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Jobe F, Kelly JT, Simpson J, Wells J, Armstrong SD, Spick M, Lacey E, Logan L, Geifman N, Hawes P, Bailey D. Viral PIC-pocketing: RSV sequestration of translational preinitiation complexes into bi-phasic biomolecular condensates. J Virol 2024; 98:e0015324. [PMID: 38421168 PMCID: PMC10949503 DOI: 10.1128/jvi.00153-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 03/02/2024] Open
Abstract
Orthopneumoviruses characteristically form membrane-less cytoplasmic inclusion bodies (IBs) wherein RNA replication and transcription occur. Here, we report a strategy whereby the orthopneumoviruses sequester various components of the translational preinitiation complex machinery into viral inclusion bodies to facilitate translation of their own mRNAs-PIC-pocketing. Electron microscopy of respiratory syncytial virus (RSV)-infected cells revealed bi-phasic organization of IBs, specifically, spherical "droplets" nested within the larger inclusion. Using correlative light and electron microscopy, combined with fluorescence in situ hybridization, we showed that the observed bi-phasic morphology represents functional compartmentalization of the inclusion body and that these domains are synonymous with the previously reported inclusion body-associated granules (IBAGs). Detailed analysis demonstrated that IBAGs concentrate nascent viral mRNA, the viral M2-1 protein as well as components of eukaryotic translation initiation factors (eIF), eIF4F and eIF3, and 40S complexes involved in translation initiation. Interestingly, although ribopuromycylation-based imaging indicates that the majority of viral mRNA translation occurs in the cytoplasm, there was some evidence for intra-IBAG translation, consistent with the likely presence of ribosomes in a subset of IBAGs imaged by electron microscopy. Mass spectrometry analysis of sub-cellular fractions from RSV-infected cells identified significant modification of the cellular translation machinery; however, interestingly, ribopuromycylation assays showed no changes to global levels of translation. The mechanistic basis for this pathway was subsequently determined to involve the viral M2-1 protein interacting with eIF4G, likely to facilitate its transport between the cytoplasm and the separate phases of the viral inclusion body. In summary, our data show that these viral organelles function to spatially regulate early steps in viral translation within a highly selective bi-phasic biomolecular condensate. IMPORTANCE Respiratory syncytial viruses (RSVs) of cows and humans are a significant cause of morbidity and mortality in their respective populations. These RNA viruses replicate in the infected cells by compartmentalizing the cell's cytoplasm into distinct viral microdomains called inclusion bodies (IBs). In this paper, we show that these IBs are further compartmentalized into smaller structures that have significantly different density, as observed by electron microscopy. Within smaller intra-IB structures, we observed ribosomal components and evidence for active translation. These findings highlight that RSV may additionally compartmentalize translation to favor its own replication in the cell. These data contribute to our understanding of how RNA viruses hijack the cell to favor replication of their own genomes and may provide new targets for antiviral therapeutics in vivo.
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Affiliation(s)
| | | | | | - Joanna Wells
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | - Stuart D. Armstrong
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Matt Spick
- School of Health Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Emily Lacey
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | - Leanne Logan
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | - Nophar Geifman
- School of Health Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | | | - Dalan Bailey
- The Pirbright Institute, Woking, Surrey, United Kingdom
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Alruwaili M, Armstrong S, Prince T, Erdmann M, Matthews DA, Luu L, Davidson A, Aljabr W, Hiscox JA. SARS-CoV-2 NSP12 associates with TRiC and the P323L substitution acts as a host adaption. J Virol 2023; 97:e0042423. [PMID: 37929963 PMCID: PMC10688337 DOI: 10.1128/jvi.00424-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/29/2023] [Indexed: 11/07/2023] Open
Abstract
IMPORTANCE SARS-CoV-2 has caused a worldwide health and economic crisis. During the course of the pandemic, genetic changes occurred in the virus, which have resulted in new properties of the virus-particularly around gains in transmission and the ability to partially evade either natural or vaccine-acquired immunity. Some of these viruses have been labeled Variants of Concern (VoCs). At the root of all VoCs are two mutations, one in the viral spike protein that has been very well characterized and the other in the virus polymerase (NSP12). This is the viral protein responsible for replicating the genome. We show that NSP12 associates with host cell proteins that act as a scaffold to facilitate the function of this protein. Furthermore, we found that different variants of NSP12 interact with host cell proteins in subtle and different ways, which affect function.
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Affiliation(s)
- Muhannad Alruwaili
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Medical Laboratory Technology Department, Northern Border University, Arar City, Saudi Arabia
| | - Stuart Armstrong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Tessa Prince
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Maximillian Erdmann
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - David A. Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Lisa Luu
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Andrew Davidson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | | | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
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García-Dorival I, Cuesta-Geijo MÁ, Galindo I, Del Puerto A, Barrado-Gil L, Urquiza J, Alonso C. Elucidation of the Cellular Interactome of African Swine Fever Virus Fusion Proteins and Identification of Potential Therapeutic Targets. Viruses 2023; 15:v15051098. [PMID: 37243184 DOI: 10.3390/v15051098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
African swine fever virus (ASFV) encodes more than 150 proteins, most of them of unknown function. We used a high-throughput proteomic analysis to elucidate the interactome of four ASFV proteins, which potentially mediate a critical step of the infection cycle, the fusion and endosomal exit of the virions. Using affinity purification and mass spectrometry, we were able to identify potential interacting partners for those ASFV proteins P34, E199L, MGF360-15R and E248R. Representative molecular pathways for these proteins were intracellular and Golgi vesicle transport, endoplasmic reticulum organization, lipid biosynthesis, and cholesterol metabolism. Rab geranyl geranylation emerged as a significant hit, and also Rab proteins, which are crucial regulators of the endocytic pathway and interactors of both p34 and E199L. Rab proteins co-ordinate a tight regulation of the endocytic pathway that is necessary for ASFV infection. Moreover, several interactors were proteins involved in the molecular exchange at ER membrane contacts. These ASFV fusion proteins shared interacting partners, suggesting potential common functions. Membrane trafficking and lipid metabolism were important categories, as we found significant interactions with several enzymes of the lipid metabolism. These targets were confirmed using specific inhibitors with antiviral effect in cell lines and macrophages.
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Affiliation(s)
- Isabel García-Dorival
- Departmento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain
| | - Miguel Ángel Cuesta-Geijo
- Departmento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain
| | - Inmaculada Galindo
- Departmento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain
| | - Ana Del Puerto
- Departmento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain
| | - Lucía Barrado-Gil
- Departmento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain
| | - Jesús Urquiza
- Departmento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain
| | - Covadonga Alonso
- Departmento de Biotecnología, INIA-CSIC, Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km 7.5, 28040 Madrid, Spain
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Wang X, Stelzer-Braid S, Scotch M, Rawlinson WD. Detection of respiratory viruses directly from clinical samples using next-generation sequencing: A literature review of recent advances and potential for routine clinical use. Rev Med Virol 2022; 32:e2375. [PMID: 35775736 PMCID: PMC9539958 DOI: 10.1002/rmv.2375] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/01/2022] [Accepted: 06/20/2022] [Indexed: 11/15/2022]
Abstract
Acute respiratory infection is the third most frequent cause of mortality worldwide, causing over 4.25 million deaths annually. Although most diagnosed acute respiratory infections are thought to be of viral origin, the aetiology often remains unclear. The advent of next‐generation sequencing (NGS) has revolutionised the field of virus discovery and identification, particularly in the detection of unknown respiratory viruses. We systematically reviewed the application of NGS technologies for detecting respiratory viruses from clinical samples and outline potential barriers to the routine clinical introduction of NGS. The five databases searched for studies published in English from 01 January 2010 to 01 February 2021, which led to the inclusion of 52 studies. A total of 14 different models of NGS platforms were summarised from included studies. Among these models, second‐generation sequencing platforms (e.g., Illumina sequencers) were used in the majority of studies (41/52, 79%). Moreover, NGS platforms have proven successful in detecting a variety of respiratory viruses, including influenza A/B viruses (9/52, 17%), SARS‐CoV‐2 (21/52, 40%), parainfluenza virus (3/52, 6%), respiratory syncytial virus (1/52, 2%), human metapneumovirus (2/52, 4%), or a viral panel including other respiratory viruses (16/52, 31%). The review of NGS technologies used in previous studies indicates the advantages of NGS technologies in novel virus detection, virus typing, mutation identification, and infection cluster assessment. Although there remain some technical and ethical challenges associated with NGS use in clinical laboratories, NGS is a promising future tool to improve understanding of respiratory viruses and provide a more accurate diagnosis with simultaneous virus characterisation.
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Affiliation(s)
- Xinye Wang
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Sacha Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew Scotch
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.,Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
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Guimerà Busquets M, Pullinger GD, Darpel KE, Cooke L, Armstrong S, Simpson J, Palmarini M, Fragkoudis R, Mertens PPC. An Early Block in the Replication of the Atypical Bluetongue Virus Serotype 26 in Culicoides Cells Is Determined by Its Capsid Proteins. Viruses 2021; 13. [PMID: 34063508 DOI: 10.3390/v13050919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 12/29/2022] Open
Abstract
Arboviruses such as bluetongue virus (BTV) replicate in arthropod vectors involved in their transmission between susceptible vertebrate-hosts. The "classical" BTV strains infect and replicate effectively in cells of their insect-vectors (Culicoides biting-midges), as well as in those of their mammalian-hosts (ruminants). However, in the last decade, some "atypical" BTV strains, belonging to additional serotypes (e.g., BTV-26), have been found to replicate efficiently only in mammalian cells, while their replication is severely restricted in Culicoides cells. Importantly, there is evidence that these atypical BTV are transmitted by direct-contact between their mammalian hosts. Here, the viral determinants and mechanisms restricting viral replication in Culicoides were investigated using a classical BTV-1, an "atypical" BTV-26 and a BTV-1/BTV-26 reassortant virus, derived by reverse genetics. Viruses containing the capsid of BTV-26 showed a reduced ability to attach to Culicoides cells, blocking early steps of the replication cycle, while attachment and replication in mammalian cells was not restricted. The replication of BTV-26 was also severely reduced in other arthropod cells, derived from mosquitoes or ticks. The data presented identifies mechanisms and potential barriers to infection and transmission by the newly emerged "atypical" BTV strains in Culicoides.
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Mann M, Brasier AR. Evolution of proteomics technologies for understanding respiratory syncytial virus pathogenesis. Expert Rev Proteomics 2021; 18:379-394. [PMID: 34018899 PMCID: PMC8277732 DOI: 10.1080/14789450.2021.1931130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/14/2021] [Indexed: 10/21/2022]
Abstract
Introduction: Respiratory syncytial virus (RSV) is a major human pathogen associated with long term morbidity. RSV replication occurs primarily in the epithelium, producing a complex cellular response associated with acute inflammation and long-lived changes in pulmonary function and allergic disease. Proteomics approaches provide important insights into post-transcriptional regulatory processes including alterations in cellular complexes regulating the coordinated innate response and epigenome.Areas covered: Peer-reviewed proteomics studies of host responses to RSV infections and proteomics techniques were analyzed. Methodologies identified include 1)." bottom-up" discovery proteomics, 2). Organellar proteomics by LC-gel fractionation; 3). Dynamic changes in protein interaction networks by LC-MS; and 4). selective reaction monitoring MS. We introduce recent developments in single-cell proteomics, top-down mass spectrometry, and photo-cleavable surfactant chemistries that will have impact on understanding how RSV induces extracellular matrix (ECM) composition and airway remodeling.Expert opinion: RSV replication induces global changes in the cellular proteome, dynamic shifts in nuclear proteins, and remodeling of epigenetic regulatory complexes linked to the innate response. Pathways discovered by proteomics technologies have led to deeper mechanistic understanding of the roles of heat shock proteins, redox response, transcriptional elongation complex remodeling and ECM secretion remodeling in host responses to RSV infections and pathological sequelae.
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Affiliation(s)
- Morgan Mann
- Department of Internal Medicine, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI, USA
| | - Allan R Brasier
- Department of Internal Medicine and Institute for Clinical and Translational Research (ICTR), University of Wisconsin-Madison, Madison, WI, USA
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Coombs KM. Update on Proteomic approaches to uncovering virus-induced protein alterations and virus -host protein interactions during the progression of viral infection. Expert Rev Proteomics 2020; 17:513-532. [PMID: 32910682 DOI: 10.1080/14789450.2020.1821656] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Viruses induce profound changes in the cells they infect. Understanding these perturbations will assist in designing better therapeutics to combat viral infection. System-based proteomic assays now provide unprecedented opportunity to monitor large numbers of cellular proteins. AREAS COVERED This review will describe various quantitative and functional mass spectrometry-based methods, and complementary non-mass spectrometry-based methods, such as aptamer profiling and proximity extension assays, and examples of how each are used to delineate how viruses affect host cells, identify which viral proteins interact with which cellular proteins, and how these change during the course of a viral infection. PubMed was searched multiple times prior to manuscript submissions and revisions, using virus, viral, proteomics; in combination with each keyword. The most recent examples of published works from each search were then analyzed. EXPERT OPINION There has been exponential growth in numbers and types of proteomic analyses in recent years. Continued development of reagents that allow increased multiplexing and deeper proteomic probing of the cell, at quantitative and functional levels, enhancements that target more important protein modifications, and improved bioinformatics software tools and pathway prediction algorithms will accelerate this growth and usher in a new era of host proteome understanding.
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Affiliation(s)
- Kevin M Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba , Winnipeg, Manitoba, Canada.,Manitoba Centre for Proteomics and Systems Biology , Winnipeg, Manitoba, Canada.,Manitoba Institute of Child Health , Winnipeg, Manitoba, Canada
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Davidson AD, Williamson MK, Lewis S, Shoemark D, Carroll MW, Heesom KJ, Zambon M, Ellis J, Lewis PA, Hiscox JA, Matthews DA. Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein. Genome Med 2020; 12:68. [PMID: 32723359 PMCID: PMC7386171 DOI: 10.1186/s13073-020-00763-0] [Citation(s) in RCA: 268] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND SARS-CoV-2 is a recently emerged respiratory pathogen that has significantly impacted global human health. We wanted to rapidly characterise the transcriptomic, proteomic and phosphoproteomic landscape of this novel coronavirus to provide a fundamental description of the virus's genomic and proteomic potential. METHODS We used direct RNA sequencing to determine the transcriptome of SARS-CoV-2 grown in Vero E6 cells which is widely used to propagate the novel coronavirus. The viral transcriptome was analysed using a recently developed ORF-centric pipeline. Allied to this, we used tandem mass spectrometry to investigate the proteome and phosphoproteome of the same virally infected cells. RESULTS Our integrated analysis revealed that the viral transcripts (i.e. subgenomic mRNAs) generally fitted the expected transcription model for coronaviruses. Importantly, a 24 nt in-frame deletion was detected in over half of the subgenomic mRNAs encoding the spike (S) glycoprotein and was predicted to remove a proposed furin cleavage site from the S glycoprotein. Tandem mass spectrometry identified over 500 viral peptides and 44 phosphopeptides in virus-infected cells, covering almost all proteins predicted to be encoded by the SARS-CoV-2 genome, including peptides unique to the deleted variant of the S glycoprotein. CONCLUSIONS Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein, a leading vaccine target, shows that this and other regions of SARS-CoV-2 proteins may readily mutate. The furin site directs cleavage of the S glycoprotein into functional subunits during virus entry or exit and likely contributes strongly to the pathogenesis and zoonosis of this virus. Our data emphasises that the viral genome sequence should be carefully monitored during the growth of viral stocks for research, animal challenge models and, potentially, in clinical samples. Such variations may result in different levels of virulence, morbidity and mortality.
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Affiliation(s)
- Andrew D Davidson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK.
| | - Maia Kavanagh Williamson
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Sebastian Lewis
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Deborah Shoemark
- School of Biochemistry, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Miles W Carroll
- Research and Development Institute, National Infection Service, Public Health, England, Porton Down, Wiltshire, UK
- National Institute Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Kate J Heesom
- Proteomics Facility Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Maria Zambon
- Virus Reference Department, Public Health England (Colindale), London, UK
| | - Joanna Ellis
- Virus Reference Department, Public Health England (Colindale), London, UK
| | - Philip A Lewis
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Julian A Hiscox
- National Institute Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Liverpool Health Partners, Liverpool, UK
| | - David A Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University Walk, University of Bristol, Bristol, BS8 1TD, UK.
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