1
|
Stancheva VG, Sanyal S. Positive-strand RNA virus replication organelles at a glance. J Cell Sci 2024; 137:jcs262164. [PMID: 39254430 PMCID: PMC11423815 DOI: 10.1242/jcs.262164] [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: 09/11/2024] Open
Abstract
Membrane-bound replication organelles (ROs) are a unifying feature among diverse positive-strand RNA viruses. These compartments, formed as alterations of various host organelles, provide a protective niche for viral genome replication. Some ROs are characterised by a membrane-spanning pore formed by viral proteins. The RO membrane separates the interior from immune sensors in the cytoplasm. Recent advances in imaging techniques have revealed striking diversity in RO morphology and origin across virus families. Nevertheless, ROs share core features such as interactions with host proteins for their biogenesis and for lipid and energy transfer. The restructuring of host membranes for RO biogenesis and maintenance requires coordinated action of viral and host factors, including membrane-bending proteins, lipid-modifying enzymes and tethers for interorganellar contacts. In this Cell Science at a Glance article and the accompanying poster, we highlight ROs as a universal feature of positive-strand RNA viruses reliant on virus-host interplay, and we discuss ROs in the context of extensive research focusing on their potential as promising targets for antiviral therapies and their role as models for understanding fundamental principles of cell biology.
Collapse
Affiliation(s)
- Viktoriya G. Stancheva
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| |
Collapse
|
2
|
den Boon JA, Nishikiori M, Zhan H, Ahlquist P. Positive-strand RNA virus genome replication organelles: structure, assembly, control. Trends Genet 2024; 40:681-693. [PMID: 38724328 DOI: 10.1016/j.tig.2024.04.003] [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: 02/27/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 08/09/2024]
Abstract
Positive-strand RNA [(+)RNA] viruses include pandemic SARS-CoV-2, tumor-inducing hepatitis C virus, debilitating chikungunya virus (CHIKV), lethal encephalitis viruses, and many other major pathogens. (+)RNA viruses replicate their RNA genomes in virus-induced replication organelles (ROs) that also evolve new viral species and variants by recombination and mutation and are crucial virus control targets. Recent cryo-electron microscopy (cryo-EM) reveals that viral RNA replication proteins form striking ringed 'crowns' at RO vesicle junctions with the cytosol. These crowns direct RO vesicle formation, viral (-)RNA and (+)RNA synthesis and capping, innate immune escape, and transfer of progeny (+)RNA genomes into translation and encapsidation. Ongoing studies are illuminating crown assembly, sequential functions, host factor interactions, etc., with significant implications for control and beneficial uses of viruses.
Collapse
Affiliation(s)
- Johan A den Boon
- Rowe Center for Virology, Morgridge Institute for Research, Madison, WI, USA; Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI; McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI
| | - Masaki Nishikiori
- Rowe Center for Virology, Morgridge Institute for Research, Madison, WI, USA; Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI; McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI
| | - Hong Zhan
- Rowe Center for Virology, Morgridge Institute for Research, Madison, WI, USA; Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI; McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI
| | - Paul Ahlquist
- Rowe Center for Virology, Morgridge Institute for Research, Madison, WI, USA; Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI; McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI.
| |
Collapse
|
3
|
Girard J, Le Bihan O, Lai-Kee-Him J, Girleanu M, Bernard E, Castellarin C, Chee M, Neyret A, Spehner D, Holy X, Favier AL, Briant L, Bron P. In situ fate of Chikungunya virus replication organelles. J Virol 2024; 98:e0036824. [PMID: 38940586 PMCID: PMC11265437 DOI: 10.1128/jvi.00368-24] [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: 02/26/2024] [Accepted: 06/02/2024] [Indexed: 06/29/2024] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne pathogen responsible for an acute musculoskeletal disease in humans. Replication of the viral RNA genome occurs in specialized membranous replication organelles (ROs) or spherules, which contain the viral replication complex. Initially generated by RNA synthesis-associated plasma membrane deformation, alphavirus ROs are generally rapidly endocytosed to produce type I cytopathic vacuoles (CPV-I), from which nascent RNAs are extruded for cytoplasmic translation. By contrast, CHIKV ROs are poorly internalized, raising the question of their fate and functionality at the late stage of infection. Here, using in situ cryogenic-electron microscopy approaches, we investigate the outcome of CHIKV ROs and associated replication machinery in infected human cells. We evidence the late persistence of CHIKV ROs at the plasma membrane with a crowned protein complex at the spherule neck similar to the recently resolved replication complex. The unexpectedly heterogeneous and large diameter of these compartments suggests a continuous, dynamic growth of these organelles beyond the replication of a single RNA genome. Ultrastructural analysis of surrounding cytoplasmic regions supports that outgrown CHIKV ROs remain dynamically active in viral RNA synthesis and export to the cell cytosol for protein translation. Interestingly, rare ROs with a homogeneous diameter are also marginally internalized in CPV-I near honeycomb-like arrangements of unknown function, which are absent in uninfected controls, thereby suggesting a temporal regulation of this internalization. Altogether, this study sheds new light on the dynamic pattern of CHIKV ROs and associated viral replication at the interface with cell membranes in infected cells.IMPORTANCEThe Chikungunya virus (CHIKV) is a positive-stranded RNA virus that requires specialized membranous replication organelles (ROs) for its genome replication. Our knowledge of this viral cycle stage is still incomplete, notably regarding the fate and functional dynamics of CHIKV ROs in infected cells. Here, we show that CHIKV ROs are maintained at the plasma membrane beyond the first viral cycle, continuing to grow and be dynamically active both in viral RNA replication and in its export to the cell cytosol, where translation occurs in proximity to ROs. This contrasts with the homogeneous diameter of ROs during internalization in cytoplasmic vacuoles, which are often associated with honeycomb-like arrangements of unknown function, suggesting a regulated mechanism. This study sheds new light on the dynamics and fate of CHIKV ROs in human cells and, consequently, on our understanding of the Chikungunya viral cycle.
Collapse
Affiliation(s)
- Justine Girard
- Centre de Biologie Structurale (CBS), Université de Montpellier, CNRS, INSERM, Montpellier, France
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
| | - Olivier Le Bihan
- Institut de Recherche Biomédicale des Armées (IRBA), Ministère des armées, Brétigny-sur-Orge, France
| | - Joséphine Lai-Kee-Him
- Centre de Biologie Structurale (CBS), Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Maria Girleanu
- Institut de Recherche Biomédicale des Armées (IRBA), Ministère des armées, Brétigny-sur-Orge, France
| | - Eric Bernard
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
| | - Cedric Castellarin
- Institut de Recherche Biomédicale des Armées (IRBA), Ministère des armées, Brétigny-sur-Orge, France
| | - Matthew Chee
- Centre de Biologie Structurale (CBS), Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Aymeric Neyret
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
| | - Danièle Spehner
- Institut de Recherche Biomédicale des Armées (IRBA), Ministère des armées, Brétigny-sur-Orge, France
| | - Xavier Holy
- Institut de Recherche Biomédicale des Armées (IRBA), Ministère des armées, Brétigny-sur-Orge, France
| | - Anne-Laure Favier
- Institut de Recherche Biomédicale des Armées (IRBA), Ministère des armées, Brétigny-sur-Orge, France
| | - Laurence Briant
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
| | - Patrick Bron
- Centre de Biologie Structurale (CBS), Université de Montpellier, CNRS, INSERM, Montpellier, France
| |
Collapse
|
4
|
Stelitano D, Cortese M. Electron microscopy: The key to resolve RNA viruses replication organelles. Mol Microbiol 2024; 121:679-687. [PMID: 37777341 DOI: 10.1111/mmi.15173] [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: 07/13/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 10/02/2023]
Abstract
Positive-sense single-stranded RNA viruses significantly reshape intracellular membranes to generate viral replication organelles that form a controlled niche in which nucleic acids, enzymes, and cofactors accumulate to assure an efficient replication of the viral genome. In recent years, advancements in electron microscopy (EM) techniques have enabled imaging of these viral factories in a near-native state providing significantly higher molecular details that have led to progress in our general understanding of virus biology. In this review, we describe the contribution of the cutting-edge EM approaches to the current knowledge of replication organelles biogenesis, structure, and functions.
Collapse
Affiliation(s)
- Debora Stelitano
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Scuola Superiore Meridionale, Naples, Italy
| | - Mirko Cortese
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Università della Campania Luigi Vanvitelli, Caserta, Italy
| |
Collapse
|
5
|
Zhang Y, Liang X, Zhao M, Qi T, Guo H, Zhao J, Zhao J, Zhan G, Kang Z, Zheng L. A novel ambigrammatic mycovirus, PsV5, works hand in glove with wheat stripe rust fungus to facilitate infection. PLANT COMMUNICATIONS 2023; 4:100505. [PMID: 36527233 DOI: 10.1016/j.xplc.2022.100505] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/16/2022] [Accepted: 12/14/2022] [Indexed: 05/11/2023]
Abstract
Here we describe a novel narnavirus, Puccinia striiformis virus 5 (PsV5), from the devastating wheat stripe rust fungus P. striiformis f. sp. tritici (Pst). The genome of PsV5 contains two predicted open reading frames (ORFs) that largely overlap on reverse strands: an RNA-dependent RNA polymerase (RdRp) and a reverse-frame ORF (rORF) with unknown function. Protein translations of both ORFs were demonstrated by immune technology. Transgenic wheat lines overexpressing PsV5 (RdRp-rORF), RdRp ORF, or rORF were more susceptible to Pst infection, whereas PsV5-RNA interference (RNAi) lines were more resistant. Overexpression of PsV5 (RdRp-rORF), RdRp ORF, or rORF in Fusarium graminearum also boosted fungal virulence. We thus report a novel ambigrammatic mycovirus that promotes the virulence of its fungal host. The results are a significant addition to our understanding of virosphere diversity and offer insights for sustainable wheat rust disease control.
Collapse
Affiliation(s)
- Yanhui Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaofei Liang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengxin Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tuo Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Hualong Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gangming Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Li Zheng
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education and School of Plant Protection, Hainan University, Haikou, Hainan 570228, China.
| |
Collapse
|
6
|
Hagedorn E, Bunnell D, Henschel B, Smith DL, Dickinson S, Brown AW, De Luca M, Turner AN, Chtarbanova S. RNA virus-mediated changes in organismal oxygen consumption rate in young and old Drosophila melanogaster males. Aging (Albany NY) 2023; 15:1748-1767. [PMID: 36947702 PMCID: PMC10085608 DOI: 10.18632/aging.204593] [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: 10/20/2022] [Accepted: 02/20/2023] [Indexed: 03/24/2023]
Abstract
Aging is accompanied by increased susceptibility to infections including with viral pathogens resulting in higher morbidity and mortality among the elderly. Significant changes in host metabolism can take place following virus infection. Efficient immune responses are energetically costly, and viruses divert host molecular resources to promote their own replication. Virus-induced metabolic reprogramming could impact infection outcomes, however, how this is affected by aging and impacts organismal survival remains poorly understood. RNA virus infection of Drosophila melanogaster with Flock House virus (FHV) is an effective model to study antiviral responses with age, where older flies die faster than younger flies due to impaired disease tolerance. Using this aged host-virus model, we conducted longitudinal, single-fly respirometry studies to determine if metabolism impacts infection outcomes. Analysis using linear mixed models on Oxygen Consumption Rate (OCR) following the first 72-hours post-infection showed that FHV modulates respiration, but age has no significant effect on OCR. However, the longitudinal assessment revealed that OCR in young flies progressively and significantly decreases, while OCR in aged flies remains constant throughout the three days of the experiment. Furthermore, we found that the OCR signature at 24-hours varied in response to both experimental treatment and survival status. FHV-injected flies that died prior to 48- or 72-hours measurements had a lower OCR compared to survivors at 48-hours. Our findings suggest the host's metabolic profile could influence the outcome of viral infections.
Collapse
Affiliation(s)
- Eli Hagedorn
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35401, USA
- Present Address: Indiana University School of Medicine-Indianapolis, Medical Scientist Training Program, Indianapolis, IN 46202, USA
| | - Dean Bunnell
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35401, USA
| | - Beate Henschel
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Biostatistics Consulting Center, Bloomington, IN 47405, USA
| | - Daniel L. Smith
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL 35233, USA
- Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Stephanie Dickinson
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Biostatistics Consulting Center, Bloomington, IN 47405, USA
| | - Andrew W. Brown
- Department of Applied Health Sciences, Indiana University, School of Public Health-Bloomington, Bloomington, IN 47405, USA
- Present Address: University of Arkansas for Medical Sciences and Arkansas Children’s Research Institute, Little Rock, AR 72202, USA
| | - Maria De Luca
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Ashley N. Turner
- Department of Biology, Jacksonville State University, Jacksonville, AL 36265, USA
| | - Stanislava Chtarbanova
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35401, USA
- Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Center for Convergent Bioscience and Medicine, University of Alabama, Tuscaloosa, AL 35401, USA
- Alabama Life Research Institute, University of Alabama, Tuscaloosa, AL 35401, USA
| |
Collapse
|
7
|
Sagan SM, Weber SC. Let's phase it: viruses are master architects of biomolecular condensates. Trends Biochem Sci 2023; 48:229-243. [PMID: 36272892 DOI: 10.1016/j.tibs.2022.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/15/2022]
Abstract
Viruses compartmentalize their replication and assembly machinery to both evade detection and concentrate the viral proteins and nucleic acids necessary for genome replication and virion production. Accumulating evidence suggests that diverse RNA and DNA viruses form replication organelles and nucleocapsid assembly sites using phase separation. In general, the biogenesis of these compartments is regulated by two types of viral protein, collectively known as antiterminators and nucleocapsid proteins, respectively. Herein, we discuss how RNA viruses establish replication organelles and nucleocapsid assembly sites, and the evidence that these compartments form through phase separation. While this review focuses on RNA viruses, accumulating evidence suggests that all viruses rely on phase separation and form biomolecular condensates important for completing the infectious cycle.
Collapse
Affiliation(s)
- Selena M Sagan
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada; Department of Biochemistry, McGill University, Montreal, QC, Canada.
| | - Stephanie C Weber
- Department of Biology, McGill University, Montreal, QC, Canada; Department of Physics, McGill University, Montreal, QC, Canada
| |
Collapse
|
8
|
Nodavirus RNA replication crown architecture reveals proto-crown precursor and viral protein A conformational switching. Proc Natl Acad Sci U S A 2023; 120:e2217412120. [PMID: 36693094 PMCID: PMC9945985 DOI: 10.1073/pnas.2217412120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Positive-strand RNA viruses replicate their genomes in virus-induced membrane vesicles, and the resulting RNA replication complexes are a major target for virus control. Nodavirus studies first revealed viral RNA replication proteins forming a 12-fold symmetric "crown" at the vesicle opening to the cytosol, an arrangement recently confirmed to extend to distantly related alphaviruses. Using cryoelectron microscopy (cryo-EM), we show that mature nodavirus crowns comprise two stacked 12-mer rings of multidomain viral RNA replication protein A. Each ring contains an ~19 nm circle of C-proximal polymerase domains, differentiated by strikingly diverged positions of N-proximal RNA capping/membrane binding domains. The lower ring is a "proto-crown" precursor that assembles prior to RNA template recruitment, RNA synthesis, and replication vesicle formation. In this proto-crown, the N-proximal segments interact to form a toroidal central floor, whose 3.1 Å resolution structure reveals many mechanistic details of the RNA capping/membrane binding domains. In the upper ring, cryo-EM fitting indicates that the N-proximal domains extend radially outside the polymerases, forming separated, membrane-binding "legs." The polymerase and N-proximal domains are connected by a long linker accommodating the conformational switch between the two rings and possibly also polymerase movements associated with RNA synthesis and nonsymmetric electron density in the lower center of mature crowns. The results reveal remarkable viral protein multifunctionality, conformational flexibility, and evolutionary plasticity and insights into (+)RNA virus replication and control.
Collapse
|
9
|
Jadhav AC, Kounatidis I. Correlative Cryo-imaging Using Soft X-Ray Tomography for the Study of Virus Biology in Cells and Tissues. Subcell Biochem 2023; 106:169-196. [PMID: 38159227 DOI: 10.1007/978-3-031-40086-5_6] [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] [Indexed: 01/03/2024]
Abstract
Viruses are obligate intracellular pathogens that depend on their host cell machinery and metabolism for their replicative life cycle. Virus entry, replication, and assembly are dynamic processes that lead to the reorganisation of host cell components. Therefore, a complete understanding of the viral processes requires their study in the cellular context where advanced imaging has been proven valuable in providing the necessary information. Among the available imaging techniques, soft X-ray tomography (SXT) at cryogenic temperatures can provide three-dimensional mapping to 25 nm resolution and is ideally suited to visualise the internal organisation of virus-infected cells. In this chapter, the principles and practices of synchrotron-based cryo-soft X-ray tomography (cryo-SXT) in virus research are presented. The potential of the cryo-SXT in correlative microscopy platforms is also demonstrated through working examples of reovirus and hepatitis research at Beamline B24 (Diamond Light Source Synchrotron, UK) and BL09-Mistral beamline (ALBA Synchrotron, Spain), respectively.
Collapse
Affiliation(s)
- Archana C Jadhav
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Ilias Kounatidis
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
- School of Life, Health and Chemical Sciences, The Open University, Milton Keynes, UK.
| |
Collapse
|
10
|
den Boon JA, Zhan H, Unchwaniwala N, Horswill M, Slavik K, Pennington J, Navine A, Ahlquist P. Multifunctional Protein A Is the Only Viral Protein Required for Nodavirus RNA Replication Crown Formation. Viruses 2022; 14:v14122711. [PMID: 36560715 PMCID: PMC9788154 DOI: 10.3390/v14122711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
Positive-strand RNA virus RNA genome replication occurs in membrane-associated RNA replication complexes (RCs). Nodavirus RCs are outer mitochondrial membrane invaginations whose necked openings to the cytosol are "crowned" by a 12-fold symmetrical proteinaceous ring that functions as the main engine of RNA replication. Similar protein crowns recently visualized at the openings of alphavirus and coronavirus RCs highlight their broad conservation and functional importance. Using cryo-EM tomography, we earlier showed that the major nodavirus crown constituent is viral protein A, whose polymerase, RNA capping, membrane interaction and multimerization domains drive RC formation and function. Other viral proteins are strong candidates for unassigned EM density in the crown. RNA-binding RNAi inhibitor protein B2 co-immunoprecipitates with protein A and could form crown subdomains that protect nascent viral RNA and dsRNA templates. Capsid protein may interact with the crown since nodavirus virion assembly has spatial and other links to RNA replication. Using cryoelectron tomography and complementary approaches, we show that, even when formed in mammalian cells, nodavirus RC crowns generated without B2 and capsid proteins are functional and structurally indistinguishable from mature crowns in infected Drosophila cells expressing all viral proteins. Thus, the only nodaviral factors essential to form functional RCs and crowns are RNA replication protein A and an RNA template. We also resolve apparent conflicts in prior results on B2 localization in infected cells, revealing at least two distinguishable pools of B2. The results have significant implications for crown structure, assembly, function and control as an antiviral target.
Collapse
Affiliation(s)
- Johan A. den Boon
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI 53705, USA
| | - Hong Zhan
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Nuruddin Unchwaniwala
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Mark Horswill
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI 53705, USA
| | - Kailey Slavik
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Janice Pennington
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Amanda Navine
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Paul Ahlquist
- John W. and Jeanne M. Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715, USA
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, WI 53706, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI 53705, USA
- Correspondence:
| |
Collapse
|
11
|
Tan YB, Chmielewski D, Law MCY, Zhang K, He Y, Chen M, Jin J, Luo D. Molecular architecture of the Chikungunya virus replication complex. SCIENCE ADVANCES 2022; 8:eadd2536. [PMID: 36449616 PMCID: PMC9710867 DOI: 10.1126/sciadv.add2536] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
To better understand how positive-strand (+) RNA viruses assemble membrane-associated replication complexes (RCs) to synthesize, process, and transport viral RNA in virus-infected cells, we determined both the high-resolution structure of the core RNA replicase of chikungunya virus and the native RC architecture in its cellular context at subnanometer resolution, using in vitro reconstitution and in situ electron cryotomography, respectively. Within the core RNA replicase, the viral polymerase nsP4, which is in complex with nsP2 helicase-protease, sits in the central pore of the membrane-anchored nsP1 RNA-capping ring. The addition of a large cytoplasmic ring next to the C terminus of nsP1 forms the holo-RNA-RC as observed at the neck of spherules formed in virus-infected cells. These results represent a major conceptual advance in elucidating the molecular mechanisms of RNA virus replication and the principles underlying the molecular architecture of RCs, likely to be shared with many pathogenic (+) RNA viruses.
Collapse
Affiliation(s)
- Yaw Bia Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - David Chmielewski
- Biophysics Graduate Program, Departments of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Michelle Cheok Yien Law
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Kuo Zhang
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Yu He
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Muyuan Chen
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Jing Jin
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
- Vitalant Research Institute, San Francisco, CA 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| |
Collapse
|
12
|
Herod MR, Ward JC, Tuplin A, Harris M, Stonehouse NJ, McCormick CJ. Positive strand RNA viruses differ in the constraints they place on the folding of their negative strand. RNA (NEW YORK, N.Y.) 2022; 28:1359-1376. [PMID: 35918125 PMCID: PMC9479745 DOI: 10.1261/rna.079125.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Genome replication of positive strand RNA viruses requires the production of a complementary negative strand RNA that serves as a template for synthesis of more positive strand progeny. Structural RNA elements are important for genome replication, but while they are readily observed in the positive strand, evidence of their existence in the negative strand is more limited. We hypothesized that this was due to viruses differing in their capacity to allow this latter RNA to adopt structural folds. To investigate this, ribozymes were introduced into the negative strand of different viral constructs; the expectation being that if RNA folding occurred, negative strand cleavage and suppression of replication would be seen. Indeed, this was what happened with hepatitis C virus (HCV) and feline calicivirus (FCV) constructs. However, little or no impact was observed for chikungunya virus (CHIKV), human rhinovirus (HRV), hepatitis E virus (HEV), and yellow fever virus (YFV) constructs. Reduced cleavage in the negative strand proved to be due to duplex formation with the positive strand. Interestingly, ribozyme-containing RNAs also remained intact when produced in vitro by the HCV polymerase, again due to duplex formation. Overall, our results show that there are important differences in the conformational constraints imposed on the folding of the negative strand between different positive strand RNA viruses.
Collapse
Affiliation(s)
- Morgan R Herod
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Joseph C Ward
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Andrew Tuplin
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Nicola J Stonehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Christopher J McCormick
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Sir Henry Wellcome Laboratories, University Hospital Southampton, Southampton SO16 6YD, United Kingdom
- Institute for Life Sciences, University of Southampton SO17 1BJ, United Kingdom
| |
Collapse
|
13
|
Nagy PD. Co-opted membranes, lipids, and host proteins: what have we learned from tombusviruses? Curr Opin Virol 2022; 56:101258. [PMID: 36166851 DOI: 10.1016/j.coviro.2022.101258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/01/2022] [Accepted: 08/21/2022] [Indexed: 11/28/2022]
Abstract
Positive-strand RNA viruses replicate in intracellular membranous structures formed after virus-driven intensive manipulation of subcellular organelles and membranes. These unique structures are called viral-replication organelles (VROs). To build VROs, the replication proteins coded by (+)RNA viruses co-opt host proteins, including membrane-shaping, lipid synthesis, and lipid-modification enzymes to create an optimal microenvironment that (i) concentrates the viral replicase and associated host proteins and the viral RNAs; (ii) regulates enzymatic activities and spatiotemporally the replication process; and (iii) protects the viral RNAs from recognition and degradation by the host innate immune defense. Tomato bushy stunt virus (TBSV), a plant (+)RNA virus, serves as an advanced model to study the interplay among viral components, co-opted host proteins, lipids, and membranes. This review presents our current understanding of the complex interaction between TBSV and host with panviral implications.
Collapse
Affiliation(s)
- Peter D Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA.
| |
Collapse
|
14
|
Feng Z, Kovalev N, Nagy PD. Multifunctional role of the co-opted Cdc48 AAA+ ATPase in tombusvirus replication. Virology 2022; 576:1-17. [PMID: 36126429 DOI: 10.1016/j.virol.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/07/2022] [Indexed: 10/31/2022]
Abstract
Replication of positive-strand RNA viruses depends on usurped cellular membranes and co-opted host proteins. Based on pharmacological inhibition and genetic and biochemical approaches, the authors identified critical roles of the cellular Cdc48 unfoldase/segregase protein in facilitating the replication of tomato bushy stunt virus (TBSV). We show that TBSV infection induces the expression of Cdc48 in Nicotiana benthamiana plants. Cdc48 binds to the TBSV replication proteins through its N-terminal region. In vitro TBSV replicase reconstitution experiments demonstrated that Cdc48 is needed for efficient replicase assembly and activity. Surprisingly, the in vitro replication experiments also showed that excess amount of Cdc48 facilitates the disassembly of the membrane-bound viral replicase-RNA template complex. Cdc48 is also needed for the recruitment of additional host proteins. Because several human viruses, including flaviviruses, utilize Cdc48, also called VCP/p97, for replication, we suggest that Cdc48 might be a common panviral host factor for plant and animal RNA viruses.
Collapse
Affiliation(s)
- Zhike Feng
- Department of Plant Pathology, University of Kentucky, Lexington, USA
| | - Nikolay Kovalev
- Department of Plant Pathology, University of Kentucky, Lexington, USA
| | - Peter D Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, USA.
| |
Collapse
|
15
|
Xue H, Zhang M, Liu J, Wang J, Ren G. Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination. Front Chem 2022; 10:889203. [PMID: 36110139 PMCID: PMC9468540 DOI: 10.3389/fchem.2022.889203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/13/2022] [Indexed: 11/28/2022] Open
Abstract
To understand the dynamic structure-function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.
Collapse
Affiliation(s)
- Han Xue
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jianjun Wang
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| |
Collapse
|
16
|
Jiang X, Luan Y, Chai M, Yang Y, Wang Y, Deng W, Li Y, Cheng X, Wu X. The N-Terminal α-Helix of Potato Virus X-Encoded RNA-Dependent RNA Polymerase Is Required for Membrane Association and Multimerization. Viruses 2022; 14:v14091907. [PMID: 36146714 PMCID: PMC9504981 DOI: 10.3390/v14091907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Positive-sense single-stranded RNA viruses replicate in virus-induced membranous organelles for maximum efficiency and immune escaping. The replication of potato virus X (PVX) takes place on the endoplasmic reticulum (ER); however, how PVX-encoded RNA-dependent RNA polymerase (RdRp) is associated with the ER is still unknown. A proline-kinked amphipathic α-helix was recently found in the MET domain of RdRp. In this study, we further illustrate that the first α-helix of the MET domain is also required for ER association. Moreover, we found that the MET domain forms multimers on ER and the first α-helix is essential for multimerization. These results suggest that the RdRp of PVX adopts more than one hydrophobic motif for membrane association and for multimerization.
Collapse
Affiliation(s)
- Xue Jiang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yameng Luan
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Mengzhu Chai
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yingshuai Yang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yuting Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Wenjia Deng
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yonggang Li
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Xiaofei Cheng
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China
- Correspondence: (X.C.); (X.W.)
| | - Xiaoyun Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
- Correspondence: (X.C.); (X.W.)
| |
Collapse
|
17
|
Neufeldt CJ, Cortese M. Membrane architects: how positive-strand RNA viruses restructure the cell. J Gen Virol 2022; 103. [PMID: 35976091 DOI: 10.1099/jgv.0.001773] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Virus infection is a process that requires combined contributions from both virus and host factors. For this process to be efficient within the crowded host environment, viruses have evolved ways to manipulate and reorganize host structures to produce cellular microenvironments. Positive-strand RNA virus replication and assembly occurs in association with cytoplasmic membranes, causing a reorganization of these membranes to create microenvironments that support viral processes. Similarities between virus-induced membrane domains and cellular organelles have led to the description of these structures as virus replication organelles (vRO). Electron microscopy analysis of vROs in positive-strand RNA virus infected cells has revealed surprising morphological similarities between genetically diverse virus species. For all positive-strand RNA viruses, vROs can be categorized into two groups: those that make invaginations into the cellular membranes (In-vRO), and those that cause the production of protrusions from cellular membranes (Pr-vRO), most often in the form of double membrane vesicles (DMVs). In this review, we will discuss the current knowledge on the structure and biogenesis of these two different vRO classes as well as comparing morphology and function of vROs between various positive-strand RNA viruses. Finally, we will discuss recent studies describing pharmaceutical intervention in vRO formation as an avenue to control virus infection.
Collapse
Affiliation(s)
- Christopher John Neufeldt
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Mirko Cortese
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| |
Collapse
|
18
|
Chen D, Zhao YG, Zhang H. Endomembrane remodeling in SARS-CoV-2 infection. CELL INSIGHT 2022; 1:100031. [PMID: 37193051 PMCID: PMC9112566 DOI: 10.1016/j.cellin.2022.100031] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 12/18/2022]
Abstract
During severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the viral proteins intimately interact with host factors to remodel the endomembrane system at various steps of the viral lifecycle. The entry of SARS-CoV-2 can be mediated by endocytosis-mediated internalization. Virus-containing endosomes then fuse with lysosomes, in which the viral S protein is cleaved to trigger membrane fusion. Double-membrane vesicles generated from the ER serve as platforms for viral replication and transcription. Virions are assembled at the ER-Golgi intermediate compartment and released through the secretory pathway and/or lysosome-mediated exocytosis. In this review, we will focus on how SARS-CoV-2 viral proteins collaborate with host factors to remodel the endomembrane system for viral entry, replication, assembly and egress. We will also describe how viral proteins hijack the host cell surveillance system-the autophagic degradation pathway-to evade destruction and benefit virus production. Finally, potential antiviral therapies targeting the host cell endomembrane system will be discussed.
Collapse
Affiliation(s)
- Di Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan G. Zhao
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
19
|
Nishikiori M, den Boon JA, Unchwaniwala N, Ahlquist P. Crowning Touches in Positive-Strand RNA Virus Genome Replication Complex Structure and Function. Annu Rev Virol 2022; 9:193-212. [PMID: 35610038 DOI: 10.1146/annurev-virology-092920-021307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Positive-strand RNA viruses, the largest genetic class of eukaryotic viruses, include coronaviruses and many other established and emerging pathogens. A major target for understanding and controlling these viruses is their genome replication, which occurs in virus-induced membrane vesicles that organize replication steps and protect double-stranded RNA intermediates from innate immune recognition. The structure of these complexes has been greatly illuminated by recent cryo-electron microscope tomography studies with several viruses. One key finding in diverse systems is the organization of crucial viral RNA replication factors in multimeric rings or crowns that among other functions serve as exit channels gating release of progeny genomes to the cytosol for translation and encapsidation. Emerging results suggest that these crowns serve additional important purposes in replication complex assembly, function, and interaction with downstream processes such as encapsidation. The findings provide insights into viral function and evolution and new bases for understanding, controlling, and engineering positive-strand RNA viruses. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Masaki Nishikiori
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Johan A den Boon
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nuruddin Unchwaniwala
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Current affiliation: Assembly Biosciences, Inc., South San Francisco, California, USA
| | - Paul Ahlquist
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
20
|
Wu K, Vedelaar TA, Damle VG, Morita A, Mougnaud J, San Martin CR, Zhang Y, van der Pol DP, Ende-Metselaar H, Zybert IR, Schirhagl R. Applying NV center-based quantum sensing to study intracellular free radical response upon viral infections. Redox Biol 2022; 52:102279. [PMID: 35349928 PMCID: PMC8965164 DOI: 10.1016/j.redox.2022.102279] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 02/08/2023] Open
|
21
|
Coronavirus RNA Synthesis Takes Place within Membrane-Bound Sites. Viruses 2021; 13:v13122540. [PMID: 34960809 PMCID: PMC8708976 DOI: 10.3390/v13122540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/01/2021] [Accepted: 12/15/2021] [Indexed: 12/22/2022] Open
Abstract
Infectious bronchitis virus (IBV), a gammacoronavirus, is an economically important virus to the poultry industry, as well as a significant welfare issue for chickens. As for all positive strand RNA viruses, IBV infection causes rearrangements of the host cell intracellular membranes to form replication organelles. Replication organelle formation is a highly conserved and vital step in the viral life cycle. Here, we investigate the localization of viral RNA synthesis and the link with replication organelles in host cells. We have shown that sites of viral RNA synthesis and virus-related dsRNA are associated with one another and, significantly, that they are located within a membrane-bound compartment within the cell. We have also shown that some viral RNA produced early in infection remains within these membranes throughout infection, while a proportion is trafficked to the cytoplasm. Importantly, we demonstrate conservation across all four coronavirus genera, including SARS-CoV-2. Understanding more about the replication of these viruses is imperative in order to effectively find ways to control them.
Collapse
|
22
|
Abstract
Alphaviruses are positive-strand RNA viruses, typically transmitted by mosquitoes between vertebrate hosts. They encode four essential replication proteins, the non-structural proteins nsP1-4, which possess the enzymatic activities of RNA capping, RNA helicase, site-specific protease, ADP-ribosyl removal and RNA polymerase. Alphaviruses have been key models in the study of membrane-associated RNA replication, which is a conserved feature among the positive-strand RNA viruses of animals and plants. We review new structural and functional information on the nsPs and their interaction with host proteins and membranes, as well as with viral RNA sequences. The dodecameric ring structure of nsP1 is likely to be one of the evolutionary innovations that facilitated the success of the progenitors of current positive-strand RNA viruses.
Collapse
Affiliation(s)
- Tero Ahola
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia.
| |
Collapse
|
23
|
Feng Z, Inaba JI, Nagy PD. Tombusviruses Target a Major Crossroad in the Endocytic and Recycling Pathways via Co-opting Rab7 Small GTPase. J Virol 2021; 95:e0107621. [PMID: 34406861 PMCID: PMC8513485 DOI: 10.1128/jvi.01076-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/13/2021] [Indexed: 12/28/2022] Open
Abstract
Positive-strand RNA viruses induce the biogenesis of unique membranous organelles called viral replication organelles (VROs), which perform virus replication in infected cells. Tombusviruses have been shown to rewire cellular trafficking and metabolic pathways, remodel host membranes, and recruit multiple host factors to support viral replication. In this work, we demonstrate that tomato bushy stunt virus (TBSV) and the closely related carnation Italian ringspot virus (CIRV) usurp Rab7 small GTPase to facilitate building VROs in the surrogate host yeast and in plants. Depletion of Rab7 small GTPase, which is needed for late endosome and retromer biogenesis, strongly inhibits TBSV and CIRV replication in yeast and in planta. The viral p33 replication protein interacts with Rab7 small GTPase, which results in the relocalization of Rab7 into the large VROs. Similar to the depletion of Rab7, the deletion of either MON1 or CCZ1 heterodimeric GEFs (guanine nucleotide exchange factors) of Rab7 inhibited TBSV RNA replication in yeast. This suggests that the activated Rab7 has proviral functions. We show that the proviral function of Rab7 is to facilitate the recruitment of the retromer complex and the endosomal sorting nexin-BAR proteins into VROs. We demonstrate that TBSV p33-driven retargeting of Rab7 into VROs results in the delivery of several retromer cargos with proviral functions. These proteins include lipid enzymes, such as Vps34 PI3K (phosphatidylinositol 3-kinase), PI4Kα-like Stt4 phosphatidylinositol 4-kinase, and Psd2 phosphatidylserine decarboxylase. In summary, based on these and previous findings, we propose that subversion of Rab7 into VROs allows tombusviruses to reroute endocytic and recycling trafficking to support virus replication. IMPORTANCE The replication of positive-strand RNA viruses depends on the biogenesis of viral replication organelles (VROs). However, the formation of membranous VROs is not well understood yet. Using tombusviruses and the model host yeast, we discovered that the endosomal Rab7 small GTPase is critical for the formation of VROs. Interaction between Rab7 and the TBSV p33 replication protein leads to the recruitment of Rab7 into VROs. TBSV-driven usurping of Rab7 has proviral functions through facilitating the delivery of the co-opted retromer complex, sorting nexin-BAR proteins, and lipid enzymes into VROs to create an optimal milieu for virus replication. These results open up the possibility that controlling cellular Rab7 activities in infected cells could be a target for new antiviral strategies.
Collapse
Affiliation(s)
- Zhike Feng
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Jun-ichi Inaba
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Peter D. Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| |
Collapse
|
24
|
Unchwaniwala N, Zhan H, den Boon JA, Ahlquist P. Cryo-electron microscopy of nodavirus RNA replication organelles illuminates positive-strand RNA virus genome replication. Curr Opin Virol 2021; 51:74-79. [PMID: 34601307 PMCID: PMC8504867 DOI: 10.1016/j.coviro.2021.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022]
Abstract
The nodavirus flock house virus recently provided a well-characterized model for the first cryo-electron microscope tomography of membrane-bound, positive-strand RNA ((+)RNA) virus genome replication complexes (RCs). The resulting first views of RC organization and complementary biochemical results showed that the viral RNA replication vesicle is tightly packed with the dsRNA genomic RNA replication intermediate, and that (+)ssRNA replication products are released through the vesicle neck to the cytosol through a 12-fold symmetric ring or crown of multi-functional viral RNA replication proteins, which likely also contribute to viral RNA synthesis. Subsequent studies identified similar crown-like RNA replication protein complexes in alphavirus and coronavirus RCs, indicating related mechanisms across highly divergent (+)RNA viruses. As outlined in this review, these results have significant implications for viral function, evolution and control.
Collapse
Affiliation(s)
- Nuruddin Unchwaniwala
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI, 53715, United States; Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, 53706, United States; McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Hong Zhan
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI, 53715, United States; Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, 53706, United States; McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Johan A den Boon
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI, 53715, United States; Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, 53706, United States; McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Paul Ahlquist
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI, 53715, United States; Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, 53706, United States; McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, 53705, United States
| |
Collapse
|
25
|
Clavel M, Dagdas Y. Proteasome and selective autophagy: Brothers-in-arms for organelle quality control. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102106. [PMID: 34487948 DOI: 10.1016/j.pbi.2021.102106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/08/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Maintaining the integrity of organelles despite the cellular disturbances that arise during stress is essential for life. To ensure organelle proteostasis (protein homeostasis), plants have evolved multitiered quality control mechanisms that work together to repair or recycle the damaged organelles. Despite recent advances, our understanding of plant organelle quality control mechanisms is far from complete. Especially, the crosstalk between different quality control pathways remains elusive. Here, we highlight recent advances on organelle quality control, focusing on the targeted protein degradation pathways that maintain the homeostasis of the endoplasmic reticulum (ER), chloroplast, and mitochondria. We discuss how plant cells decide to employ different degradation pathways and propose tools that could be used to discover the missing components in organelle quality control.
Collapse
Affiliation(s)
- Marion Clavel
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
| | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
| |
Collapse
|
26
|
Nguyen-Dinh V, Herker E. Ultrastructural Features of Membranous Replication Organelles Induced by Positive-Stranded RNA Viruses. Cells 2021; 10:cells10092407. [PMID: 34572055 PMCID: PMC8464962 DOI: 10.3390/cells10092407] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/12/2021] [Accepted: 09/02/2021] [Indexed: 11/25/2022] Open
Abstract
All intracellular pathogens critically depend on host cell organelles and metabolites for successful infection and replication. One hallmark of positive-strand RNA viruses is to induce alterations of the (endo)membrane system in order to shield their double-stranded RNA replication intermediates from detection by the host cell’s surveillance systems. This spatial seclusion also allows for accruing host and viral factors and building blocks required for efficient replication of the genome and prevents access of antiviral effectors. Even though the principle is iterated by almost all positive-strand RNA viruses infecting plants and animals, the specific structure and the organellar source of membranes differs. Here, we discuss the characteristic ultrastructural features of the virus-induced membranous replication organelles in plant and animal cells and the scientific progress gained by advanced microscopy methods.
Collapse
|
27
|
Wang J, Maschietto F, Guberman-Pfeffer MJ, Reiss K, Allen B, Xiong Y, Lolis E, Batista VS. Computational insights into the membrane fusion mechanism of SARS-CoV-2 at the cellular level. Comput Struct Biotechnol J 2021; 19:5019-5028. [PMID: 34540146 PMCID: PMC8442599 DOI: 10.1016/j.csbj.2021.08.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 08/14/2021] [Accepted: 08/31/2021] [Indexed: 12/25/2022] Open
Abstract
The membrane fusion mechanism of SARS-CoV-2 offers an attractive target for the development of small molecule antiviral inhibitors. Fusion involves an initial binding of the crown-like trimeric spike glycoproteins of SARS-CoV-2 to the receptor angiotensin II-converting enzyme 2 (ACE2) on the permissive host cellular membrane and a prefusion to post-fusion conversion of the spike trimer. During this conversion, the fusion peptides of the spike trimer are inserted into the host membrane to bring together the host and viral membranes for membrane fusion in highly choreographic events. However, geometric constraints due to interactions with the membranes remain poorly understood. In this study, we build structural models of super-complexes of spike trimer/ACE2 dimers based on the molecular structures of the ACE2/neutral amino acid transporter B(0)AT heterodimer. We determine the conformational constraints due to the membrane geometry on the enzymatic activity of ACE2 and on the viral fusion process. Furthermore, we find that binding three ACE2 dimers per spike trimer is essential to open the central pore as necessary for triggering productive membrane fusion through an elongation of the central stalk. The reported findings thus provide valuable insights for targeting the membrane fusion mechanism for drug design at the molecular level.
Collapse
Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, United States
| | - Federica Maschietto
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, United States
| | | | - Krystle Reiss
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, United States
| | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, United States
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, United States
| | - Elias Lolis
- Department of Pharmacology, Yale University, New Haven, CT 06520-8066, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, United States
| |
Collapse
|
28
|
Zhang S, Sun R, Perdoncini Carvalho C, Han J, Zheng L, Qu F. Replication-Dependent Biogenesis of Turnip Crinkle Virus Long Noncoding RNAs. J Virol 2021; 95:e0016921. [PMID: 34160262 PMCID: PMC8387050 DOI: 10.1128/jvi.00169-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/14/2021] [Indexed: 12/24/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) of virus origin accumulate in cells infected by many positive-strand (+) RNA viruses to bolster viral infectivity. Their biogenesis mostly utilizes exoribonucleases of host cells that degrade viral genomic or subgenomic RNAs in the 5'-to-3' direction until being stalled by well-defined RNA structures. Here, we report a viral lncRNA that is produced by a novel replication-dependent mechanism. This lncRNA corresponds to the last 283 nucleotides of the turnip crinkle virus (TCV) genome and hence is designated tiny TCV subgenomic RNA (ttsgR). ttsgR accumulated to high levels in TCV-infected Nicotiana benthamiana cells when the TCV-encoded RNA-dependent RNA polymerase (RdRp), also known as p88, was overexpressed. Both (+) and (-) strand forms of ttsgR were produced in a manner dependent on the RdRp functionality. Strikingly, templates as short as ttsgR itself were sufficient to program ttsgR amplification, as long as the TCV-encoded replication proteins p28 and p88 were provided in trans. Consistent with its replicational origin, ttsgR accumulation required a 5' terminal carmovirus consensus sequence (CCS), a sequence motif shared by genomic and subgenomic RNAs of many viruses phylogenetically related to TCV. More importantly, introducing a new CCS motif elsewhere in the TCV genome was alone sufficient to cause the emergence of another lncRNA. Finally, abolishing ttsgR by mutating its 5' CCS gave rise to a TCV mutant that failed to compete with wild-type TCV in Arabidopsis. Collectively, our results unveil a replication-dependent mechanism for the biogenesis of viral lncRNAs, thus suggesting that multiple mechanisms, individually or in combination, may be responsible for viral lncRNA production. IMPORTANCE Many positive-strand (+) RNA viruses produce long noncoding RNAs (lncRNAs) during the process of cellular infections and mobilize these lncRNAs to counteract antiviral defenses, as well as coordinate the translation of viral proteins. Most viral lncRNAs arise from 5'-to-3' degradation of longer viral RNAs being stalled at stable secondary structures. Here, we report a viral lncRNA that is produced by the replication machinery of turnip crinkle virus (TCV). This lncRNA, designated ttsgR, shares the terminal characteristics with TCV genomic and subgenomic RNAs and overaccumulates in the presence of moderately overexpressed TCV RNA-dependent RNA polymerase (RdRp). Furthermore, templates that are of similar sizes as ttsgR are readily replicated by TCV replication proteins (p28 and RdRp) provided from nonviral sources. In summary, this study establishes an approach for uncovering low abundance viral lncRNAs, and characterizes a replicating TCV lncRNA. Similar investigations on human-pathogenic (+) RNA viruses could yield novel therapeutic targets.
Collapse
Affiliation(s)
- Shaoyan Zhang
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Rong Sun
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Camila Perdoncini Carvalho
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Junping Han
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Limin Zheng
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| | - Feng Qu
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, Ohio, USA
| |
Collapse
|
29
|
Burt A, Gaifas L, Dendooven T, Gutsche I. A flexible framework for multi-particle refinement in cryo-electron tomography. PLoS Biol 2021; 19:e3001319. [PMID: 34437530 PMCID: PMC8389456 DOI: 10.1371/journal.pbio.3001319] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/09/2021] [Indexed: 11/19/2022] Open
Abstract
Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) are increasingly used for macromolecular structure determination in situ. Here, we introduce a set of computational tools and resources designed to enable flexible approaches to STA through increased automation and simplified metadata handling. We create a bidirectional interface between the Dynamo software package and the Warp-Relion-M pipeline, providing a framework for ab initio and geometrical approaches to multiparticle refinement in M. We illustrate the power of working within this framework by applying it to EMPIAR-10164, a publicly available dataset containing immature HIV-1 virus-like particles (VLPs), and a challenging in situ dataset containing chemosensory arrays in bacterial minicells. Additionally, we provide a comprehensive, step-by-step guide to obtaining a 3.4-Å reconstruction from EMPIAR-10164. The guide is hosted on https://teamtomo.org/, a collaborative online platform we establish for sharing knowledge about cryo-ET.
Collapse
Affiliation(s)
- Alister Burt
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Lorenzo Gaifas
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Tom Dendooven
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| |
Collapse
|
30
|
Mendonça L, Howe A, Gilchrist JB, Sheng Y, Sun D, Knight ML, Zanetti-Domingues LC, Bateman B, Krebs AS, Chen L, Radecke J, Li VD, Ni T, Kounatidis I, Koronfel MA, Szynkiewicz M, Harkiolaki M, Martin-Fernandez ML, James W, Zhang P. Correlative multi-scale cryo-imaging unveils SARS-CoV-2 assembly and egress. Nat Commun 2021; 12:4629. [PMID: 34330917 PMCID: PMC8324836 DOI: 10.1038/s41467-021-24887-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/11/2021] [Indexed: 02/07/2023] Open
Abstract
Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified viral components and inactivated viruses. However, structural and ultrastructural evidence on how the SARS-CoV-2 infection progresses in the native cellular context is scarce, and there is a lack of comprehensive knowledge on the SARS-CoV-2 replicative cycle. To correlate cytopathic events induced by SARS-CoV-2 with virus replication processes in frozen-hydrated cells, we established a unique multi-modal, multi-scale cryo-correlative platform to image SARS-CoV-2 infection in Vero cells. This platform combines serial cryoFIB/SEM volume imaging and soft X-ray cryo-tomography with cell lamellae-based cryo-electron tomography (cryoET) and subtomogram averaging. Here we report critical SARS-CoV-2 structural events - e.g. viral RNA transport portals, virus assembly intermediates, virus egress pathway, and native virus spike structures, in the context of whole-cell volumes revealing drastic cytppathic changes. This integrated approach allows a holistic view of SARS-CoV-2 infection, from the whole cell to individual molecules.
Collapse
Affiliation(s)
- Luiza Mendonça
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Andrew Howe
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - James B. Gilchrist
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Yuewen Sheng
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Dapeng Sun
- grid.21925.3d0000 0004 1936 9000Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Michael L. Knight
- grid.4991.50000 0004 1936 8948Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Laura C. Zanetti-Domingues
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - Benji Bateman
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - Anna-Sophia Krebs
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Long Chen
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Julika Radecke
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Vivian D. Li
- grid.5335.00000000121885934Murray Edwards College, University of Cambridge, Cambridge, UK
| | - Tao Ni
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ilias Kounatidis
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Mohamed A. Koronfel
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Marta Szynkiewicz
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - Maria Harkiolaki
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Marisa L. Martin-Fernandez
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - William James
- grid.4991.50000 0004 1936 8948Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Peijun Zhang
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK ,grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK ,grid.21925.3d0000 0004 1936 9000Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
31
|
Kril V, Aïqui-Reboul-Paviet O, Briant L, Amara A. New Insights into Chikungunya Virus Infection and Pathogenesis. Annu Rev Virol 2021; 8:327-347. [PMID: 34255544 DOI: 10.1146/annurev-virology-091919-102021] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chikungunya virus (CHIKV) is a re-emerging mosquito-borne alphavirus responsible for major outbreaks of disease since 2004 in the Indian Ocean islands, South east Asia, and the Americas. CHIKV causes debilitating musculoskeletal disorders in humans that are characterized by fever, rash, polyarthralgia, and myalgia. The disease is often self-limiting and nonlethal; however, some patients experience atypical or severe clinical manifestations, as well as a chronic rheumatic syndrome. Unfortunately, no efficient antivirals against CHIKV infection are available so far, highlighting the importance of deepening our knowledge of CHIKV host cell interactions and viral replication strategies. In this review, we discuss recent breakthroughs in the molecular mechanisms that regulate CHIKV infection and lay down the foundations to understand viral pathogenesis. We describe the role of the recently identified host factors co-opted by the virus for infection and pathogenesis, and emphasize the importance of CHIKV nonstructural proteins in both replication complex assembly and host immune response evasion. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Vasiliya Kril
- Biology of Emerging Virus Team, INSERM U944, CNRS UMR 7212, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, 75010 Paris, France;
| | - Olivier Aïqui-Reboul-Paviet
- RNA Viruses and Metabolism Team, CNRS UMR 9004, Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, 34293 Montpellier, France;
| | - Laurence Briant
- RNA Viruses and Metabolism Team, CNRS UMR 9004, Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, 34293 Montpellier, France;
| | - Ali Amara
- Biology of Emerging Virus Team, INSERM U944, CNRS UMR 7212, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, 75010 Paris, France;
| |
Collapse
|
32
|
Nagy PD, Feng Z. Tombusviruses orchestrate the host endomembrane system to create elaborate membranous replication organelles. Curr Opin Virol 2021; 48:30-41. [PMID: 33845410 DOI: 10.1016/j.coviro.2021.03.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/19/2021] [Accepted: 03/21/2021] [Indexed: 02/09/2023]
Abstract
Positive-strand RNA viruses depend on intensive manipulation of subcellular organelles and membranes to create unique viral replication organelles (VROs), which represent the sites of robust virus replication. The host endomembrane-based protein-trafficking and vesicle-trafficking pathways are specifically targeted by many (+)RNA viruses to take advantage of their rich resources. We summarize the critical roles of co-opted endoplasmic reticulum subdomains and associated host proteins and COPII vesicles play in tombusvirus replication. We also present the surprising contribution of the early endosome and the retromer tubular transport carriers to VRO biogenesis. The central player is tomato bushy stunt virus (TBSV), which provides an outstanding system based on the identification of a complex network of interactions with the host cells. We present the emerging theme on how TBSV uses tethering and membrane-shaping proteins and lipid modifying enzymes to build the sophisticated VRO membranes with unique lipid composition.
Collapse
Affiliation(s)
- Peter D Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA.
| | - Zhike Feng
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
| |
Collapse
|
33
|
Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review. Viruses 2021; 13:v13030412. [PMID: 33807625 PMCID: PMC7999175 DOI: 10.3390/v13030412] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 12/24/2022] Open
Abstract
Plant viral diseases are the foremost threat to sustainable agriculture, leading to several billion dollars in losses every year. Many viruses infecting several crops have been described in the literature; however, new infectious viruses are emerging frequently through outbreaks. For the effective treatment and prevention of viral diseases, there is great demand for new techniques that can provide accurate identification on the causative agents. With the advancements in biochemical and molecular biology techniques, several diagnostic methods with improved sensitivity and specificity for the detection of prevalent and/or unknown plant viruses are being continuously developed. Currently, serological and nucleic acid methods are the most widely used for plant viral diagnosis. Nucleic acid-based techniques that amplify target DNA/RNA have been evolved with many variants. However, there is growing interest in developing techniques that can be based in real-time and thus facilitate in-field diagnosis. Next-generation sequencing (NGS)-based innovative methods have shown great potential to detect multiple viruses simultaneously; however, such techniques are in the preliminary stages in plant viral disease diagnostics. This review discusses the recent progress in the use of NGS-based techniques for the detection, diagnosis, and identification of plant viral diseases. New portable devices and technologies that could provide real-time analyses in a relatively short period of time are prime important for in-field diagnostics. Current development and application of such tools and techniques along with their potential limitations in plant virology are likewise discussed in detail.
Collapse
|
34
|
Abstract
The ongoing pandemic of the new severe acute respiratory syndrome coronavirus (SARS-CoV-2) has caused more than one million deaths, overwhelmed many public health systems, and led to a worldwide economic recession. This has raised an unprecedented need to develop antiviral drugs and vaccines, which requires profound knowledge of the fundamental pathology of the virus, including its entry, replication, and release from host cells. The genome of coronaviruses comprises around 30 kb of positive single-stranded RNA, representing one of the largest RNA genomes of viruses. The 5′ part of the genome encodes a large polyprotein, PP1ab, which gives rise to 16 non-structural proteins (nsp1– nsp16). Two proteases encoded in nsp3 and nsp5 cleave the polyprotein into individual proteins. Most nsps belong to the viral replicase complex that promotes replication of the viral genome and translation of structural proteins by producing subgenomic mRNAs. The replicase complexes are found on double-membrane vesicles (DMVs) that contain viral double-stranded RNA. Expression of a small subset of viral proteins, including nsp3 and nsp4, is sufficient to induce formation of these DMVs in human cells, suggesting that both proteins deform host membranes into such structures. We will discuss the formation of DMVs and provide an overview of other membrane remodeling processes that are induced by coronaviruses.
Collapse
Affiliation(s)
- Jagan Mohan
- Membrane Biochemistry and Transport, Institut Pasteur, UMR3691 CNRS, F-75015, Paris, France
| | - Thomas Wollert
- Membrane Biochemistry and Transport, Institut Pasteur, UMR3691 CNRS, F-75015, Paris, France
| |
Collapse
|
35
|
Yang JE, Larson MR, Sibert BS, Shrum S, Wright ER. CorRelator: Interactive software for real-time high precision cryo-correlative light and electron microscopy. J Struct Biol 2021; 213:107709. [PMID: 33610654 PMCID: PMC8601405 DOI: 10.1016/j.jsb.2021.107709] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/06/2021] [Accepted: 02/11/2021] [Indexed: 12/31/2022]
Abstract
Cryo-correlative light and electron microscopy (CLEM) is a technique that uses the spatiotemporal cues from fluorescence light microscopy (FLM) to investigate the high-resolution ultrastructure of biological samples by cryo-electron microscopy (cryo-EM). Cryo-CLEM provides advantages for identifying and distinguishing fluorescently labeled proteins, macromolecular complexes, and organelles from the cellular environment. Challenges remain on how correlation workflows and software tools are implemented on different microscope platforms to support automated cryo-EM data acquisition. Here, we present CorRelator: an open-source desktop application that bridges between cryo-FLM and real-time cryo-EM/ET automated data collection. CorRelator implements a pixel-coordinate-to-stage-position transformation for flexible, high accuracy on-the-fly and post-acquisition correlation. CorRelator can be integrated into cryo-CLEM workflows and easily adapted to standard fluorescence and transmission electron microscope (TEM) system configurations. CorRelator was benchmarked under live-cell and cryogenic conditions using several FLM and TEM instruments, demonstrating that CorRelator reliably supports real-time, automated correlative cryo-EM/ET acquisition, through a combination of software-aided and interactive alignment. CorRelator is a cross-platform software package featuring an intuitive Graphical User Interface (GUI) that guides the user through the correlation process. CorRelator source code is available at: https://github.com/wright-cemrc-projects/corr.
Collapse
Affiliation(s)
- Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States
| | - Matthew R Larson
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States
| | - Bryan S Sibert
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States
| | - Samantha Shrum
- Biophysics Graduate Program, University of Wisconsin, Madison, WI 53706, United States
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States; Biophysics Graduate Program, University of Wisconsin, Madison, WI 53706, United States; Morgridge Institute for Research, Madison, WI, 53715, United States; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI 53706, United States.
| |
Collapse
|
36
|
Multiscale Electron Microscopy for the Study of Viral Replication Organelles. Viruses 2021; 13:v13020197. [PMID: 33525547 PMCID: PMC7912242 DOI: 10.3390/v13020197] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 11/17/2022] Open
Abstract
During infection with positive-strand RNA viruses, viral RNA synthesis associates with modified intracellular membranes that form unique and captivating structures in the cytoplasm of the infected cell. These viral replication organelles (ROs) play a key role in the replicative cycle of important human pathogens like coronaviruses, enteroviruses, or flaviviruses. From their discovery to date, progress in our understanding of viral ROs has closely followed new developments in electron microscopy (EM). This review gives a chronological account of this progress and an introduction to the different EM techniques that enabled it. With an ample repertoire of imaging modalities, EM is nowadays a versatile technique that provides structural and functional information at a wide range of scales. Together with well-established approaches like electron tomography or labeling methods, we examine more recent developments, such as volume scanning electron microscopy (SEM) and in situ cryotomography, which are only beginning to be applied to the study of viral ROs. We also highlight the first cryotomography analyses of viral ROs, which have led to the discovery of macromolecular complexes that may serve as RO channels that control the export of newly-made viral RNA. These studies are key first steps towards elucidating the macromolecular complexity of viral ROs.
Collapse
|
37
|
Zhang P, Mendonca L, Howe A, Gilchrist J, Sun D, Knight M, Zanetti-Domingues L, Bateman B, Krebs AS, Chen L, Radecke J, Sheng Y, Li V, Ni T, Kounatidis I, Koronfel M, Szynkiewicz M, Harkiolaki M, Martin-Fernandez M, James W. Correlative Multi-scale Cryo-imaging Unveils SARS-CoV-2 Assembly and Egress. RESEARCH SQUARE 2021. [PMID: 33501431 PMCID: PMC7836121 DOI: 10.21203/rs.3.rs-134794/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified recombinant viral components and inactivated viruses. However, structural and ultrastructural evidence on how the SARS-CoV-2 infection progresses in the frozen-hydrated native cellular context is scarce, and there is a lack of comprehensive knowledge on the SARS-CoV-2 replicative cycle. To correlate the cytopathic events induced by SARS-CoV-2 with virus replication process under the frozen-hydrated condition, here we established a unique multi-modal, multi-scale cryo-correlative platform to image SARS-CoV-2 infection in Vero cells. This platform combines serial cryoFIB/SEM volume imaging and soft X-ray cryo-tomography with cell lamellae-based cryo-electron tomography (cryoET) and subtomogram averaging. The results place critical SARS-CoV-2 structural events – e.g. viral RNA transport portals on double membrane vesicles, virus assembly and budding intermediates, virus egress pathways, and native virus spike structures from intracellular assembled and extracellular released virus - in the context of whole-cell images. The latter revealed numerous heterogeneous cytoplasmic vesicles, the formation of membrane tunnels through which viruses exit, and the drastic cytoplasm invasion into the nucleus. This integrated approach allows a holistic view of SARS-CoV-2 infection, from the whole cell to individual molecules.
Collapse
|
38
|
[Activation of positive-strand RNA virus genome replication complexes by host oxidation machinery and viroporins]. Uirusu 2021; 71:55-62. [PMID: 35526995 DOI: 10.2222/jsv.71.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
39
|
Transmembrane redox regulation of genome replication functions in positive-strand RNA viruses. Curr Opin Virol 2020; 47:25-31. [PMID: 33383355 DOI: 10.1016/j.coviro.2020.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023]
Abstract
Positive-strand RNA virus genome replication takes place on intracellular membranes that separate the reduced cytosol from the oxidized extracellular/luminal milieu. Ongoing studies of these membrane-bounded genome replication complexes have revealed underlying common principles in their structure, assembly and functionalization, including transmembrane features and redox dependencies. Among these, members of the alphavirus, flavivirus, and picornavirus supergroups all encode membrane-permeabilizing viroporins required for efficient RNA replication. For flaviviruses and particularly alphavirus supergroup members, these viroporins are linked to activating viral RNA capping and potentially other later-stage RNA replication functions, and to local transmembrane release of oxidizing potential to trigger these changes in cytoplasmic RNA replication complexes. Further exploration of these emerging shared principles could spur development of broad-spectrum antivirals.
Collapse
|
40
|
Enterovirus Infection Induces Massive Recruitment of All Isoforms of Small Cellular Arf GTPases to the Replication Organelles. J Virol 2020; 95:JVI.01629-20. [PMID: 33087467 DOI: 10.1128/jvi.01629-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/18/2020] [Indexed: 12/12/2022] Open
Abstract
Enterovirus replication requires the cellular protein GBF1, a guanine nucleotide exchange factor for small Arf GTPases. When activated, Arfs associate with membranes, where they regulate numerous steps of membrane homeostasis. The requirement for GBF1 implies that Arfs are important for replication, but which of the different Arfs function(s) during replication remains poorly understood. Here, we established cell lines expressing each of the human Arfs fused to a fluorescent tag and investigated their behavior during enterovirus infection. Arf1 was the first to be recruited to the replication organelles, where it strongly colocalized with the viral antigen 2B and mature virions but not double-stranded RNA. By the end of the infectious cycle, Arf3, Arf4, Arf5, and Arf6 were also concentrated on the replication organelles. Once on the replication membranes, all Arfs except Arf3 were no longer sensitive to inhibition of GBF1, suggesting that in infected cells they do not actively cycle between GTP- and GDP-bound states. Only the depletion of Arf1, but not other class 1 and 2 Arfs, significantly increased the sensitivity of replication to GBF1 inhibition. Surprisingly, depletion of Arf6, a class 3 Arf, normally implicated in plasma membrane events, also increased the sensitivity to GBF1 inhibition. Together, our results suggest that GBF1-dependent Arf1 activation directly supports the development and/or functioning of the replication complexes and that Arf6 plays a previously unappreciated role in viral replication. Our data reveal a complex pattern of Arf activation in enterovirus-infected cells that may contribute to the resilience of viral replication in different cellular environments.IMPORTANCE Enteroviruses include many known and emerging pathogens, such as poliovirus, enteroviruses 71 and D68, and others. However, licensed vaccines are available only against poliovirus and enterovirus 71, and specific anti-enterovirus therapeutics are lacking. Enterovirus infection induces the massive remodeling of intracellular membranes and the development of specialized domains harboring viral replication complexes, replication organelles. Here, we investigated the roles of small Arf GTPases during enterovirus infection. Arfs control distinct steps in intracellular membrane traffic, and one of the Arf-activating proteins, GBF1, is a cellular factor required for enterovirus replication. We found that all Arfs expressed in human cells, including Arf6, normally associated with the plasma membrane, are recruited to the replication organelles and that Arf1 appears to be the most important Arf for enterovirus replication. These results document the rewiring of the cellular membrane pathways in infected cells and may provide new ways of controlling enterovirus infections.
Collapse
|
41
|
Varkey J, Zhang J, Kim J, George G, He G, Belov G, Langen R, Wang X. An Amphipathic Alpha-Helix Domain from Poliovirus 2C Protein Tubulate Lipid Vesicles. Viruses 2020; 12:v12121466. [PMID: 33353144 PMCID: PMC7766222 DOI: 10.3390/v12121466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 02/01/2023] Open
Abstract
Positive-strand RNA viruses universally remodel host intracellular membranes to form membrane-bound viral replication complexes, where viral offspring RNAs are synthesized. In the majority of cases, viral replication proteins are targeted to and play critical roles in the modulation of the designated organelle membranes. Many viral replication proteins do not have transmembrane domains, but contain single or multiple amphipathic alpha-helices. It has been conventionally recognized that these helices serve as an anchor for viral replication protein to be associated with membranes. We report here that a peptide representing the amphipathic α-helix at the N-terminus of the poliovirus 2C protein not only binds to liposomes, but also remodels spherical liposomes into tubules. The membrane remodeling ability of this amphipathic alpha-helix is similar to that recognized in other amphipathic alpha-helices from cellular proteins involved in membrane remodeling, such as BAR domain proteins. Mutations affecting the hydrophobic face of the amphipathic alpha-helix severely compromised membrane remodeling of vesicles with physiologically relevant phospholipid composition. These mutations also affected the ability of poliovirus to form plaques indicative of reduced viral replication, further underscoring the importance of membrane remodeling by the amphipathic alpha-helix in possible relation to the formation of viral replication complexes.
Collapse
Affiliation(s)
- Jobin Varkey
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA; (J.V.); (G.G.)
| | - Jiantao Zhang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (J.Z.); (G.H.)
| | - Junghyun Kim
- Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA; (J.K.); (G.B.)
| | - Gincy George
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA; (J.V.); (G.G.)
| | - Guijuan He
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (J.Z.); (G.H.)
| | - George Belov
- Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA; (J.K.); (G.B.)
| | - Ralf Langen
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA; (J.V.); (G.G.)
- Correspondence: (R.L.); (X.W.); Tel.: +1-323-442-1323 (R.L.); +1-540-231-1868 (X.W.)
| | - Xiaofeng Wang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (J.Z.); (G.H.)
- Correspondence: (R.L.); (X.W.); Tel.: +1-323-442-1323 (R.L.); +1-540-231-1868 (X.W.)
| |
Collapse
|
42
|
Feng Z, Kovalev N, Nagy PD. Key interplay between the co-opted sorting nexin-BAR proteins and PI3P phosphoinositide in the formation of the tombusvirus replicase. PLoS Pathog 2020; 16:e1009120. [PMID: 33370420 PMCID: PMC7833164 DOI: 10.1371/journal.ppat.1009120] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/25/2021] [Accepted: 10/31/2020] [Indexed: 12/27/2022] Open
Abstract
Positive-strand RNA viruses replicate in host cells by forming large viral replication organelles, which harbor numerous membrane-bound viral replicase complexes (VRCs). In spite of its essential role in viral replication, the biogenesis of the VRCs is not fully understood. The authors identified critical roles of cellular membrane-shaping proteins and PI(3)P (phosphatidylinositol 3-phosphate) phosphoinositide, a minor lipid with key functions in endosomal vesicle trafficking and autophagosome biogenesis, in VRC formation for tomato bushy stunt virus (TBSV). The authors show that TBSV co-opts the endosomal SNX-BAR (sorting nexin with Bin/Amphiphysin/Rvs- BAR domain) proteins, which bind to PI(3)P and have membrane-reshaping function during retromer tubular vesicle formation, directly into the VRCs to boost progeny viral RNA synthesis. We find that the viral replication protein-guided recruitment and pro-viral function of the SNX-BAR proteins depends on enrichment of PI(3)P at the site of viral replication. Depletion of SNX-BAR proteins or PI(3)P renders the viral double-stranded (ds)RNA replication intermediate RNAi-sensitive within the VRCs in the surrogate host yeast and in planta and ribonuclease-sensitive in cell-free replicase reconstitution assays in yeast cell extracts or giant unilamellar vesicles (GUVs). Based on our results, we propose that PI(3)P and the co-opted SNX-BAR proteins are coordinately exploited by tombusviruses to promote VRC formation and to play structural roles and stabilize the VRCs during viral replication. Altogether, the interplay between the co-opted SNX-BAR membrane-shaping proteins, PI(3)P and the viral replication proteins leads to stable VRCs, which provide the essential protection of the viral RNAs against the host antiviral responses.
Collapse
Affiliation(s)
- Zhike Feng
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Nikolay Kovalev
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Peter D. Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
| |
Collapse
|
43
|
Klein S, Cortese M, Winter SL, Wachsmuth-Melm M, Neufeldt CJ, Cerikan B, Stanifer ML, Boulant S, Bartenschlager R, Chlanda P. SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography. Nat Commun 2020; 11:5885. [PMID: 33208793 PMCID: PMC7676268 DOI: 10.1038/s41467-020-19619-7] [Citation(s) in RCA: 446] [Impact Index Per Article: 111.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/23/2020] [Indexed: 01/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID19 pandemic, is a highly pathogenic β-coronavirus. As other coronaviruses, SARS-CoV-2 is enveloped, replicates in the cytoplasm and assembles at intracellular membranes. Here, we structurally characterize the viral replication compartment and report critical insights into the budding mechanism of the virus, and the structure of extracellular virions close to their native state by in situ cryo-electron tomography and subtomogram averaging. We directly visualize RNA filaments inside the double membrane vesicles, compartments associated with viral replication. The RNA filaments show a diameter consistent with double-stranded RNA and frequent branching likely representing RNA secondary structures. We report that assembled S trimers in lumenal cisternae do not alone induce membrane bending but laterally reorganize on the envelope during virion assembly. The viral ribonucleoprotein complexes (vRNPs) are accumulated at the curved membrane characteristic for budding sites suggesting that vRNP recruitment is enhanced by membrane curvature. Subtomogram averaging shows that vRNPs are distinct cylindrical assemblies. We propose that the genome is packaged around multiple separate vRNP complexes, thereby allowing incorporation of the unusually large coronavirus genome into the virion while maintaining high steric flexibility between the vRNPs.
Collapse
Affiliation(s)
- Steffen Klein
- Schaller Research Groups, Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany.,Research Group "Membrane Biology of Viral Infection," Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases-Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Sophie L Winter
- Schaller Research Groups, Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany.,Research Group "Membrane Biology of Viral Infection," Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany
| | - Moritz Wachsmuth-Melm
- Schaller Research Groups, Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany.,Research Group "Membrane Biology of Viral Infection," Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany
| | - Christopher J Neufeldt
- Department of Infectious Diseases-Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Berati Cerikan
- Department of Infectious Diseases-Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Megan L Stanifer
- Department of Infectious Diseases-Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Steeve Boulant
- Research Group "Host/Pathogen Interactions at Intestinal Epithelial Surfaces," Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases-Molecular Virology, Heidelberg University, Heidelberg, Germany. .,Division Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany. .,German Center for Infection Research (DZIF), (Heidelberg Partner Site), Heidelberg, Germany.
| | - Petr Chlanda
- Schaller Research Groups, Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany. .,Research Group "Membrane Biology of Viral Infection," Department of Infectious Diseases-Virology, Heidelberg University, Heidelberg, Germany.
| |
Collapse
|
44
|
Qu F, Zheng L, Zhang S, Sun R, Slot J, Miyashita S. Bottleneck, Isolate, Amplify, Select (BIAS) as a mechanistic framework for intracellular population dynamics of positive-sense RNA viruses. Virus Evol 2020; 6:veaa086. [PMID: 33343926 PMCID: PMC7733609 DOI: 10.1093/ve/veaa086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many positive-sense RNA viruses, especially those infecting plants, are known to experience stringent, stochastic population bottlenecks inside the cells they invade, but exactly how and why these populations become bottlenecked are unclear. A model proposed ten years ago advocates that such bottlenecks are evolutionarily favored because they cause the isolation of individual viral variants in separate cells. Such isolation in turn allows the viral variants to manifest the phenotypic differences they encode. Recently published observations lend mechanistic support to this model and prompt us to refine the model with novel molecular details. The refined model, designated Bottleneck, Isolate, Amplify, Select (BIAS), postulates that these viruses impose population bottlenecks on themselves by encoding bottleneck-enforcing proteins (BNEPs) that function in a concentration-dependent manner. In cells simultaneously invaded by numerous virions of the same virus, BNEPs reach the bottleneck-ready concentration sufficiently early to arrest nearly all internalized viral genomes. As a result, very few (as few as one) viral genomes stochastically escape to initiate reproduction. Repetition of this process in successively infected cells isolates viral genomes with different mutations in separate cells. This isolation prevents mutant viruses encoding defective viral proteins from hitchhiking on sister genome-encoded products, leading to the swift purging of such mutants. Importantly, genome isolation also ensures viral genomes harboring beneficial mutations accrue the cognate benefit exclusively to themselves, leading to the fixation of such beneficial mutations. Further interrogation of the BIAS hypothesis promises to deepen our understanding of virus evolution and inspire new solutions to virus disease mitigation.
Collapse
Affiliation(s)
- Feng Qu
- Department of Plant Pathology and.,Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | - Limin Zheng
- Department of Plant Pathology and.,Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | - Shaoyan Zhang
- Department of Plant Pathology and.,Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | - Rong Sun
- Department of Plant Pathology and.,Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | | | - Shuhei Miyashita
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-aoba, Aoba-ku, Sendai 980-0845, Japan
| |
Collapse
|
45
|
Quemin ERJ, Machala EA, Vollmer B, Pražák V, Vasishtan D, Rosch R, Grange M, Franken LE, Baker LA, Grünewald K. Cellular Electron Cryo-Tomography to Study Virus-Host Interactions. Annu Rev Virol 2020; 7:239-262. [PMID: 32631159 DOI: 10.1146/annurev-virology-021920-115935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses are obligatory intracellular parasites that reprogram host cells upon infection to produce viral progeny. Here, we review recent structural insights into virus-host interactions in bacteria, archaea, and eukaryotes unveiled by cellular electron cryo-tomography (cryoET). This advanced three-dimensional imaging technique of vitreous samples in near-native state has matured over the past two decades and proven powerful in revealing molecular mechanisms underlying viral replication. Initial studies were restricted to cell peripheries and typically focused on early infection steps, analyzing surface proteins and viral entry. Recent developments including cryo-thinning techniques, phase-plate imaging, and correlative approaches have been instrumental in also targeting rare events inside infected cells. When combined with advances in dedicated image analyses and processing methods, details of virus assembly and egress at (sub)nanometer resolution were uncovered. Altogether, we provide a historical and technical perspective and discuss future directions and impacts of cryoET for integrative structural cell biology analyses of viruses.
Collapse
Affiliation(s)
- Emmanuelle R J Quemin
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
| | - Emily A Machala
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Benjamin Vollmer
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Vojtěch Pražák
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Daven Vasishtan
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Rene Rosch
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
| | - Michael Grange
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Linda E Franken
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
| | - Lindsay A Baker
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Kay Grünewald
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| |
Collapse
|
46
|
Affiliation(s)
- Nuruddin Unchwaniwala
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI, USA. .,University of Wisconsin-Madison, Madison, WI, USA
| | - Paul Ahlquist
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI, USA. .,University of Wisconsin-Madison, Madison, WI, USA.,Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
47
|
Li X, Wang M, Cheng A, Wen X, Ou X, Mao S, Gao Q, Sun D, Jia R, Yang Q, Wu Y, Zhu D, Zhao X, Chen S, Liu M, Zhang S, Liu Y, Yu Y, Zhang L, Tian B, Pan L, Chen X. Enterovirus Replication Organelles and Inhibitors of Their Formation. Front Microbiol 2020; 11:1817. [PMID: 32973693 PMCID: PMC7468505 DOI: 10.3389/fmicb.2020.01817] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/10/2020] [Indexed: 12/23/2022] Open
Abstract
Enteroviral replication reorganizes the cellular membrane. Upon infection, viral proteins and hijacked host factors generate unique structures called replication organelles (ROs) to replicate their viral genomes. ROs promote efficient viral genome replication, coordinate the steps of the viral replication cycle, and protect viral RNA from host immune responses. More recent researches have focused on the ultrastructure structures, formation mechanism, and functions in the virus life cycle of ROs. Dynamic model of enterovirus ROs structure is proposed, and the secretory pathway, the autophagy pathway, and lipid metabolism are found to be associated in the formation of ROs. With deeper understanding of ROs, some compounds have been found to show inhibitory effects on viral replication by targeting key proteins in the process of ROs formation. Here, we review the recent findings concerning the role, morphology, biogenesis, formation mechanism, and inhibitors of enterovirus ROs.
Collapse
Affiliation(s)
- Xinhong Li
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xingjian Wen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yunya Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Leichang Pan
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyue Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
48
|
Wolff G, Limpens RWAL, Zevenhoven-Dobbe JC, Laugks U, Zheng S, de Jong AWM, Koning RI, Agard DA, Grünewald K, Koster AJ, Snijder EJ, Bárcena M. A molecular pore spans the double membrane of the coronavirus replication organelle. Science 2020; 369:1395-1398. [PMID: 32763915 PMCID: PMC7665310 DOI: 10.1126/science.abd3629] [Citation(s) in RCA: 325] [Impact Index Per Article: 81.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022]
Abstract
Coronaviruses transform host cell membranes into peculiar double-membrane vesicles that have long been thought to accommodate viral genome replication. However, because these compartments appeared to be completely sealed, it has remained unknown how the newly made viral RNA could be exported to the cytosol for translation and packaging into new virions. Wolff et al. used cryo–electron microscopy to identify a molecular pore that spans the double membrane (see the Perspective by Unchwaniwala and Ahlquist). Six copies of a large coronavirus transmembrane protein formed the core of this structure, which may constitute a viral RNA export channel and provide a target for future antiviral interventions. Science, this issue p. 1395; see also p. 1306 Coronavirus genome replication is associated with virus-induced cytosolic double-membrane vesicles, which may provide a tailored microenvironment for viral RNA synthesis in the infected cell. However, it is unclear how newly synthesized genomes and messenger RNAs can travel from these sealed replication compartments to the cytosol to ensure their translation and the assembly of progeny virions. In this study, we used cellular cryo–electron microscopy to visualize a molecular pore complex that spans both membranes of the double-membrane vesicle and would allow export of RNA to the cytosol. A hexameric assembly of a large viral transmembrane protein was found to form the core of the crown-shaped complex. This coronavirus-specific structure likely plays a key role in coronavirus replication and thus constitutes a potential drug target.
Collapse
Affiliation(s)
- Georg Wolff
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands
| | - Ronald W A L Limpens
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands
| | - Jessika C Zevenhoven-Dobbe
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, Netherlands
| | - Ulrike Laugks
- Department of Structural Cell Biology of Viruses, Centre for Structural Systems Biology, Heinrich Pette Institute, Leibnitz Institute of Experimental Virology, 22607 Hamburg, Germany
| | - Shawn Zheng
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Anja W M de Jong
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands
| | - Roman I Koning
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands
| | - David A Agard
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Kay Grünewald
- Department of Structural Cell Biology of Viruses, Centre for Structural Systems Biology, Heinrich Pette Institute, Leibnitz Institute of Experimental Virology, 22607 Hamburg, Germany.,Department of Chemistry, MIN Faculty, Universität Hamburg, 20146 Hamburg, Germany
| | - Abraham J Koster
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, Netherlands
| | - Montserrat Bárcena
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZC, Netherlands.
| |
Collapse
|
49
|
Unchwaniwala N, Zhan H, Pennington J, Horswill M, den Boon JA, Ahlquist P. Subdomain cryo-EM structure of nodaviral replication protein A crown complex provides mechanistic insights into RNA genome replication. Proc Natl Acad Sci U S A 2020; 117:18680-18691. [PMID: 32690711 PMCID: PMC7414174 DOI: 10.1073/pnas.2006165117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
For positive-strand RNA [(+)RNA] viruses, the major target for antiviral therapies is genomic RNA replication, which occurs at poorly understood membrane-bound viral RNA replication complexes. Recent cryoelectron microscopy (cryo-EM) of nodavirus RNA replication complexes revealed that the viral double-stranded RNA replication template is coiled inside a 30- to 90-nm invagination of the outer mitochondrial membrane, whose necked aperture to the cytoplasm is gated by a 12-fold symmetric, 35-nm diameter "crown" complex that contains multifunctional viral RNA replication protein A. Here we report optimizing cryo-EM tomography and image processing to improve crown resolution from 33 to 8.5 Å. This resolves the crown into 12 distinct vertical segments, each with 3 major subdomains: A membrane-connected basal lobe and an apical lobe that together comprise the ∼19-nm-diameter central turret, and a leg emerging from the basal lobe that connects to the membrane at ∼35-nm diameter. Despite widely varying replication vesicle diameters, the resulting two rings of membrane interaction sites constrain the vesicle neck to a highly uniform shape. Labeling protein A with a His-tag that binds 5-nm Ni-nanogold allowed cryo-EM tomography mapping of the C terminus of protein A to the apical lobe, which correlates well with the predicted structure of the C-proximal polymerase domain of protein A. These and other results indicate that the crown contains 12 copies of protein A arranged basally to apically in an N-to-C orientation. Moreover, the apical polymerase localization has significant mechanistic implications for template RNA recruitment and (-) and (+)RNA synthesis.
Collapse
Affiliation(s)
- Nuruddin Unchwaniwala
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706
| | - Hong Zhan
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706
| | - Janice Pennington
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706
| | - Mark Horswill
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706
| | - Johan A den Boon
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706
| | - Paul Ahlquist
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI 53715;
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI 53706
| |
Collapse
|
50
|
Nagy PD. Host protein chaperones, RNA helicases and the ubiquitin network highlight the arms race for resources between tombusviruses and their hosts. Adv Virus Res 2020; 107:133-158. [PMID: 32711728 PMCID: PMC7342006 DOI: 10.1016/bs.aivir.2020.06.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Positive-strand RNA viruses need to arrogate many cellular resources to support their replication and infection cycles. These viruses co-opt host factors, lipids and subcellular membranes and exploit cellular metabolites to built viral replication organelles in infected cells. However, the host cells have their defensive arsenal of factors to protect themselves from easy exploitation by viruses. In this review, the author discusses an emerging arms race for cellular resources between viruses and hosts, which occur during the early events of virus-host interactions. Recent findings with tomato bushy stunt virus and its hosts revealed that the need of the virus to exploit and co-opt given members of protein families provides an opportunity for the host to deploy additional members of the same or associated protein family to interfere with virus replication. Three examples with well-established heat shock protein 70 and RNA helicase protein families and the ubiquitin network will be described to illustrate this model on the early arms race for cellular resources between tombusviruses and their hosts. We predict that arms race for resources with additional cellular protein families will be discovered with tombusviruses. These advances will fortify research on interactions among other plant and animal viruses and their hosts.
Collapse
Affiliation(s)
- Peter D Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States.
| |
Collapse
|