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Jiao Y, Zhao P, Xu LD, Yu JQ, Cai HL, Zhang C, Tong C, Yang YL, Xu P, Sun Q, Chen N, Wang B, Huang YW. Enteric coronavirus nsp2 is a virulence determinant that recruits NBR1 for autophagic targeting of TBK1 to diminish the innate immune response. Autophagy 2024; 20:1762-1779. [PMID: 38597182 DOI: 10.1080/15548627.2024.2340420] [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: 09/22/2023] [Accepted: 04/04/2024] [Indexed: 04/11/2024] Open
Abstract
Non-structural protein 2 (nsp2) exists in all coronaviruses (CoVs), while its primary function in viral pathogenicity, is largely unclear. One such enteric CoV, porcine epidemic diarrhea virus (PEDV), causes high mortality in neonatal piglets worldwide. To determine the biological role of nsp2, we generated a PEDV mutant containing a complete nsp2 deletion (rPEDV-Δnsp2) from a highly pathogenic strain by reverse genetics, showing that nsp2 was dispensable for PEDV infection, while its deficiency reduced viral replication in vitro. Intriguingly, rPEDV-Δnsp2 was entirely avirulent in vivo, with significantly increased productions of IFNB (interferon beta) and IFN-stimulated genes (ISGs) in various intestinal tissues of challenged newborn piglets. Notably, nsp2 targets and degrades TBK1 (TANK binding kinase 1), the critical kinase in the innate immune response. Mechanistically, nsp2 induced the macroautophagy/autophagy process and recruited a selective autophagic receptor, NBR1 (NBR1 autophagy cargo receptor). NBR1 subsequently facilitated the K48-linked ubiquitination of TBK1 and delivered it for autophagosome-mediated degradation. Accordingly, the replication of rPEDV-Δnsp2 CoV was restrained by reduced autophagy and excess productions of type I IFNs and ISGs. Our data collectively define enteric CoV nsp2 as a novel virulence determinant, propose a crucial role of nsp2 in diminishing innate antiviral immunity by targeting TBK1 for NBR1-mediated selective autophagy, and pave the way to develop a new type of nsp2-based attenuated PEDV vaccine. The study also provides new insights into the prevention and treatment of other pathogenic CoVs.Abbreviations: 3-MA: 3-methyladenine; Baf A1: bafilomycin A1; CoV: coronavirus; CQ: chloroquine; dpi: days post-inoculation; DMVs: double-membrane vesicles; GABARAP: GABA type A receptor-associated protein; GFP: green fluorescent protein; GIGYF2: GRB10 interacting GYF protein 2; hpi: hours post-infection; IFA: immunofluorescence assay; IFIH1: interferon induced with helicase C domain 1; IFIT2: interferon induced protein with tetratricopeptide repeats 2; IFITM1: interferon induced transmembrane protein 1; IFNB: interferon beta; IRF3: interferon regulatory factor 3; ISGs: interferon-stimulated genes; mAb: monoclonal antibody; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAVS: mitochondrial antiviral signaling protein; NBR1: NBR1 autophagy cargo receptor; nsp2: non-structural protein 2; OAS1: 2'-5'-oligoadenylate synthetase 1; PEDV: porcine epidemic diarrhea virus; PRRs: pattern recognition receptors; RIGI: RNA sensor RIG-I; RT-qPCR: reverse transcription quantitative polymerase chain reaction; SQSTM1: sequestosome 1; TBK1: TANK binding kinase 1; TCID50: 50% tissue culture infectious doses; VSV: vesicular stomatitis virus.
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Affiliation(s)
- Yajuan Jiao
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Pengwei Zhao
- Department of Biochemistry and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ling-Dong Xu
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jia-Qi Yu
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Hou-Li Cai
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Chong Zhang
- Boehringer Ingelheim Vetmedica (China) Co. Ltd, Taizhou, China
| | - Chao Tong
- Boehringer Ingelheim Vetmedica (China) Co. Ltd, Taizhou, China
| | - Yong-Le Yang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Pinglong Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Qiming Sun
- Department of Biochemistry and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ning Chen
- Boehringer Ingelheim Vetmedica (China) Co. Ltd, Taizhou, China
| | - Bin Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, China
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Davies JP, Plate L. The glycoprotein quality control factor Malectin promotes coronavirus replication and viral protein biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.02.597051. [PMID: 38895409 PMCID: PMC11185542 DOI: 10.1101/2024.06.02.597051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Coronaviruses (CoV) rewire host protein homeostasis (proteostasis) networks through interactions between viral nonstructural proteins (nsps) and host factors to promote infection. With the emergence of SARS-CoV-2, it is imperative to characterize host interactors shared across nsp homologs. Using quantitative proteomics and functional genetic screening, we identify conserved proteostasis interactors of nsp2 and nsp4 that serve pro-viral roles during infection of murine hepatitis virus - a model betacoronavirus. We uncover a glycoprotein quality control factor, Malectin (MLEC), which significantly reduces infectious titers when knocked down. During infection, nsp2 interacts with MLEC-associated proteins and the MLEC-interactome is drastically altered, stabilizing association with the Oligosaccheryltransferase (OST) complex, a crucial component of viral glycoprotein production. MLEC promotes viral protein levels and genome replication through its quality control activity. Lastly, we show MLEC promotes SARS-CoV-2 replication. Our results reveal a role for MLEC in mediating CoV infection and identify a potential target for pan-CoV antivirals.
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Wang M, Bo Z, Zhang C, Guo M, Wu Y, Zhang X. Deciphering the Genetic Variation: A Comparative Analysis of Parental and Attenuated Strains of the QXL87 Vaccine for Infectious Bronchitis. Animals (Basel) 2024; 14:1784. [PMID: 38929403 PMCID: PMC11200882 DOI: 10.3390/ani14121784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The QXL87 live attenuated vaccine strain for infectious bronchitis represents the first approved QX type (GI-19 lineage) vaccine in China. This strain was derived from the parental strain CK/CH/JS/2010/12 through continuous passage in SPF chicken embryos. To elucidate the molecular mechanism behind its attenuation, whole-genome sequencing was conducted on both the parental and attenuated strains. Analysis revealed 145 nucleotide mutations in the attenuated strain, leading to 48 amino acid mutations in various proteins, including Nsp2 (26), Nsp3 (14), Nsp4 (1), S (4), 3a (1), E (1), and N (1). Additionally, a frameshift mutation caused by a single base insertion in the ORFX resulted in a six-amino-acid extension. Subsequent comparison of post-translational modification sites, protein structure, and protein-protein binding sites between the parental and attenuated strains identified three potential virulence genes: Nsp2, Nsp3, and S. The amino acid mutations in these proteins not only altered their conformation but also affected the distribution of post-translational modification sites and protein-protein interaction sites. Furthermore, three potential functional mutation sites-P106S, A352T, and L472F, all located in the Nsp2 protein-were identified through PROVEAN, PolyPhen, and I-Mutant. Overall, our findings suggest that Nsp2, Nsp3, and S proteins may play a role in modulating IBV pathogenicity, with a particular focus on the significance of the Nsp2 protein. This study contributes to our understanding of the molecular mechanisms underlying IBV attenuation and holds promise for the development of safer live attenuated IBV vaccines using reverse genetic approaches.
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Affiliation(s)
- Mengmeng Wang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
| | - Zongyi Bo
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Chengcheng Zhang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
| | - Mengjiao Guo
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
| | - Yantao Wu
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Xiaorong Zhang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
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Kumawat P, Agarwal LK, Sharma K. An Overview of SARS-CoV-2 Potential Targets, Inhibitors, and Computational Insights to Enrich the Promising Treatment Strategies. Curr Microbiol 2024; 81:169. [PMID: 38733424 DOI: 10.1007/s00284-024-03671-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 03/18/2024] [Indexed: 05/13/2024]
Abstract
The rapid spread of the SARS-CoV-2 virus has emphasized the urgent need for effective therapies to combat COVID-19. Investigating the potential targets, inhibitors, and in silico approaches pertinent to COVID-19 are of utmost need to develop novel therapeutic agents and reprofiling of existing FDA-approved drugs. This article reviews the viral enzymes and their counter receptors involved in the entry of SARS-CoV-2 into host cells, replication of genomic RNA, and controlling the host cell physiology. In addition, the study provides an overview of the computational techniques such as docking simulations, molecular dynamics, QSAR modeling, and homology modeling that have been used to find the FDA-approved drugs and other inhibitors against SARS-CoV-2. Furthermore, a comprehensive overview of virus-based and host-based druggable targets from a structural point of view, together with the reported therapeutic compounds against SARS-CoV-2 have also been presented. The current study offers future perspectives for research in the field of network pharmacology investigating the large unexplored molecular libraries. Overall, the present in-depth review aims to expedite the process of identifying and repurposing drugs for researchers involved in the field of COVID-19 drug discovery.
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Affiliation(s)
- Pooja Kumawat
- Department of Chemistry, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India
| | - Lokesh Kumar Agarwal
- Department of Chemistry, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India.
| | - Kuldeep Sharma
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India
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Liao Y, Wang H, Liao H, Sun Y, Tan L, Song C, Qiu X, Ding C. Classification, replication, and transcription of Nidovirales. Front Microbiol 2024; 14:1291761. [PMID: 38328580 PMCID: PMC10847374 DOI: 10.3389/fmicb.2023.1291761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 02/09/2024] Open
Abstract
Nidovirales is one order of RNA virus, with the largest single-stranded positive sense RNA genome enwrapped with membrane envelope. It comprises four families (Arterividae, Mesoniviridae, Roniviridae, and Coronaviridae) and has been circulating in humans and animals for almost one century, posing great threat to livestock and poultry,as well as to public health. Nidovirales shares similar life cycle: attachment to cell surface, entry, primary translation of replicases, viral RNA replication in cytoplasm, translation of viral proteins, virion assembly, budding, and release. The viral RNA synthesis is the critical step during infection, including genomic RNA (gRNA) replication and subgenomic mRNAs (sg mRNAs) transcription. gRNA replication requires the synthesis of a negative sense full-length RNA intermediate, while the sg mRNAs transcription involves the synthesis of a nested set of negative sense subgenomic intermediates by a discontinuous strategy. This RNA synthesis process is mediated by the viral replication/transcription complex (RTC), which consists of several enzymatic replicases derived from the polyprotein 1a and polyprotein 1ab and several cellular proteins. These replicases and host factors represent the optimal potential therapeutic targets. Hereby, we summarize the Nidovirales classification, associated diseases, "replication organelle," replication and transcription mechanisms, as well as related regulatory factors.
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Affiliation(s)
- Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huiyu Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
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Ni X, Han Y, Zhou R, Zhou Y, Lei J. Structural insights into ribonucleoprotein dissociation by nucleocapsid protein interacting with non-structural protein 3 in SARS-CoV-2. Commun Biol 2023; 6:193. [PMID: 36806252 PMCID: PMC9938351 DOI: 10.1038/s42003-023-04570-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 02/09/2023] [Indexed: 02/20/2023] Open
Abstract
The coronavirus nucleocapsid (N) protein interacts with non-structural protein 3 (Nsp3) to facilitate viral RNA synthesis and stabilization. However, structural information on the N-Nsp3 complex is limited. Here, we report a 2.6 Å crystal structure of the N-terminal domain (NTD) of the N protein in complex with the ubiquitin-like domain 1 (Ubl1) of Nsp3 in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). One NTD and two Ubl1s formed a stable heterotrimer. We performed mutational analysis to reveal the key residues for this interaction. We confirmed the colocalization of SARS-CoV-2 N and Nsp3 in Huh-7 cells. N-Ubl1 interaction also exists in SARS-CoV and Middle East respiratory syndrome coronavirus. We found that SARS-CoV-2 Ubl1 competes with RNA to bind N protein in a dose-dependent manner. Based on our results, we propose a model for viral ribonucleoprotein dissociation through N protein binding to Ubl1 of Nsp3.
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Affiliation(s)
- Xincheng Ni
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yinze Han
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Renjie Zhou
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yanmei Zhou
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Jian Lei
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China. .,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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Xing Y, Zhang Q, Jiu Y. Coronavirus and the Cytoskeleton of Virus-Infected Cells. Subcell Biochem 2023; 106:333-364. [PMID: 38159233 DOI: 10.1007/978-3-031-40086-5_12] [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
The cytoskeleton, which includes actin filaments, microtubules, and intermediate filaments, is one of the most important networks in the cell and undertakes many fundamental life activities. Among them, actin filaments are mainly responsible for maintaining cell shape and mediating cell movement, microtubules are in charge of coordinating all cargo transport within the cell, and intermediate filaments are mainly thought to guard against external mechanical pressure. In addition to this, cytoskeleton networks are also found to play an essential role in multiple viral infections. Due to the COVID-19 epidemic, including SARS-CoV-2, SARS-CoV and MERS-CoV, so many variants have caused wide public concern, that any virus infection can potentially bring great harm to human beings and society. Therefore, it is of great importance to study coronavirus infection and develop antiviral drugs and vaccines. In this chapter, we summarize in detail how the cytoskeleton responds and participates in coronavirus infection by analyzing the possibility of the cytoskeleton and its related proteins as antiviral targets, thereby providing ideas for finding more effective treatments.
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Affiliation(s)
- Yifan Xing
- Shanghai Institute of Immunity and Infection (Formerly Institut Pasteur of Shanghai), Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qian Zhang
- Unit of Cell Biology and Imaging Study of Pathogen Host Interaction, The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Yaming Jiu
- Shanghai Institute of Immunity and Infection (Formerly Institut Pasteur of Shanghai), Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Unit of Cell Biology and Imaging Study of Pathogen Host Interaction, The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.
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Koči J, Novotová M, Sláviková M, Klempa B, Zahradník I. SARS-CoV-2 Exploits Non-Canonical Autophagic Processes to Replicate, Mature, and Egress the Infected Vero E6 Cells. Pathogens 2022; 11:pathogens11121535. [PMID: 36558869 PMCID: PMC9781122 DOI: 10.3390/pathogens11121535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
The coronavirus transforms the cytoplasm of susceptible cells to support virus replication. It also activates autophagy-like processes, the role of which is not well understood. Here, we studied SARS-CoV-2-infected Vero E6 cells using transmission electron microscopy and autophagy PCR array. After 6-24 h post-infection (hpi), the cytoplasm of infected cells only contained double-membrane vesicles, phagophores, and phagosomes engulfing virus particles and cytoplasmic debris, including damaged mitochondria. The phagosomes interacted with the viral nucleoprotein complex, virus particles, mitochondria, and lipid droplets. The phagosomes transformed into egress vacuoles, which broke through the plasmalemma and discharged the virus particles. The Vero E6 cells exhibited pronounced virus replication at 6 hpi, which stabilized at 18-24 hpi at a high level. The autophagy PCR array tests revealed a significant upregulation of 10 and downregulation of 8 autophagic gene markers out of 84. Altogether, these results underline the importance of autophagy-like processes for SARS-CoV-2 maturation and egress, and point to deviations from a canonical autophagy response.
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Affiliation(s)
- Juraj Koči
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, 84505 Bratislava, Slovakia
- Correspondence: (J.K.); (I.Z.)
| | - Marta Novotová
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, 84505 Bratislava, Slovakia
| | - Monika Sláviková
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, 84505 Bratislava, Slovakia
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, 84505 Bratislava, Slovakia
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | - Ivan Zahradník
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, 84505 Bratislava, Slovakia
- Correspondence: (J.K.); (I.Z.)
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Ichikawa T, Torii S, Suzuki H, Takada A, Suzuki S, Nakajima M, Tampo A, Kakinoki Y. Mutations in the nonstructural proteins of SARS-CoV-2 may contribute to adverse clinical outcome in patients with COVID-19. Int J Infect Dis 2022; 122:123-129. [PMID: 35562044 PMCID: PMC9088090 DOI: 10.1016/j.ijid.2022.05.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/13/2022] [Accepted: 05/05/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND From late March through April 2021, we experienced a cluster of patients with COVID-19, named "Cluster K", with rapid severe illness compared with those who were infected before. METHODS Patients with COVID-19 who were enrolled in this study were divided into two groups: 66 patients from November 2020 to March 2021 (group A) and 37 patients whose infection links were traced from Cluster K (group B). The primary outcome was mortality rate, and the secondary outcome was maximal oxygen flow rate as the severity of the disease. Viral genome sequences were compared between the two groups. RESULTS Mortality rates were 6.1% in group A and 16.2% in group B (odds ratio: 2.97, 95% confidence interval: 0.65-15.38). The patients in group B required high oxygen flow rate (O2 ≥10 l/min) in the earlier clinical course (P = 0.029). Viral genome sequences revealed five amino acid mutations; of these, four were found on three nonstructural proteins (NSPs): one in nsp3 and nsp15, two in nsp6 (one of them is near the potential sites under positive selective pressure). Another one was on the S protein. CONCLUSION This study suggests that mutations in NSPs, especially nsp6, are associated with adverse clinical outcome in patients with COVID-19.
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Affiliation(s)
- Takaya Ichikawa
- Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan.
| | - Shiho Torii
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | | | - Akio Takada
- Department of Pathology, Asahikawa City Hospital, Asahikawa, Japan
| | - Satoshi Suzuki
- Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan
| | | | - Akihito Tampo
- Department of Emergency Medicine, Asahikawa City Hospital, Asahikawa, Japan
| | - Yasutaka Kakinoki
- Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan
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Singh E, Jha RK, Khan RJ, Kumar A, Jain M, Muthukumaran J, Singh AK. A computational essential dynamics approach to investigate structural influences of ligand binding on Papain like protease from SARS-CoV-2. Comput Biol Chem 2022; 99:107721. [PMID: 35835027 PMCID: PMC9238113 DOI: 10.1016/j.compbiolchem.2022.107721] [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] [Received: 05/11/2022] [Revised: 06/21/2022] [Accepted: 06/25/2022] [Indexed: 11/28/2022]
Abstract
Papain like protease (PLpro) is a cysteine protease from the coronaviridae family of viruses. Coronaviruses possess a positive sense, single-strand RNA, leading to the translation of two viral polypeptides containing viral structural, non-structural and accessory proteins. PLpro is responsible for the cleavage of nsp1–3 from the viral polypeptide. PLpro also possesses deubiquitinating and deISGlyating activity, which sequesters the virus from the host's immune system. This indispensable attribute of PLpro makes it a protein of interest as a drug target. The present study aims to analyze the structural influences of ligand binding on PLpro. First, PLpro was screened against the ZINC-in-trials library, from which four lead compounds were identified based on estimated binding affinity and interaction patterns. Next, based on molecular docking results, ZINC000000596945, ZINC000064033452 and VIR251 (control molecule) were subjected to molecular dynamics simulation. The study evaluated global and essential dynamics analyses utilising principal component analyses, dynamic cross-correlation matrix, free energy landscape and time-dependant essential dynamics to predict the structural changes observed in PLpro upon ligand binding in a simulated environment. The MM/PBSA-based binding free energy calculations of the two selected molecules, ZINC000000596945 (−41.23 ± 3.70 kcal/mol) and ZINC000064033452 (−25.10 ± 2.65 kcal/mol), displayed significant values which delineate them as potential inhibitors of PLpro from SARS-CoV-2.
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Affiliation(s)
- Ekampreet Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, 201310 Greater Noida, Uttar Pradesh, India
| | - Rajat Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, 201310 Greater Noida, Uttar Pradesh, India
| | - Rameez Jabeer Khan
- Department of Biotechnology, School of Engineering and Technology, Sharda University, 201310 Greater Noida, Uttar Pradesh, India
| | - Ankit Kumar
- Department of Biotechnology, School of Engineering and Technology, Sharda University, 201310 Greater Noida, Uttar Pradesh, India
| | - Monika Jain
- Department of Biotechnology, School of Engineering and Technology, Sharda University, 201310 Greater Noida, Uttar Pradesh, India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, School of Engineering and Technology, Sharda University, 201310 Greater Noida, Uttar Pradesh, India.
| | - Amit Kumar Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, 201310 Greater Noida, Uttar Pradesh, India.
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Khazaneha M, Tajedini O, Esmaeili O, Abdi M, Khasseh AA, Sadatmoosavi A. Thematic evolution of coronavirus disease: a longitudinal co-word analysis. LIBRARY HI TECH 2022. [DOI: 10.1108/lht-10-2021-0370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PurposeUsing science mapping analysis approach and co-word analysis, the present study explores and visualizes research fields and thematic evolution of the coronavirus. Based on this method, one can get a picture of the real content of the themes in the mentioned thematic area and identify the main minor and emerging themes.Design/methodology/approachThis study was conducted based on co-word science mapping analysis under a longitudinal study (from 1988 to 2020). The collection of documents in this study was further divided into three subperiods: 1988–1998, 1999–2009 and 2010–2020. In order to perform science mapping analysis based on co-word bibliographic networks, SciMAT was utilized as a bibliometric tool. Moreover, WoS, PubMed and Scopus bibliographic databases were used to download all records.FindingsIn this study, strategic diagrams were demonstrated for the coronavirus research for a chronological period to assess the most relevant themes. Each diagram depended on the sum of documents linked to each research topic. In the first period (1988–1998), the most centralizations were on virology and evaluation of coronavirus structure and its structural and nonstructural proteins. In the second period (1999–2009), with due attention to high population density in eastern Asia and the increasing number of people affected with the new generation of coronavirus (named severe acute respiratory syndrome virus or SARS virus), publications have been concentrated on “antiviral activity.” In the third period (2010–2020), there was a tendency to investigate clinical syndromes, and most of the publications and citations were about hot topics like “severe acute respiratory syndrome,” “coronavirus” and “respiratory tract disease.” Scientometric analysis of the field of coronavirus can be regarded as a roadmap for future research and policymaking in this important area.Originality/valueThe originality of this research can be considered in two ways. First, the strategic diagrams of coronavirus are drawn in four thematic areas including motor cluster, basic and transversal cluster, highly developed cluster and emerging and declining cluster. Second, COVID-19 is mentioned as a hot topic of research.
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12
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Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing. Curr Microbiol 2022; 79:48. [PMID: 34982246 PMCID: PMC8750362 DOI: 10.1007/s00284-021-02743-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 12/06/2021] [Indexed: 11/18/2022]
Abstract
This study aimed to characterize the whole genome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) isolated from an oropharyngeal swab specimen of a Pashtun Pakistani patient using next-generation sequencing. Upon comparing the SARS-CoV2 genome to the reference genome, a total of 10 genetic variants were identified. Among the 10 genetic variants, 1 missense mutation (c.1139A > G, p.Lys292Glu) in the Open Reading Frame 1ab (ORF1ab) positioned at 112 in the non-structural protein 2 (NSP2) was found to be unique. Phylogenetic analysis (n = 84) revealed that the current SARS-CoV2 genome was closely clustered with 8 Pakistani strains belonging to Punjab, Federal Capital, Azad Jammu and Kashmir (AJK), and Khyber Pakhtunkhwa (KP). In addition, the current SARS-CoV2 genome was very similar to the genome of SARS-CoV2 reported from Guam, Taiwan, India, the USA, and France. Overall, this study reports a slight mismatch in the SARS-CoV2 genome, indicating the presence of a single unique missense mutation. However, phylogenetic analysis revealed that the current SARS-CoV2 genome was closely clustered with 8 other Pakistani strains.
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13
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Ávila-Pérez G, Rejas MT, Chichón FJ, Guerra M, Fernández JJ, Rodríguez D. Architecture of torovirus replicative organelles. Mol Microbiol 2021; 117:837-850. [PMID: 34967475 DOI: 10.1111/mmi.14875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 11/29/2022]
Abstract
Plus-stranded RNA viruses replicate in the cytosol of infected cells, in membrane-bound replication complexes. We previously identified double membrane vesicles (DMVs) in the cytoplasm of cells infected with Berne virus (BEV), the prototype member of Torovirus genus (Nidovirales Order). Our previous analysis by transmission electron microscopy suggested that the DMVs form a reticulovesicular network (RVN) analogous those described for the related severe acute respiratory syndrome coronavirus (SARS-CoV-1). Here, we used serial sectioning and electron tomography to characterize the architecture of torovirus replication organelles, and to learn about their biogenesis and dynamics during the infection. The formation of a RVN in BEV infected cells was confirmed, where the outer membranes of the DMVs are interconnected with each other and with the ER. Paired or zippered ER membranes connected with the DMVs were also observed, and likely represent early structures that evolve to give rise to DMVs. Also, paired membranes forming small spherule-like invaginations were observed at late time post-infection. Although resembling in size, the tomographic analysis show that these structures are clearly different from the true spherules described previously for coronaviruses. Hence, BEV shows important similarities, but also some differences, in the architecture of the replication organelles with other nidoviruses.
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Affiliation(s)
- Ginés Ávila-Pérez
- Department of Molecular and Cellular Biology, Centro de Biología Molecular Severo Ochoa, CSIC, C/Nicolás Cabrera 1, 28049, Madrid, Spain
| | - María Teresa Rejas
- Servicio de Microscopía Electrónica, Centro de Biología Molecular Severo Ochoa, CSIC, C/Nicolás Cabrera 1, 28049, Madrid, Spain
| | - Francisco Javier Chichón
- Servicio de Criomicroscopía Electrónica (cryoEM-CSIC) and Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049, Madrid, Spain
| | - Milagros Guerra
- Servicio de Microscopía Electrónica, Centro de Biología Molecular Severo Ochoa, CSIC, C/Nicolás Cabrera 1, 28049, Madrid, Spain
| | - José Jesús Fernández
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), CINN-CSIC, Av Hospital Universitario s/n, 33011, Oviedo, Spain
| | - Dolores Rodríguez
- Department of Molecular and Cellular Biology, Centro de Biología Molecular Severo Ochoa, CSIC, C/Nicolás Cabrera 1, 28049, Madrid, Spain
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14
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Razali R, Asis H, Budiman C. Structure-Function Characteristics of SARS-CoV-2 Proteases and Their Potential Inhibitors from Microbial Sources. Microorganisms 2021; 9:2481. [PMID: 34946083 PMCID: PMC8706127 DOI: 10.3390/microorganisms9122481] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/07/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is considered the greatest challenge to the global health community of the century as it continues to expand. This has prompted immediate urgency to discover promising drug targets for the treatment of COVID-19. The SARS-CoV-2 viral proteases, 3-chymotrypsin-like protease (3CLpro) and papain-like cysteine protease (PLpro), have become the promising target to study due to their essential functions in spreading the virus by RNA transcription, translation, protein synthesis, processing and modification, virus replication, and infection of the host. As such, understanding of the structure and function of these two proteases is unavoidable as platforms for the development of inhibitors targeting this protein which further arrest the infection and spread of the virus. While the abundance of reports on the screening of natural compounds such as SARS-CoV-2 proteases inhibitors are available, the microorganisms-based compounds (peptides and non-peptides) remain less studied. Indeed, microorganisms-based compounds are also one of the potent antiviral candidates against COVID-19. Microbes, especially bacteria and fungi, are other resources to produce new drugs as well as nucleosides, nucleotides, and nucleic acids. Thus, we have compiled various reported literature in detail on the structures, functions of the SARS-CoV-2 proteases, and potential inhibitors from microbial sources as assistance to other researchers working with COVID-19. The compounds are also compared to HIV protease inhibitors which suggested the microorganisms-based compounds are advantageous as SARS-CoV2 proteases inhibitors. The information should serve as a platform for further development of COVID-19 drug design strategies.
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Affiliation(s)
| | | | - Cahyo Budiman
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia; (R.R.); (H.A.)
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15
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Ryu JK, Hwang DE, Choi JM. Current Understanding of Molecular Phase Separation in Chromosomes. Int J Mol Sci 2021; 22:10736. [PMID: 34639077 PMCID: PMC8509192 DOI: 10.3390/ijms221910736] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular phase separation denotes the demixing of a specific set of intracellular components without membrane encapsulation. Recent studies have found that biomolecular phase separation is involved in a wide range of cellular processes. In particular, phase separation is involved in the formation and regulation of chromosome structures at various levels. Here, we review the current understanding of biomolecular phase separation related to chromosomes. First, we discuss the fundamental principles of phase separation and introduce several examples of nuclear/chromosomal biomolecular assemblies formed by phase separation. We also briefly explain the experimental and computational methods used to study phase separation in chromosomes. Finally, we discuss a recent phase separation model, termed bridging-induced phase separation (BIPS), which can explain the formation of local chromosome structures.
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Affiliation(s)
- Je-Kyung Ryu
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Da-Eun Hwang
- Department of Chemistry, Pusan National University, Busan 46241, Korea;
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan 46241, Korea;
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16
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Zheng YX, Wang L, Kong WS, Chen H, Wang XN, Meng Q, Zhang HN, Guo SJ, Jiang HW, Tao SC. Nsp2 has the potential to be a drug target revealed by global identification of SARS-CoV-2 Nsp2-interacting proteins. Acta Biochim Biophys Sin (Shanghai) 2021; 53:1134-1141. [PMID: 34159380 DOI: 10.1093/abbs/gmab088] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 01/09/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global health threat since December 2019, and there is still no highly effective drug to control the pandemic. To facilitate drug target identification for drug development, studies on molecular mechanisms, such as SARS-CoV-2 protein interactions, are urgently needed. In this study, we focused on Nsp2, a non-structural protein with largely unknown function and mechanism. The interactome of Nsp2 was revealed through the combination of affinity purification mass spectrometry (AP-MS) and stable isotope labeling by amino acids in cell culture (SILAC), and 84 proteins of high-confidence were identified. Gene ontology analysis demonstrated that Nsp2-interacting proteins are involved in several biological processes such as endosome transport and translation. Network analysis generated two clusters, including ribosome assembly and vesicular transport. Bio-layer interferometry (BLI) assay confirmed the bindings between Nsp2- and 4-interacting proteins, i.e. STAU2 (Staufen2), HNRNPLL, ATP6V1B2, and RAP1GDS1 (SmgGDS), which were randomly selected from the list of 84 proteins. Our findings provide insights into the Nsp2-host interplay and indicate that Nsp2 may play important roles in SARS-CoV-2 infection and serve as a potential drug target for anti-SARS-CoV-2 drug development.
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Affiliation(s)
- Yun-Xiao Zheng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei-Sha Kong
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Ning Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qingfeng Meng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Nan Zhang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-Juan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - He-Wei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
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17
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Slavin M, Zamel J, Zohar K, Eliyahu T, Braitbard M, Brielle E, Baraz L, Stolovich-Rain M, Friedman A, Wolf DG, Rouvinski A, Linial M, Schneidman-Duhovny D, Kalisman N. Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of three proteins from SARS-CoV-2. Proc Natl Acad Sci U S A 2021; 118:e2103554118. [PMID: 34373319 PMCID: PMC8403911 DOI: 10.1073/pnas.2103554118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Atomic structures of several proteins from the coronavirus family are still partial or unavailable. A possible reason for this gap is the instability of these proteins outside of the cellular context, thereby prompting the use of in-cell approaches. In situ cross-linking and mass spectrometry (in situ CLMS) can provide information on the structures of such proteins as they occur in the intact cell. Here, we applied targeted in situ CLMS to structurally probe Nsp1, Nsp2, and nucleocapsid (N) proteins from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and obtained cross-link sets with an average density of one cross-link per 20 residues. We then employed integrative modeling that computationally combined the cross-linking data with domain structures to determine full-length atomic models. For the Nsp2, the cross-links report on a complex topology with long-range interactions. Integrative modeling with structural prediction of individual domains by the AlphaFold2 system allowed us to generate a single consistent all-atom model of the full-length Nsp2. The model reveals three putative metal binding sites and suggests a role for Nsp2 in zinc regulation within the replication-transcription complex. For the N protein, we identified multiple intra- and interdomain cross-links. Our integrative model of the N dimer demonstrates that it can accommodate three single RNA strands simultaneously, both stereochemically and electrostatically. For the Nsp1, cross-links with the 40S ribosome were highly consistent with recent cryogenic electron microscopy structures. These results highlight the importance of cellular context for the structural probing of recalcitrant proteins and demonstrate the effectiveness of targeted in situ CLMS and integrative modeling.
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Affiliation(s)
- Moriya Slavin
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Joanna Zamel
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Keren Zohar
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Tsiona Eliyahu
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Merav Braitbard
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Esther Brielle
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Leah Baraz
- Hadassah Academic College Jerusalem, Jerusalem 9101001, Israel
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Miri Stolovich-Rain
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ahuva Friedman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Dana G Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, 9190401 Jerusalem, Israel
| | - Alexander Rouvinski
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
| | - Dina Schneidman-Duhovny
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Kalisman
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
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18
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Gupta M, Azumaya CM, Moritz M, Pourmal S, Diallo A, Merz GE, Jang G, Bouhaddou M, Fossati A, Brilot AF, Diwanji D, Hernandez E, Herrera N, Kratochvil HT, Lam VL, Li F, Li Y, Nguyen HC, Nowotny C, Owens TW, Peters JK, Rizo AN, Schulze-Gahmen U, Smith AM, Young ID, Yu Z, Asarnow D, Billesbølle C, Campbell MG, Chen J, Chen KH, Chio US, Dickinson MS, Doan L, Jin M, Kim K, Li J, Li YL, Linossi E, Liu Y, Lo M, Lopez J, Lopez KE, Mancino A, Moss FR, Paul MD, Pawar KI, Pelin A, Pospiech TH, Puchades C, Remesh SG, Safari M, Schaefer K, Sun M, Tabios MC, Thwin AC, Titus EW, Trenker R, Tse E, Tsui TKM, Wang F, Zhang K, Zhang Y, Zhao J, Zhou F, Zhou Y, Zuliani-Alvarez L, Agard DA, Cheng Y, Fraser JS, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Swaney DL, Krogan NJ, Frost A, Rosenberg OS, Verba KA. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. RESEARCH SQUARE 2021:rs.3.rs-515215. [PMID: 34031651 PMCID: PMC8142659 DOI: 10.21203/rs.3.rs-515215/v1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design.
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Affiliation(s)
- Meghna Gupta
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Caleigh M. Azumaya
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Michelle Moritz
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Sergei Pourmal
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Amy Diallo
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Gregory E. Merz
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Gwendolyn Jang
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Andrea Fossati
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Axel F. Brilot
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Devan Diwanji
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Evelyn Hernandez
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Nadia Herrera
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Huong T. Kratochvil
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Victor L. Lam
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Fei Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yang Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Henry C. Nguyen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Carlos Nowotny
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Tristan W. Owens
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Jessica K. Peters
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Alexandrea N. Rizo
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Ursula Schulze-Gahmen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Amber M. Smith
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Iris D. Young
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Zanlin Yu
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Daniel Asarnow
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Christian Billesbølle
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Melody G. Campbell
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Current affiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jen Chen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kuei-Ho Chen
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Un Seng Chio
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Miles Sasha Dickinson
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Loan Doan
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Mingliang Jin
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kate Kim
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Junrui Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yen-Li Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Edmond Linossi
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yanxin Liu
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Megan Lo
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Jocelyne Lopez
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kyle E. Lopez
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Adamo Mancino
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Frank R. Moss
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Michael D. Paul
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Komal Ishwar Pawar
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Adrian Pelin
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Thomas H. Pospiech
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Cristina Puchades
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Soumya Govinda Remesh
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Maliheh Safari
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kaitlin Schaefer
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Ming Sun
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Current affiliation: Beam Therapeutics, Cambridge, MA 02139, USA
| | - Mariano C Tabios
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Aye C. Thwin
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Erron W. Titus
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Raphael Trenker
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Eric Tse
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Tsz Kin Martin Tsui
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Feng Wang
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kaihua Zhang
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yang Zhang
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Jianhua Zhao
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Fengbo Zhou
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yuan Zhou
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Lorena Zuliani-Alvarez
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | | | - David A Agard
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Yifan Cheng
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - James S Fraser
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Natalia Jura
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Tanja Kortemme
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
- The University of California, Berkeley–University of California, San Francisco Graduate Program in Bioengineering, University of California, San Francisco, CA 94158, USA
| | - Aashish Manglik
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Daniel R. Southworth
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Robert M Stroud
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Danielle L Swaney
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adam Frost
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Oren S Rosenberg
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Kliment A Verba
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
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19
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Gupta M, Azumaya CM, Moritz M, Pourmal S, Diallo A, Merz GE, Jang G, Bouhaddou M, Fossati A, Brilot AF, Diwanji D, Hernandez E, Herrera N, Kratochvil HT, Lam VL, Li F, Li Y, Nguyen HC, Nowotny C, Owens TW, Peters JK, Rizo AN, Schulze-Gahmen U, Smith AM, Young ID, Yu Z, Asarnow D, Billesbølle C, Campbell MG, Chen J, Chen KH, Chio US, Dickinson MS, Doan L, Jin M, Kim K, Li J, Li YL, Linossi E, Liu Y, Lo M, Lopez J, Lopez KE, Mancino A, Moss FR, Paul MD, Pawar KI, Pelin A, Pospiech TH, Puchades C, Remesh SG, Safari M, Schaefer K, Sun M, Tabios MC, Thwin AC, Titus EW, Trenker R, Tse E, Tsui TKM, Wang F, Zhang K, Zhang Y, Zhao J, Zhou F, Zhou Y, Zuliani-Alvarez L, Agard DA, Cheng Y, Fraser JS, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Swaney DL, Krogan NJ, Frost A, Rosenberg OS, Verba KA. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.05.10.443524. [PMID: 34013269 PMCID: PMC8132225 DOI: 10.1101/2021.05.10.443524] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design.
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Affiliation(s)
- Meghna Gupta
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Caleigh M Azumaya
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Michelle Moritz
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Sergei Pourmal
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Amy Diallo
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Gregory E Merz
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Gwendolyn Jang
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Andrea Fossati
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Axel F Brilot
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Devan Diwanji
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Evelyn Hernandez
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Nadia Herrera
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Huong T Kratochvil
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Victor L Lam
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Fei Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yang Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Henry C Nguyen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Carlos Nowotny
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Tristan W Owens
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Jessica K Peters
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Alexandrea N Rizo
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Ursula Schulze-Gahmen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Amber M Smith
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Iris D Young
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Zanlin Yu
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Daniel Asarnow
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Christian Billesbølle
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Melody G Campbell
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Current affiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jen Chen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kuei-Ho Chen
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Un Seng Chio
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Miles Sasha Dickinson
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Loan Doan
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Mingliang Jin
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kate Kim
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Junrui Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yen-Li Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Edmond Linossi
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yanxin Liu
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Megan Lo
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Jocelyne Lopez
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kyle E Lopez
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Adamo Mancino
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Frank R Moss
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Michael D Paul
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Komal Ishwar Pawar
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Adrian Pelin
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Thomas H Pospiech
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Cristina Puchades
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Soumya Govinda Remesh
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Maliheh Safari
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kaitlin Schaefer
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Ming Sun
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Current affiliation: Beam Therapeutics, Cambridge, MA 02139, USA
| | - Mariano C Tabios
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Aye C Thwin
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Erron W Titus
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Raphael Trenker
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Eric Tse
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Tsz Kin Martin Tsui
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Feng Wang
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kaihua Zhang
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yang Zhang
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Jianhua Zhao
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Fengbo Zhou
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yuan Zhou
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Lorena Zuliani-Alvarez
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - David A Agard
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Yifan Cheng
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - James S Fraser
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Natalia Jura
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Tanja Kortemme
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
- The University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, San Francisco, CA 94158, USA
| | - Aashish Manglik
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Daniel R Southworth
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Robert M Stroud
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Danielle L Swaney
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adam Frost
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Oren S Rosenberg
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Kliment A Verba
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
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Zekri ARN, Mohanad M, Hafez MM, Soliman HK, Hassan ZK, Abouelhoda M, Amer KE, Seadawy MG, Ahmed OS. Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166154. [PMID: 33932525 PMCID: PMC8079944 DOI: 10.1016/j.bbadis.2021.166154] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/03/2021] [Accepted: 04/22/2021] [Indexed: 12/13/2022]
Abstract
Background Severe acute respiratory syndrome-2 (SARS-CoV-2) exhibits a broad spectrum of clinical manifestations. Despite the fact that SARS-CoV-2 has slower evolutionary rate than other coronaviruses, different mutational hotspots have been identified along the SARS-CoV-2 genome. Methods We performed whole-genome high throughput sequencing on isolates from 50 Egyptian patients to see if the variation in clinical symptoms was related to mutations in the SARS-CoV-2 genome. Then, we investigated the relationship between the observed mutations and the clinical characteristics of the patients. Results Among the 36 most common mutations, we found two frameshift deletions linked to an increased risk of shortness of breath, a V6 deletion in the spike glycoprotein's signal peptide region linked to an increased risk of fever, longer fever duration and nasal congestion, and L3606-nsp6 deletion linked to a higher prevalence of cough and conjunctival congestion. S5398L nsp13-helicase was linked to an increased risk of fever duration and progression. The most common mutations (241, 3037, 14,408, and 23,403) were not linked to clinical variability. However, the E3909G-nsp7 variant was more common in children (2–13 years old) and was associated with a shorter duration of symptoms. The duration of fever was significantly reduced with E1363D-nsp3 and E3073A-nsp4. Conclusions The most common mutations, D614G/spike-glycoprotein and P4715L/RNA-dependent-RNA-polymerase, were linked to transmissibility regardless of symptom variability. E3909G-nsp7 could explain why children recover so quickly. Nsp6-L3606fs, spike-glycoprotein-V6fs, and nsp13-S5398L variants may be linked to clinical symptom worsening. These variations related to host-virus interactions might open new therapeutic avenues for symptom relief and disease containment.
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Affiliation(s)
- Abdel-Rahman N Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Marwa Mohanad
- Biochemistry Department, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, Egypt.
| | - Mohammed M Hafez
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Hany K Soliman
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Zainab K Hassan
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo 12613, Egypt
| | - Khaled E Amer
- Egypt Center for Research and Regenerative Medicine, Egypt
| | | | - Ola S Ahmed
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
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21
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Wen Z, Zhang Y, Lin Z, Shi K, Jiu Y. Cytoskeleton-a crucial key in host cell for coronavirus infection. J Mol Cell Biol 2021; 12:968-979. [PMID: 32717049 PMCID: PMC7454755 DOI: 10.1093/jmcb/mjaa042] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/21/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
The emerging coronavirus (CoV) pandemic is threatening the public health all over the world. Cytoskeleton is an intricate network involved in controlling cell shape, cargo transport, signal transduction, and cell division. Infection biology studies have illuminated essential roles for cytoskeleton in mediating the outcome of host‒virus interactions. In this review, we discuss the dynamic interactions between actin filaments, microtubules, intermediate filaments, and CoVs. In one round of viral life cycle, CoVs surf along filopodia on the host membrane to the entry sites, utilize specific intermediate filament protein as co-receptor to enter target cells, hijack microtubules for transportation to replication and assembly sites, and promote actin filaments polymerization to provide forces for egress. During CoV infection, disruption of host cytoskeleton homeostasis and modification state is tightly connected to pathological processes, such as defective cytokinesis, demyelinating, cilia loss, and neuron necrosis. There are increasing mechanistic studies on cytoskeleton upon CoV infection, such as viral protein‒cytoskeleton interaction, changes in the expression and post-translation modification, related signaling pathways, and incorporation with other host factors. Collectively, these insights provide new concepts for fundamental virology and the control of CoV infection.
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Affiliation(s)
- Zeyu Wen
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Zhang
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhekai Lin
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun Shi
- Department of Gynecology and Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Yaming Jiu
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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22
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Platt DE, Parida L, Zalloua P. Lies, Gosh Darn Lies, and not enough good statistics: why epidemic model parameter estimation fails. Sci Rep 2021; 11:408. [PMID: 33432032 PMCID: PMC7801491 DOI: 10.1038/s41598-020-79745-6] [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] [Received: 05/07/2020] [Accepted: 12/02/2020] [Indexed: 12/03/2022] Open
Abstract
We sought to investigate whether epidemiological parameters that define epidemic models could be determined from the epidemic trajectory of infections, recovery, and hospitalizations prior to peak, and also to evaluate the comparability of data between jurisdictions reporting their statistics. We found that, analytically, the pre-peak growth of an epidemic underdetermines the model variates, and that the rate limiting variables are dominated by the exponentially expanding eigenmode of their equations. The variates quickly converge to the ratio of eigenvector components of the positive growth mode, which determines the doubling time. Without a sound epidemiological study framework, measurements of infection rates and other parameters are highly corrupted by uneven testing rates, uneven counting, and under reporting of relevant values. We argue that structured experiments must be performed to estimate these parameters in order to perform genetic association studies, or to construct viable models accurately predicting critical quantities such as hospitalization loads.
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Affiliation(s)
- Daniel E Platt
- Computational Genomics, IBM T. J. Watson Research Center, New York, USA.
| | - Laxmi Parida
- Computational Genomics, IBM T. J. Watson Research Center, New York, USA
| | - Pierre Zalloua
- TH Chan Harvard School of Public Health, Harvard University, Cambridge, USA.
- School of Medicine, University of Balamand, P.O. Box 33, Amioun, Lebanon.
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23
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Coronavirus infection induces progressive restructuring of the endoplasmic reticulum involving the formation and degradation of double membrane vesicles. Virology 2020; 556:9-22. [PMID: 33524849 PMCID: PMC7836250 DOI: 10.1016/j.virol.2020.12.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/25/2020] [Accepted: 12/13/2020] [Indexed: 01/02/2023]
Abstract
Coronaviruses rearrange endoplasmic reticulum (ER) membranes to form a reticulovesicular network (RVN) comprised predominantly of double membrane vesicles (DMVs) involved in viral replication. While portions of the RVN have been analyzed by electron tomography (ET), the full extent of the RVN is not known, nor how RVN formation affects ER morphology. Additionally the precise mechanism of DMV formation has not been observed. In this work, we examined large volumes of coronavirus-infected cells at multiple timepoints during infection using serial-section ET. We provide a comprehensive 3D analysis of the ER and RVN which gives insight into the formation mechanism of DMVs as well as the first evidence for their lysosomal degradation. We also show that the RVN breaks down late in infection, concurrent with the ER becoming the main budding compartment for new virions. This work provides a broad view of the multifaceted involvement of ER membranes in coronavirus infection.
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24
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Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread worldwide since its first incidence in Wuhan, China, in December 2019. Although the case fatality rate of COVID-19 appears to be lower than that of SARS and Middle East respiratory syndrome (MERS), the higher transmissibility of SARS-CoV-2 has caused the total fatality to surpass other viral diseases, reaching more than 1 million globally as of October 6, 2020. The rate at which the disease is spreading calls for a therapy that is useful for treating a large population. Multiple intersecting viral and host factor targets involved in the life cycle of the virus are being explored. Because of the frequent mutations, many coronaviruses gain zoonotic potential, which is dependent on the presence of cell receptors and proteases, and therefore the targeting of the viral proteins has some drawbacks, as strain-specific drug resistance can occur. Moreover, the limited number of proteins in a virus makes the number of available targets small. Although SARS-CoV and SARS-CoV-2 share common mechanisms of entry and replication, there are substantial differences in viral proteins such as the spike (S) protein. In contrast, targeting cellular factors may result in a broader range of therapies, reducing the chances of developing drug resistance. In this Review, we discuss the role of primary host factors such as the cell receptor angiotensin-converting enzyme 2 (ACE2), cellular proteases of S protein priming, post-translational modifiers, kinases, inflammatory cells, and their pharmacological intervention in the infection of SARS-CoV-2 and related viruses.
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Affiliation(s)
- Anil Mathew Tharappel
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Subodh Kumar Samrat
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Zhong Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Hongmin Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY 12201, USA
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25
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Wan H, Aravamuthan V, Pearlstein RA. Probing the Dynamic Structure-Function and Structure-Free Energy Relationships of the Coronavirus Main Protease with Biodynamics Theory. ACS Pharmacol Transl Sci 2020; 3:1111-1143. [PMID: 33330838 PMCID: PMC7671103 DOI: 10.1021/acsptsci.0c00089] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Indexed: 02/01/2023]
Abstract
![]()
The
SARS-CoV-2 main protease (Mpro) is of major interest
as an antiviral drug target. Structure-based virtual screening efforts,
fueled by a growing list of apo and inhibitor-bound SARS-CoV/CoV-2
Mpro crystal structures, are underway in many laboratories.
However, little is known about the dynamic enzyme mechanism, which
is needed to inform both assay development and structure-based inhibitor
design. Here, we apply biodynamics theory to characterize the structural
dynamics of substrate-induced Mpro activation under nonequilibrium conditions. The catalytic cycle
is governed by concerted dynamic structural
rearrangements of domain 3 and the m-shaped loop (residues 132–147)
on which Cys145 (comprising the thiolate nucleophile and half of the
oxyanion hole) and Gly143 (comprising the second half of the oxyanion
hole) reside. In particular, we observed the following: (1) Domain
3 undergoes dynamic rigid-body rotation about the domain 2–3
linker, alternately visiting two primary conformational states (denoted
as M1pro ↔
M2pro); (2)
The Gly143-containing crest of the m-shaped loop undergoes up and
down translations caused by conformational changes within the rising
stem of the loop (Lys137–Asn142) in response to domain 3 rotation
and dimerization (denoted as M1/downpro ↔ 2·M2/uppro) (noting that the Cys145-containing
crest is fixed in the up position). We propose that substrates associate
to the M1/downpro state, which promotes the M2/downpro state, dimerization (denoted as 2·M2/uppro–substrate),
and catalysis. Here, we explore the state transitions of Mpro under nonequilibrium conditions, the mechanisms by which they are
powered, and the implications thereof for efficacious inhibition under in vivo conditions.
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Affiliation(s)
- Hongbin Wan
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Vibhas Aravamuthan
- Vibhas Aravamuthan - NIBR Informatics, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Robert A Pearlstein
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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26
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Greco S, Madè A, Gaetano C, Devaux Y, Emanueli C, Martelli F. Noncoding RNAs implication in cardiovascular diseases in the COVID-19 era. J Transl Med 2020; 18:408. [PMID: 33129318 PMCID: PMC7602761 DOI: 10.1186/s12967-020-02582-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/24/2020] [Indexed: 12/21/2022] Open
Abstract
COronaVIrus Disease 19 (COVID-19) is caused by the infection of the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2). Although the main clinical manifestations of COVID-19 are respiratory, many patients also display acute myocardial injury and chronic damage to the cardiovascular system. Understanding both direct and indirect damage caused to the heart and the vascular system by SARS-CoV-2 infection is necessary to identify optimal clinical care strategies. The homeostasis of the cardiovascular system requires a tight regulation of the gene expression, which is controlled by multiple types of RNA molecules, including RNA encoding proteins (messenger RNAs) (mRNAs) and those lacking protein-coding potential, the noncoding-RNAs. In the last few years, dysregulation of noncoding-RNAs has emerged as a crucial component in the pathophysiology of virtually all cardiovascular diseases. Here we will discuss the potential role of noncoding RNAs in COVID-19 disease mechanisms and their possible use as biomarkers of clinical use.
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Affiliation(s)
- S Greco
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097, Milan, Italy
| | - A Madè
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097, Milan, Italy
| | - C Gaetano
- Laboratory of Epigenetics, Istituti Clinici Scientifici Maugeri IRCCS, 27100, Pavia, Italy
| | - Y Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - C Emanueli
- Imperial College London, National Heart and Lung Institute, Hammersmith Campus, London, W12 0NN, UK
| | - F Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097, Milan, Italy.
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27
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Safavi A, Kefayat A, Mahdevar E, Abiri A, Ghahremani F. Exploring the out of sight antigens of SARS-CoV-2 to design a candidate multi-epitope vaccine by utilizing immunoinformatics approaches. Vaccine 2020; 38:7612-7628. [PMID: 33082015 PMCID: PMC7546226 DOI: 10.1016/j.vaccine.2020.10.016] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/25/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 causes a severe respiratory disease called COVID-19. Currently, global health is facing its devastating outbreak. However, there is no vaccine available against this virus up to now. In this study, a novel multi-epitope vaccine against SARS-CoV-2 was designed to provoke both innate and adaptive immune responses. The immunodominant regions of six non-structural proteins (nsp7, nsp8, nsp9, nsp10, nsp12 and nsp14) of SARS-CoV-2 were selected by multiple immunoinformatic tools to provoke T cell immune response. Also, immunodominant fragment of the functional region of SARS-CoV-2 spike (400-510 residues) protein was selected for inducing neutralizing antibodies production. The selected regions' sequences were connected to each other by furin-sensitive linker (RVRR). Moreover, the functional region of β-defensin as a well-known agonist for the TLR-4/MD complex was added at the N-terminus of the vaccine using (EAAAK)3 linker. Also, a CD4 + T-helper epitope, PADRE, was used at the C-terminal of the vaccine by GPGPG and A(EAAAK)2A linkers to form the final vaccine construct. The physicochemical properties, allergenicity, antigenicity, functionality and population coverage of the final vaccine construct were analyzed. The final vaccine construct was an immunogenic, non-allergen and unfunctional protein which contained multiple CD8 + and CD4 + overlapping epitopes, IFN-γ inducing epitopes, linear and conformational B cell epitopes. It could form stable and significant interactions with TLR-4/MD according to molecular docking and dynamics simulations. Global population coverage of the vaccine for HLA-I and II were estimated 96.2% and 97.1%, respectively. At last, the final vaccine construct was reverse translated to design the DNA vaccine. Although the designed vaccine exhibited high efficacy in silico, further experimental validation is necessary.
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Affiliation(s)
- Ashkan Safavi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Amirhosein Kefayat
- Department of Oncology, Cancer Prevention Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Mahdevar
- Department of Biology, Faculty of Science and Engineering, Science and Arts University, Yazd, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Fatemeh Ghahremani
- Department of Medical Physics and Radiotherapy, Arak School of Paramedicine, Arak University of Medical Sciences, Arak, Iran.
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28
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Lisi L, Lacal PM, Barbaccia ML, Graziani G. Approaching coronavirus disease 2019: Mechanisms of action of repurposed drugs with potential activity against SARS-CoV-2. Biochem Pharmacol 2020; 180:114169. [PMID: 32710969 PMCID: PMC7375972 DOI: 10.1016/j.bcp.2020.114169] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
Abstract
On March 11, 2020, the World Health Organization (WHO) declared the severe acute respiratory syndrome caused by coronavirus 2 (SARS-CoV-2) a global pandemic. As of July 2020, SARS-CoV-2 has infected more than 14 million people and provoked more than 590,000 deaths, worldwide. From the beginning, a variety of pharmacological treatments has been empirically used to cope with the life-threatening complications associated with Corona Virus Disease 2019 (COVID-19). Thus far, only a couple of them and not consistently across reports have been shown to further decrease mortality, respect to what can be achieved with supportive care. In most cases, and due to the urgency imposed by the number and severity of the patients' clinical conditions, the choice of treatment has been limited to repurposed drugs, approved for other indications, or investigational agents used for other viral infections often rendered available on a compassionate-use basis. The rationale for drug selection was mainly, though not exclusively, based either i) on the activity against other coronaviruses or RNA viruses in order to potentially hamper viral entry and replication in the epithelial cells of the airways, and/or ii) on the ability to modulate the excessive inflammatory reaction deriving from dysregulated host immune responses against the SARS-CoV-2. In several months, an exceptionally large number of clinical trials have been designed to evaluate the safety and efficacy of anti-COVID-19 therapies in different clinical settings (treatment or pre- and post-exposure prophylaxis) and levels of disease severity, but only few of them have been completed so far. This review focuses on the molecular mechanisms of action that have provided the scientific rationale for the empirical use and evaluation in clinical trials of structurally different and often functionally unrelated drugs during the SARS-CoV-2 pandemic.
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Affiliation(s)
- Lucia Lisi
- Dipartimento di Bioetica e Sicurezza, Sezione di Farmacologia, Catholic University Medical School, 00168 Rome, Italy
| | | | | | - Grazia Graziani
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy.
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29
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Levy E, Delvin E, Marcil V, Spahis S. Can phytotherapy with polyphenols serve as a powerful approach for the prevention and therapy tool of novel coronavirus disease 2019 (COVID-19)? Am J Physiol Endocrinol Metab 2020; 319:E689-E708. [PMID: 32755302 PMCID: PMC7518070 DOI: 10.1152/ajpendo.00298.2020] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Much more serious than the previous severe acute respiratory syndrome (SARS) coronavirus (CoV) outbreaks, the novel SARS-CoV-2 infection has spread speedily, affecting 213 countries and causing ∼17,300,000 cases and ∼672,000 (∼+1,500/day) deaths globally (as of July 31, 2020). The potentially fatal coronavirus disease (COVID-19), caused by air droplets and airborne as the main transmission modes, clearly induces a spectrum of respiratory clinical manifestations, but it also affects the immune, gastrointestinal, hematological, nervous, and renal systems. The dramatic scale of disorders and complications arises from the inadequacy of current treatments and absence of a vaccine and specific anti-COVID-19 drugs to suppress viral replication, inflammation, and additional pathogenic conditions. This highlights the importance of understanding the SARS-CoV-2 mechanisms of actions and the urgent need of prospecting for new or alternative treatment options. The main objective of the present review is to discuss the challenging issue relative to the clinical utility of plants-derived polyphenols in fighting viral infections. Not only is the strong capacity of polyphenols highlighted in magnifying health benefits, but the underlying mechanisms are also stressed. Finally, emphasis is placed on the potential ability of polyphenols to combat SARS-CoV-2 infection via the regulation of its molecular targets of human cellular binding and replication, as well as through the resulting host inflammation, oxidative stress, and signaling pathways.
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Affiliation(s)
- Emile Levy
- Research Centre, Sainte-Justine University Health Center, Montreal, Quebec, Canada
- Department of Nutrition, Université de Montréal, Montreal, Quebec, Canada
- Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec City, Quebec, Canada
| | - Edgard Delvin
- Research Centre, Sainte-Justine University Health Center, Montreal, Quebec, Canada
| | - Valérie Marcil
- Research Centre, Sainte-Justine University Health Center, Montreal, Quebec, Canada
- Department of Nutrition, Université de Montréal, Montreal, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec City, Quebec, Canada
| | - Schohraya Spahis
- Research Centre, Sainte-Justine University Health Center, Montreal, Quebec, Canada
- Department of Nutrition, Université de Montréal, Montreal, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec City, Quebec, Canada
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30
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Nebigil CG, Moog C, Vagner S, Benkirane-Jessel N, Smith DR, Désaubry L. Flavaglines as natural products targeting eIF4A and prohibitins: From traditional Chinese medicine to antiviral activity against coronaviruses. Eur J Med Chem 2020; 203:112653. [PMID: 32693294 PMCID: PMC7362831 DOI: 10.1016/j.ejmech.2020.112653] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/19/2022]
Abstract
Flavaglines are cyclopenta[b]benzofurans found in plants of the genus Aglaia, several species of which are used in traditional Chinese medicine. These compounds target the initiation factor of translation eIF4A and the scaffold proteins prohibitins-1 and 2 (PHB1/2) to exert various pharmacological activities, including antiviral effects against several types of viruses, including coronaviruses. This review is focused on the antiviral effects of flavaglines and their therapeutic potential against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Canan G Nebigil
- INSERM U 1260, Regenerative Nanomedicine (RNM), FMTS, 11 Rue Humann, 67000, Strasbourg, France
| | - Christiane Moog
- INSERM U1109, LabEx TRANSPLANTEX, Fédération Hospitalo-Universitaire (FHU) OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), University of Strasbourg, Strasbourg, France
| | - Stéphan Vagner
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Sud, Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France
| | - Nadia Benkirane-Jessel
- INSERM U 1260, Regenerative Nanomedicine (RNM), FMTS, 11 Rue Humann, 67000, Strasbourg, France; Université de Strasbourg, Faculté de Chirurgie Dentaire, Hôpitaux Universitaires de Strasbourg, 8 Rue de Ste Elisabeth, 67000, Strasbourg, France
| | - Duncan R Smith
- Institute of Molecular Biosciences, Mahidol University, Salaya, 73170, Thailand
| | - Laurent Désaubry
- INSERM U 1260, Regenerative Nanomedicine (RNM), FMTS, 11 Rue Humann, 67000, Strasbourg, France.
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31
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Santerre M, Arjona SP, Allen CN, Shcherbik N, Sawaya BE. Why do SARS-CoV-2 NSPs rush to the ER? J Neurol 2020; 268:2013-2022. [PMID: 32870373 PMCID: PMC7461160 DOI: 10.1007/s00415-020-10197-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/15/2020] [Accepted: 08/27/2020] [Indexed: 12/18/2022]
Abstract
SARS-CoV-2, which led to the 2020 global pandemic, is responsible for the Coronavirus Disease 2019 (COVID-19), a respiratory illness, and presents a tropism for the central nervous system. Like most members of this family, the virus is composed of structural and non-structural proteins (NSPs). The non-structural proteins are critical elements of the replication and transcription complex (RTC), as well as immune system evasion. Through hijacking the endoplasmic reticulum (ER) membrane, NSPs help the virus establish the RTC, inducing ER stress after membrane rearrangement and causing severe neuronal disturbance. In this review, we focus on the role of Nsp3, 4, and 6 in intracellular membrane rearrangement and evaluate the potential disruption of the central nervous system and the neurodegeneration which it could trigger. Studies of these NSPs will not only bring to light their specific role in viral infection but also facilitate the discovery of novel targeted drugs.
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Affiliation(s)
- Maryline Santerre
- Molecular Studies of Neurodegenerative Diseases Lab, Lewis Katz School of Medicine, Fels Institute for Cancer Research, Temple University, 3307 North Broad Street, Philadelphia, PA, 19140, USA.
| | - Sterling P Arjona
- Molecular Studies of Neurodegenerative Diseases Lab, Lewis Katz School of Medicine, Fels Institute for Cancer Research, Temple University, 3307 North Broad Street, Philadelphia, PA, 19140, USA
| | - Charles Ns Allen
- Molecular Studies of Neurodegenerative Diseases Lab, Lewis Katz School of Medicine, Fels Institute for Cancer Research, Temple University, 3307 North Broad Street, Philadelphia, PA, 19140, USA
| | - Natalia Shcherbik
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, 2 Medical Center Drive, Stratford, NJ, 08084, USA
| | - Bassel E Sawaya
- Molecular Studies of Neurodegenerative Diseases Lab, Lewis Katz School of Medicine, Fels Institute for Cancer Research, Temple University, 3307 North Broad Street, Philadelphia, PA, 19140, USA. .,Department of Neurology, Lewis Katz School of Medicine - Temple University Philadelphia, Philadelphia, PA, 19140, USA.
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32
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Dadhich R, Kapoor S. Various Facets of Pathogenic Lipids in Infectious Diseases: Exploring Virulent Lipid-Host Interactome and Their Druggability. J Membr Biol 2020; 253:399-423. [PMID: 32833058 PMCID: PMC7443855 DOI: 10.1007/s00232-020-00135-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
Lipids form an integral, structural, and functional part of all life forms. They play a significant role in various cellular processes such as membrane fusion, fission, endocytosis, protein trafficking, and protein functions. Interestingly, recent studies have revealed their more impactful and critical involvement in infectious diseases, starting with the manipulation of the host membrane to facilitate pathogenic entry. Thereafter, pathogens recruit specific host lipids for the maintenance of favorable intracellular niche to augment their survival and proliferation. In this review, we showcase the lipid-mediated host pathogen interplay in context of life-threatening viral and bacterial diseases including the recent SARS-CoV-2 infection. We evaluate the emergent lipid-centric approaches adopted by these pathogens, while delineating the alterations in the composition and organization of the cell membrane within the host, as well as the pathogen. Lastly, crucial nexus points in their interaction landscape for therapeutic interventions are identified. Lipids act as critical determinants of bacterial and viral pathogenesis by altering the host cell membrane structure and functions.
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Affiliation(s)
- Ruchika Dadhich
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India.
- Wadhwani Research Centre for Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
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33
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Zhou R, Zeng R, von Brunn A, Lei J. Structural characterization of the C-terminal domain of SARS-CoV-2 nucleocapsid protein. MOLECULAR BIOMEDICINE 2020; 1:2. [PMID: 34765991 PMCID: PMC7406681 DOI: 10.1186/s43556-020-00001-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 07/12/2020] [Indexed: 12/18/2022] Open
Abstract
The newly emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in a global human health crisis. The CoV nucleocapsid (N) protein plays essential roles both in the viral genomic RNA packaging and the regulation of host cellular machinery. Here, to contribute to the structural information of the N protein, we describe the 2.0 Å crystal structure of the SARS-CoV-2 N protein C-terminal domain (N-CTD). The structure indicates an extensive interaction dimer in a domain-swapped manner. The interface of this dimer was first thoroughly illustrated. Also, the SARS-CoV-2 N-CTD dimerization form was verified in solution using size-exclusion chromatography. Based on the structural comparison of the N-CTDs from alpha-, beta-, and gamma-CoVs, we demonstrate the common and specific characteristics of the SARS-CoV-2 N-CTD. Furthermore, we provide evidence that the SARS-CoV-2 N-CTD possesses the binding ability to single-stranded RNA, single-stranded DNA as well as double-stranded DNA in vitro. In conclusion, this study could potentially accelerate research to understand the complete biological functions of the new CoV N protein.
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Asghari A, Naseri M, Safari H, Saboory E, Parsamanesh N. The Novel Insight of SARS-CoV-2 Molecular Biology and Pathogenesis and Therapeutic Options. DNA Cell Biol 2020; 39:1741-1753. [PMID: 32716648 DOI: 10.1089/dna.2020.5703] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
On December 31, 2019, a novel coronavirus, being the third highly infective CoV and named as coronavirus disease 2019 (COVID-19) in the city of Wuhan, was announced by the World Health Organization. COVID-19 has a 2% mortality rate, is known as the third extremely infective CoV infection, and has a mortality rate less than MERS-CoV and SARS-CoV. The CoV family comprises a chief number of positive single-stranded ss (+) RNA viruses that are recognized in mammals. The 2019-nCoV patients showed that the angiotensin-converting enzyme II (ACE2) was the same for SARS-CoV. Structural proteins have an essential role in virus released and budding to various host cells. Notably, evidence indicated human-to-human transmission, along with several exported patients of virus infection worldwide. Nowadays, no licensed antivirals drugs or vaccines for being utilized against these coronavirus infections are recognized. There is an urgent requirement for an extensive research of CoV infections to disclose the route of extension, pathogenesis, and diagnosis and then to recognize the therapeutic targets to facilitate disease control and surveillance. In this article, we present an overview of the common biological criteria of CoVs and explain pathogenesis with a focus on the therapeutic approach to suggest potential goals for treating and monitoring this emerging zoonotic disease.
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Affiliation(s)
- Arghavan Asghari
- Student Research Committee and Birjand University of Medical Sciences, Birjand, Iran
| | - Mohsen Naseri
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Hamidreza Safari
- Department of Immunology, Torbat Jam Faculty of Medical Sciences, Torbat Jam, Iran
| | - Ehsan Saboory
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Negin Parsamanesh
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
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Abstract
Novel beta-coronavirus SARS-CoV-2 is the pathogenic agent responsible for coronavirus disease-2019 (COVID-19), a globally pandemic infectious disease. Due to its high virulence and the absence of immunity among the general population, SARS-CoV-2 has quickly spread to all countries. This pandemic highlights the urgent unmet need to expand and focus our research tools on what are considered "neglected infectious diseases" and to prepare for future inevitable pandemics. This global emergency has generated unprecedented momentum and scientific efforts around the globe unifying scientists from academia, government and the pharmaceutical industry to accelerate the discovery of vaccines and treatments. Herein, we shed light on the virus structure and life cycle and the potential therapeutic targets in SARS-CoV-2 and briefly refer to both active and passive immunization modalities, drug repurposing focused on speed to market, and novel agents against specific viral targets as therapeutic interventions for COVID-19.
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Affiliation(s)
- Essam Eldin A. Osman
- Department of Medicinal Chemistry, College of Pharmacy and
Michigan Drug Discovery, Life Sciences Institute,
University of Michigan, Ann Arbor, Michigan 48109,
United States
- Department of Pharmaceutical Chemistry, Faculty of
Pharmacy, Cairo University, Cairo 11562,
Egypt
| | - Peter L. Toogood
- Department of Medicinal Chemistry, College of Pharmacy and
Michigan Drug Discovery, Life Sciences Institute,
University of Michigan, Ann Arbor, Michigan 48109,
United States
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy and
Michigan Drug Discovery, Life Sciences Institute,
University of Michigan, Ann Arbor, Michigan 48109,
United States
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Carlson CR, Asfaha JB, Ghent CM, Howard CJ, Hartooni N, Morgan DO. Phosphorylation modulates liquid-liquid phase separation of the SARS-CoV-2 N protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32637943 DOI: 10.1101/2020.06.28.176248] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The nucleocapsid (N) protein of coronaviruses serves two major functions: compaction of the RNA genome in the virion and regulation of viral gene transcription in the infected cell 1-3 . The N protein contains two globular RNA-binding domains surrounded by regions of intrinsic disorder 4 . Phosphorylation of the central disordered region is required for normal viral genome transcription 5,6 , which occurs in a cytoplasmic structure called the replication transcription complex (RTC) 7-11 . It is not known how phosphorylation controls N protein function. Here we show that the N protein of SARS-CoV-2, together with viral RNA, forms biomolecular condensates 12-15 . Unmodified N protein forms partially ordered gel-like structures that depend on multivalent RNA-protein and protein-protein interactions. Phosphorylation reduces a subset of these interactions, generating a more liquid-like droplet. We speculate that distinct oligomeric states support the two functions of the N protein: unmodified protein forms a structured oligomer that is suited for nucleocapsid assembly, and phosphorylated protein forms a liquid-like compartment for viral genome processing. Inhibitors of N protein phosphorylation could therefore serve as antiviral therapy.
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Prajapat M, Sarma P, Shekhar N, Prakash A, Avti P, Bhattacharyya A, Kaur H, Kumar S, Bansal S, Sharma AR, Medhi B. Update on the target structures of SARS-CoV-2: A systematic review. Indian J Pharmacol 2020; 52:142-149. [PMID: 32565603 PMCID: PMC7282679 DOI: 10.4103/ijp.ijp_338_20] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 01/18/2023] Open
Abstract
Knowledge of structural details is very much essential from the drug-design perspective. In the systematic review, we systematically reviewed the structural basis of different target proteins of SARS-corona virus (CoV2) from a viral life cycle and from drug design perspective. We searched four literature (PubMed, EMBASE, NATURE, and Willey online library) databases and one structural database (RCSB.org) with appropriate keywords till April 18, and finally, 26 articles were included in the systematic review. The published literature mainly centered upon the structural details of “spike protein,” “main protease/M Pro/3CL pro,” “RNA-dependent RNA polymerase,” and “nonstructural protein 15 Endoribonuclease” of SARS-CoV-2. However, inhibitor bound structures were very less. We need better structures elucidating the interactions between different targets and their inhibitors which will help us in understanding the atomic level importance of different amino acid residues in the functionality of the target structures. To summarize, we need structures with fine resolution, co-crystallized structures with biologically validated inhibitors, and functional characterization of different target proteins. Some other routes of entry of SARS-CoV-2 are also mentioned (e.g., CD147); however, these findings are not structurally validated. This review may pave way for better understanding of SARS-CoV-2 life cycle from structural biology perspective.
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Affiliation(s)
- Manisha Prajapat
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Phulen Sarma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Nishant Shekhar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ajay Prakash
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pramod Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anusuya Bhattacharyya
- Departments of Ophthalmology, Government Medical College and Hospital, Chandigarh, India
| | - Hardeep Kaur
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Subodh Kumar
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Seema Bansal
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Amit Raj Sharma
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Nucleocapsid Protein Recruitment to Replication-Transcription Complexes Plays a Crucial Role in Coronaviral Life Cycle. J Virol 2020; 94:JVI.01925-19. [PMID: 31776274 PMCID: PMC6997762 DOI: 10.1128/jvi.01925-19] [Citation(s) in RCA: 225] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 11/17/2019] [Indexed: 12/21/2022] Open
Abstract
CoVs have long been regarded as relatively harmless pathogens for humans. Severe respiratory tract infection outbreaks caused by severe acute respiratory syndrome CoV and Middle East respiratory syndrome CoV, however, have caused high pathogenicity and mortality rates in humans. These outbreaks highlighted the relevance of being able to control CoV infections. We used a model CoV, MHV, to investigate the importance of the recruitment of N protein, a central component of CoV virions, to intracellular platforms where CoVs replicate, transcribe, and translate their genomes. By identifying the principal binding partner at these intracellular platforms and generating a specific mutant, we found that N protein recruitment to these locations is crucial for promoting viral RNA synthesis. Moreover, blocking this recruitment strongly inhibits viral infection. Thus, our results explain an important aspect of the CoV life cycle and reveal an interaction of viral proteins that could be targeted in antiviral therapies. Coronavirus (CoV) nucleocapsid (N) proteins are key for incorporating genomic RNA into progeny viral particles. In infected cells, N proteins are present at the replication-transcription complexes (RTCs), the sites of CoV RNA synthesis. It has been shown that N proteins are important for viral replication and that the one of mouse hepatitis virus (MHV), a commonly used model CoV, interacts with nonstructural protein 3 (nsp3), a component of the RTCs. These two aspects of the CoV life cycle, however, have not been linked. We found that the MHV N protein binds exclusively to nsp3 and not other RTC components by using a systematic yeast two-hybrid approach, and we identified two distinct regions in the N protein that redundantly mediate this interaction. A selective N protein variant carrying point mutations in these two regions fails to bind nsp3 in vitro, resulting in inhibition of its recruitment to RTCs in vivo. Furthermore, in contrast to the wild-type N protein, this N protein variant impairs the stimulation of genomic RNA and viral mRNA transcription in vivo and in vitro, which in turn leads to impairment of MHV replication and progeny production. Altogether, our results show that N protein recruitment to RTCs, via binding to nsp3, is an essential step in the CoV life cycle because it is critical for optimal viral RNA synthesis. IMPORTANCE CoVs have long been regarded as relatively harmless pathogens for humans. Severe respiratory tract infection outbreaks caused by severe acute respiratory syndrome CoV and Middle East respiratory syndrome CoV, however, have caused high pathogenicity and mortality rates in humans. These outbreaks highlighted the relevance of being able to control CoV infections. We used a model CoV, MHV, to investigate the importance of the recruitment of N protein, a central component of CoV virions, to intracellular platforms where CoVs replicate, transcribe, and translate their genomes. By identifying the principal binding partner at these intracellular platforms and generating a specific mutant, we found that N protein recruitment to these locations is crucial for promoting viral RNA synthesis. Moreover, blocking this recruitment strongly inhibits viral infection. Thus, our results explain an important aspect of the CoV life cycle and reveal an interaction of viral proteins that could be targeted in antiviral therapies.
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Sachse M, Fernández de Castro I, Tenorio R, Risco C. The viral replication organelles within cells studied by electron microscopy. Adv Virus Res 2019; 105:1-33. [PMID: 31522702 PMCID: PMC7112055 DOI: 10.1016/bs.aivir.2019.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Transmission electron microscopy (TEM) has been crucial to study viral infections. As a result of recent advances in light and electron microscopy, we are starting to be aware of the variety of structures that viruses assemble inside cells. Viruses often remodel cellular compartments to build their replication factories. Remarkably, viruses are also able to induce new membranes and new organelles. Here we revise the most relevant imaging technologies to study the biogenesis of viral replication organelles. Live cell microscopy, correlative light and electron microscopy, cryo-TEM, and three-dimensional imaging methods are unveiling how viruses manipulate cell organization. In particular, methods for molecular mapping in situ in two and three dimensions are revealing how macromolecular complexes build functional replication complexes inside infected cells. The combination of all these imaging approaches is uncovering the viral life cycle events with a detail never seen before.
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Affiliation(s)
- Martin Sachse
- Unité Technologie et service BioImagerie Ultrastructurale, Institut Pasteur, Paris, France.
| | | | - Raquel Tenorio
- Cell Structure Laboratory, National Center for Biotechnology, CSIC, Madrid, Spain
| | - Cristina Risco
- Cell Structure Laboratory, National Center for Biotechnology, CSIC, Madrid, Spain.
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V'kovski P, Gerber M, Kelly J, Pfaender S, Ebert N, Braga Lagache S, Simillion C, Portmann J, Stalder H, Gaschen V, Bruggmann R, Stoffel MH, Heller M, Dijkman R, Thiel V. Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling. eLife 2019; 8:42037. [PMID: 30632963 PMCID: PMC6372286 DOI: 10.7554/elife.42037] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/11/2019] [Indexed: 12/31/2022] Open
Abstract
Positive-sense RNA viruses hijack intracellular membranes that provide niches for viral RNA synthesis and a platform for interactions with host proteins. However, little is known about host factors at the interface between replicase complexes and the host cytoplasm. We engineered a biotin ligase into a coronaviral replication/transcription complex (RTC) and identified >500 host proteins constituting the RTC microenvironment. siRNA-silencing of each RTC-proximal host factor demonstrated importance of vesicular trafficking pathways, ubiquitin-dependent and autophagy-related processes, and translation initiation factors. Notably, detection of translation initiation factors at the RTC was instrumental to visualize and demonstrate active translation proximal to replication complexes of several coronaviruses. Collectively, we establish a spatial link between viral RNA synthesis and diverse host factors of unprecedented breadth. Our data may serve as a paradigm for other positive-strand RNA viruses and provide a starting point for a comprehensive analysis of critical virus-host interactions that represent targets for therapeutic intervention. Coronaviruses can infect the nose and throat and are a main cause of the common cold. Infections are usually mild and short-lived, but sometimes they can turn nasty. In 2002 and 2012, two dangerous new coronaviruses emerged and caused diseases known as SARS and MERS. These viruses caused much more serious symptoms and in some cases proved deadly. The question is, why are some coronaviruses more dangerous than others? Scientists know that the body's response to virus infection can make a difference to whether someone had mild or severe disease. So, to understand why some coronaviruses cause a cold and others kill, they also need to learn how people react to virus infection. Coronaviruses hijack membranes inside cells and turn them into virus factories. Within these factories, the viruses build molecular machinery called replicase complexes to copy their genetic code, which is needed for the next generation of virus particles. The viruses steal and repurpose proteins from their host cell that will assist in the copying process. However, scientists do not yet know which host proteins are essential for the virus to multiply. So, to find out, V’kovski et al. developed a way to tag any host protein that came near the virus factories. The new technique involved attaching an enzyme called a biotin ligase to the replicase complex. This enzyme acts as a molecular label gun, attaching a chemical tag to any protein that comes within ten nanometres. The label gun revealed that more than 500 different proteins come into contact with the replicase complex. To find out what these proteins were doing, the next step was to switch off their genes one by one. This revealed the key cell machinery that coronaviruses hijack when they are replicating. It included the cell's cargo transport system, the waste disposal system, and the protein production system. Using these systems allows the viruses to copy their genetic code next to machines that can turn it straight into viral proteins. These new results provide clues about which proteins viruses actually need from their host cells. They also do not just apply to coronaviruses. Other viruses use similar strategies to complete their infection cycle. These findings could help researchers to understand more generally about how viruses multiply. In the future, this knowledge could lead to new ways to combat virus infections.
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Affiliation(s)
- Philip V'kovski
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Markus Gerber
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna Kelly
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Interfaculty Bioinformatics Unit, SIB Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Stephanie Pfaender
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sophie Braga Lagache
- Mass Spectrometry and Proteomics Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Cedric Simillion
- Mass Spectrometry and Proteomics Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland.,Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Jasmine Portmann
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Véronique Gaschen
- Division of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit, SIB Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Michael H Stoffel
- Division of Veterinary Anatomy, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Manfred Heller
- Mass Spectrometry and Proteomics Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Ronald Dijkman
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology IVI, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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Müller C, Hardt M, Schwudke D, Neuman BW, Pleschka S, Ziebuhr J. Inhibition of Cytosolic Phospholipase A 2α Impairs an Early Step of Coronavirus Replication in Cell Culture. J Virol 2018; 92:e01463-17. [PMID: 29167338 PMCID: PMC5790932 DOI: 10.1128/jvi.01463-17] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/14/2017] [Indexed: 12/15/2022] Open
Abstract
Coronavirus replication is associated with intracellular membrane rearrangements in infected cells, resulting in the formation of double-membrane vesicles (DMVs) and other membranous structures that are referred to as replicative organelles (ROs). The latter provide a structural scaffold for viral replication/transcription complexes (RTCs) and help to sequester RTC components from recognition by cellular factors involved in antiviral host responses. There is increasing evidence that plus-strand RNA (+RNA) virus replication, including RO formation and virion morphogenesis, affects cellular lipid metabolism and critically depends on enzymes involved in lipid synthesis and processing. Here, we investigated the role of cytosolic phospholipase A2α (cPLA2α) in coronavirus replication using a low-molecular-weight nonpeptidic inhibitor, pyrrolidine-2 (Py-2). The inhibition of cPLA2α activity, which produces lysophospholipids (LPLs) by cleaving at the sn-2 position of phospholipids, had profound effects on viral RNA and protein accumulation in human coronavirus 229E-infected Huh-7 cells. Transmission electron microscopy revealed that DMV formation in infected cells was significantly reduced in the presence of the inhibitor. Furthermore, we found that (i) viral RTCs colocalized with LPL-containing membranes, (ii) cellular LPL concentrations were increased in coronavirus-infected cells, and (iii) this increase was diminished in the presence of the cPLA2α inhibitor Py-2. Py-2 also displayed antiviral activities against other viruses representing the Coronaviridae and Togaviridae families, while members of the Picornaviridae were not affected. Taken together, the study provides evidence that cPLA2α activity is critically involved in the replication of various +RNA virus families and may thus represent a candidate target for broad-spectrum antiviral drug development.IMPORTANCE Examples of highly conserved RNA virus proteins that qualify as drug targets for broad-spectrum antivirals remain scarce, resulting in increased efforts to identify and specifically inhibit cellular functions that are essential for the replication of RNA viruses belonging to different genera and families. The present study supports and extends previous conclusions that enzymes involved in cellular lipid metabolism may be tractable targets for broad-spectrum antivirals. We obtained evidence to show that a cellular phospholipase, cPLA2α, which releases fatty acid from the sn-2 position of membrane-associated glycerophospholipids, is critically involved in coronavirus replication, most likely by producing lysophospholipids that are required to form the specialized membrane compartments in which viral RNA synthesis takes place. The importance of this enzyme in coronavirus replication and DMV formation is supported by several lines of evidence, including confocal and electron microscopy, viral replication, and lipidomics studies of coronavirus-infected cells treated with a highly specific cPLA2α inhibitor.
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Affiliation(s)
- Christin Müller
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Martin Hardt
- Imaging Unit, Biomedical Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Priority Area Infection, Research Center Borstel, Leibniz Center for Medicine and Bioscience, Borstel, Germany
| | | | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
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In Situ Tagged nsp15 Reveals Interactions with Coronavirus Replication/Transcription Complex-Associated Proteins. mBio 2017; 8:mBio.02320-16. [PMID: 28143984 PMCID: PMC5285509 DOI: 10.1128/mbio.02320-16] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Coronavirus (CoV) replication and transcription are carried out in close proximity to restructured endoplasmic reticulum (ER) membranes in replication/transcription complexes (RTC). Many of the CoV nonstructural proteins (nsps) are required for RTC function; however, not all of their functions are known. nsp15 contains an endoribonuclease domain that is conserved in the CoV family. While the enzymatic activity and crystal structure of nsp15 are well defined, its role in replication remains elusive. nsp15 localizes to sites of RNA replication, but whether it acts independently or requires additional interactions for its function remains unknown. To begin to address these questions, we created an in situ tagged form of nsp15 using the prototypic CoV, mouse hepatitis virus (MHV). In MHV, nsp15 contains the genomic RNA packaging signal (P/S), a 95-bp RNA stem-loop structure that is not required for viral replication or nsp15 function. Utilizing this knowledge, we constructed an internal hemagglutinin (HA) tag that replaced the P/S. We found that nsp15-HA was localized to discrete perinuclear puncta and strongly colocalized with nsp8 and nsp12, both well-defined members of the RTC, but not the membrane (M) protein, involved in virus assembly. Finally, we found that nsp15 interacted with RTC-associated proteins nsp8 and nsp12 during infection, and this interaction was RNA independent. From this, we conclude that nsp15 localizes and interacts with CoV proteins in the RTC, suggesting it plays a direct or indirect role in virus replication. Furthermore, the use of in situ epitope tags could be used to determine novel nsp-nsp interactions in coronaviruses. IMPORTANCE Despite structural and biochemical data demonstrating that the coronavirus nsp15 protein contains an endoribonuclease domain, its precise function during coronavirus infection remains unknown. In this work, we created a novel in situ tagged form of nsp15 to study interactions and localization during infection. This in situ tag was tolerated by MHV and did not affect viral replication. Utilizing this tag, we established that nsp15 localized to sites of replication but not sites of assembly throughout infection. Furthermore, we found that nsp15 interacted with the putative viral primase nsp8 and polymerase nsp12 during CoV infection. The strong association of nsp15 with replication complexes and interactions with replicative CoV enzymes suggest nsp15 is involved in CoV replication. These data and tools developed in this study help elucidate the function of nsp15 during infection and may be used to uncover other novel viral protein interactions.
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Müller C, Ulyanova V, Ilinskaya O, Pleschka S, Shah Mahmud R. A Novel Antiviral Strategy against MERS-CoV and HCoV-229E Using Binase to Target Viral Genome Replication. BIONANOSCIENCE 2016; 7:294-299. [PMID: 32219056 PMCID: PMC7090624 DOI: 10.1007/s12668-016-0341-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
RNA viruses cause most of the dangerous communicable diseases. Due to their high mutation rates, RNA viruses quickly evade selective pressures and can adapt to a new host. Therefore, new antiviral approaches are urgently needed, which target more than one specific virus variant and which would optimally prevent development of viral resistance. Among the family of coronaviruses (CoV), several human pathogenic strains (HCoV) are known to cause respiratory diseases and are implied in enteric diseases. While most strains contribute to common cold-like illnesses, others lead to severe infections. One of these viruses is the newly emerged (2012), highly pathogenic Middle East respiratory syndrome coronavirus (MERS-CoV) of zoonotic origin. MERS-CoV causes a severe respiratory infection with a high mortality rate of 35 %. There is no specific treatment or infection prevention available. Here, we show that the bacterial ribonuclease Binase is able to inhibit the replication of MERS-CoV and of the low-pathogenic human coronavirus 229E (HCoV-229E) in cell culture. We demonstrate that at non-toxic concentrations, Binase decreased the titers of MERS-CoV and HCoV-229E. On a molecular level, Binase treatment reduced (i) the viral subgenomic RNAs and (ii) the viral nucleocapsidprotein (N) and non-structural protein 13 (nsp13) accumulation. Furthermore, we show that the quantity of the replication/transcription complexes within the infected cells is diminished. Thus, the data obtained might allow further development of new anti-coronaviral approaches affecting viral replication, independent of the specific virus strain.
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Affiliation(s)
- Christin Müller
- Institute of Medical Virology, Justus Liebig University, Schubertstrasse 81, 35392 Giessen, Germany
| | - Vera Ulyanova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 18 Kremlyovskaya Str, Kazan, 420008 Russia
| | - Olga Ilinskaya
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 18 Kremlyovskaya Str, Kazan, 420008 Russia
| | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University, Schubertstrasse 81, 35392 Giessen, Germany
| | - Raihan Shah Mahmud
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 18 Kremlyovskaya Str, Kazan, 420008 Russia
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Neuman BW. Bioinformatics and functional analyses of coronavirus nonstructural proteins involved in the formation of replicative organelles. Antiviral Res 2016; 135:97-107. [PMID: 27743916 PMCID: PMC7113682 DOI: 10.1016/j.antiviral.2016.10.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/23/2016] [Accepted: 10/12/2016] [Indexed: 12/13/2022]
Abstract
Replication of eukaryotic positive-stranded RNA viruses is usually linked to the presence of membrane-associated replicative organelles. The purpose of this review is to discuss the function of proteins responsible for formation of the coronavirus replicative organelle. This will be done by identifying domains that are conserved across the order Nidovirales, and by summarizing what is known about function and structure at the level of protein domains. Bioinformatics reveals a new domain-level map of coronavirus nsp3-nsp6. Domain-level protein variability is a tool for functional annotation. Ten nsp3 domains are conserved in all known coronaviruses. Review of the role of the nsp5 main protease in RNA synthesis.
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Affiliation(s)
- Benjamin W Neuman
- University of Reading, School of Biological Sciences, RG6 6AH, United Kingdom; College of STEM, Texas A&M University-Texarkana, Texarkana, TX 75503, USA.
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Illuminating the Sites of Enterovirus Replication in Living Cells by Using a Split-GFP-Tagged Viral Protein. mSphere 2016; 1:mSphere00104-16. [PMID: 27390781 PMCID: PMC4935779 DOI: 10.1128/msphere.00104-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/02/2016] [Indexed: 12/13/2022] Open
Abstract
Enteroviruses induce the formation of membranous structures (replication organelles [ROs]) with a unique protein and lipid composition specialized for genome replication. Electron microscopy has revealed the morphology of enterovirus ROs, and immunofluorescence studies have been conducted to investigate their origin and formation. Yet, immunofluorescence analysis of fixed cells results in a rather static view of RO formation, and the results may be compromised by immunolabeling artifacts. While live-cell imaging of ROs would be preferred, enteroviruses encoding a membrane-anchored viral protein fused to a large fluorescent reporter have thus far not been described. Here, we tackled this constraint by introducing a small tag from a split-GFP system into an RO-resident enterovirus protein. This new tool bridges a methodological gap by circumventing the need for immunolabeling fixed cells and allows the study of the dynamics and formation of enterovirus ROs in living cells. Like all other positive-strand RNA viruses, enteroviruses generate new organelles (replication organelles [ROs]) with a unique protein and lipid composition on which they multiply their viral genome. Suitable tools for live-cell imaging of enterovirus ROs are currently unavailable, as recombinant enteroviruses that carry genes that encode RO-anchored viral proteins tagged with fluorescent reporters have not been reported thus far. To overcome this limitation, we used a split green fluorescent protein (split-GFP) system, comprising a large fragment [strands 1 to 10; GFP(S1-10)] and a small fragment [strand 11; GFP(S11)] of only 16 residues. The GFP(S11) (GFP with S11 fragment) fragment was inserted into the 3A protein of the enterovirus coxsackievirus B3 (CVB3), while the large fragment was supplied by transient or stable expression in cells. The introduction of GFP(S11) did not affect the known functions of 3A when expressed in isolation. Using correlative light electron microscopy (CLEM), we showed that GFP fluorescence was detected at ROs, whose morphologies are essentially identical to those previously observed for wild-type CVB3, indicating that GFP(S11)-tagged 3A proteins assemble with GFP(S1-10) to form GFP for illumination of bona fide ROs. It is well established that enterovirus infection leads to Golgi disintegration. Through live-cell imaging of infected cells expressing an mCherry-tagged Golgi marker, we monitored RO development and revealed the dynamics of Golgi disassembly in real time. Having demonstrated the suitability of this virus for imaging ROs, we constructed a CVB3 encoding GFP(S1-10) and GFP(S11)-tagged 3A to bypass the need to express GFP(S1-10) prior to infection. These tools will have multiple applications in future studies on the origin, location, and function of enterovirus ROs. IMPORTANCE Enteroviruses induce the formation of membranous structures (replication organelles [ROs]) with a unique protein and lipid composition specialized for genome replication. Electron microscopy has revealed the morphology of enterovirus ROs, and immunofluorescence studies have been conducted to investigate their origin and formation. Yet, immunofluorescence analysis of fixed cells results in a rather static view of RO formation, and the results may be compromised by immunolabeling artifacts. While live-cell imaging of ROs would be preferred, enteroviruses encoding a membrane-anchored viral protein fused to a large fluorescent reporter have thus far not been described. Here, we tackled this constraint by introducing a small tag from a split-GFP system into an RO-resident enterovirus protein. This new tool bridges a methodological gap by circumventing the need for immunolabeling fixed cells and allows the study of the dynamics and formation of enterovirus ROs in living cells.
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Wang H, Tai AW. Mechanisms of Cellular Membrane Reorganization to Support Hepatitis C Virus Replication. Viruses 2016; 8:v8050142. [PMID: 27213428 PMCID: PMC4885097 DOI: 10.3390/v8050142] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/20/2016] [Accepted: 05/15/2016] [Indexed: 12/13/2022] Open
Abstract
Like all positive-sense RNA viruses, hepatitis C virus (HCV) induces host membrane alterations for its replication termed the membranous web (MW). Assembling replication factors at a membranous structure might facilitate the processes necessary for genome replication and packaging and shield viral components from host innate immune defenses. The biogenesis of the HCV MW is a complex process involving a concerted effort of HCV nonstructural proteins with a growing list of host factors. Although a comprehensive understanding of MW formation is still missing, a number of important viral and host determinants have been identified. This review will summarize the recent studies that have led to our current knowledge of the role of viral and host factors in the biogenesis of the MWs and discuss how HCV uses this specialized membrane structure for its replication.
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Affiliation(s)
- Hongliang Wang
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Andrew W Tai
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
- Medicine Service, Ann Arbor Veterans Administration Health System, Ann Arbor, MI 48105, USA.
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Abstract
Coronaviruses (CoVs) generate specialized membrane compartments, which consist of double membrane vesicles connected to convoluted membranes, the so-called replicative structures, where viral RNA synthesis takes place. These sites harbor the CoV replication-transcription complexes (RTCs): multi-protein complexes consisting of 16 nonstructural proteins (nsps), the CoV nucleocapsid protein (N) and presumably host proteins. To successfully establish functional membrane-bound RTCs all of the viral and host constituents need to be correctly spatiotemporally organized during viral infection. Few studies, however, have investigated the dynamic processes involved in the formation and functioning of the (subunits of) CoV RTCs and the replicative structures in living cells. In this chapter we describe several protocols to perform time-lapse imaging of CoV-infected cells and to study the kinetics of (subunits of) the CoV replicative structures. The approaches described are not limited to CoV-infected cells; they can also be applied to other virus-infected or non-infected cells.
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Venkatagopalan P, Daskalova SM, Lopez LA, Dolezal KA, Hogue BG. Coronavirus envelope (E) protein remains at the site of assembly. Virology 2015; 478:75-85. [PMID: 25726972 PMCID: PMC4550588 DOI: 10.1016/j.virol.2015.02.005] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 09/19/2014] [Accepted: 02/04/2015] [Indexed: 01/01/2023]
Abstract
Coronaviruses (CoVs) assemble at endoplasmic reticulum Golgi intermediate compartment (ERGIC) membranes and egress from cells in cargo vesicles. Only a few molecules of the envelope (E) protein are assembled into virions. The role of E in morphogenesis is not fully understood. The cellular localization and dynamics of mouse hepatitis CoV A59 (MHV) E protein were investigated to further understanding of its role during infection. E protein localized in the ERGIC and Golgi with the amino and carboxy termini in the lumen and cytoplasm, respectively. E protein does not traffic to the cell surface. MHV was genetically engineered with a tetracysteine tag at the carboxy end of E. Fluorescence recovery after photobleaching (FRAP) showed that E is mobile in ERGIC/Golgi membranes. Correlative light electron microscopy (CLEM) confirmed the presence of E in Golgi cisternae. The results provide strong support that E proteins carry out their function(s) at the site of budding/assembly. Mouse hepatitis coronavirus (MHV-CoV) E protein localizes in the ERGIC and Golgi. MHV-CoV E does not transport to the cell surface. MHV-CoV can be genetically engineered with a tetracysteine tag appended to E. First FRAP and correlative light electron microscopy of a CoV E protein. Live-cell imaging shows that E is mobile in ERGIC/Golgi membranes.
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Affiliation(s)
- Pavithra Venkatagopalan
- The Biodesign Institute, Center for Infectious Diseases and Vaccinology, Arizona State University, Tempe, AZ 85287-5401, United States; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5401, United States; Microbiology Graduate Program, Arizona State University, Tempe, AZ 85287-5401, United States
| | - Sasha M Daskalova
- The Biodesign Institute, Center for Infectious Diseases and Vaccinology, Arizona State University, Tempe, AZ 85287-5401, United States; Department of Biochemistry and Chemistry, Arizona State University, Tempe, AZ 85287-5401, United States
| | - Lisa A Lopez
- The Biodesign Institute, Center for Infectious Diseases and Vaccinology, Arizona State University, Tempe, AZ 85287-5401, United States; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5401, United States; Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ 85287-5401, United States
| | - Kelly A Dolezal
- The Biodesign Institute, Center for Infectious Diseases and Vaccinology, Arizona State University, Tempe, AZ 85287-5401, United States; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5401, United States; Microbiology Graduate Program, Arizona State University, Tempe, AZ 85287-5401, United States
| | - Brenda G Hogue
- The Biodesign Institute, Center for Infectious Diseases and Vaccinology, Arizona State University, Tempe, AZ 85287-5401, United States; School of Life Sciences, Arizona State University, Tempe, AZ 85287-5401, United States.
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Báez-Santos YM, St John SE, Mesecar AD. The SARS-coronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds. Antiviral Res 2014; 115:21-38. [PMID: 25554382 PMCID: PMC5896749 DOI: 10.1016/j.antiviral.2014.12.015] [Citation(s) in RCA: 573] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/17/2014] [Accepted: 12/19/2014] [Indexed: 02/06/2023]
Abstract
HTS and structure-based design produced naphthalene-based lead compounds with inhibition of SARS-CoV PLpro in the nM range. These naphthalene-based lead compounds have antiviral potency against SARS-CoV in cell culture. SARS-CoV PLpro naphthalene-based inhibitors are non-toxic and highly selective for SARS-CoV PLpro. Designed SARS-CoV PLpro inhibitors act through a non-covalent, competitive mechanism of inhibition. Lessons from design of SARS-CoV PLpro inhibitors have profound implications for other USPs implicated in disease processes.
Over 10 years have passed since the deadly human coronavirus that causes severe acute respiratory syndrome (SARS-CoV) emerged from the Guangdong Province of China. Despite the fact that the SARS-CoV pandemic infected over 8500 individuals, claimed over 800 lives and cost billions of dollars in economic loss worldwide, there still are no clinically approved antiviral drugs, vaccines or monoclonal antibody therapies to treat SARS-CoV infections. The recent emergence of the deadly human coronavirus that causes Middle East respiratory syndrome (MERS-CoV) is a sobering reminder that new and deadly coronaviruses can emerge at any time with the potential to become pandemics. Therefore, the continued development of therapeutic and prophylactic countermeasures to potentially deadly coronaviruses is warranted. The coronaviral proteases, papain-like protease (PLpro) and 3C-like protease (3CLpro), are attractive antiviral drug targets because they are essential for coronaviral replication. Although the primary function of PLpro and 3CLpro are to process the viral polyprotein in a coordinated manner, PLpro has the additional function of stripping ubiquitin and ISG15 from host-cell proteins to aid coronaviruses in their evasion of the host innate immune responses. Therefore, targeting PLpro with antiviral drugs may have an advantage in not only inhibiting viral replication but also inhibiting the dysregulation of signaling cascades in infected cells that may lead to cell death in surrounding, uninfected cells. This review provides an up-to-date discussion on the SARS-CoV papain-like protease including a brief overview of the SARS-CoV genome and replication followed by a more in-depth discussion on the structure and catalytic mechanism of SARS-CoV PLpro, the multiple cellular functions of SARS-CoV PLpro, the inhibition of SARS-CoV PLpro by small molecule inhibitors, and the prospect of inhibiting papain-like protease from other coronaviruses. This paper forms part of a series of invited articles in Antiviral Research on “From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses.”
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Affiliation(s)
- Yahira M Báez-Santos
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA; Department of Chemistry, Purdue University, West Lafayette, IN, USA; Center for Drug Discovery, Purdue University, West Lafayette, IN, USA; Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Sarah E St John
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA; Department of Chemistry, Purdue University, West Lafayette, IN, USA; Center for Drug Discovery, Purdue University, West Lafayette, IN, USA; Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Andrew D Mesecar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA; Department of Chemistry, Purdue University, West Lafayette, IN, USA; Center for Drug Discovery, Purdue University, West Lafayette, IN, USA; Center for Cancer Research, Purdue University, West Lafayette, IN, USA.
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Neuman BW, Angelini MM, Buchmeier MJ. Does form meet function in the coronavirus replicative organelle? Trends Microbiol 2014; 22:642-7. [PMID: 25037114 PMCID: PMC7127430 DOI: 10.1016/j.tim.2014.06.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/10/2014] [Accepted: 06/13/2014] [Indexed: 12/14/2022]
Abstract
If we use the analogy of a virus as a living entity, then the replicative organelle is the part of the body where its metabolic and reproductive activities are concentrated. Recent studies have illuminated the intricately complex replicative organelles of coronaviruses, a group that includes the largest known RNA virus genomes. This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle.
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Affiliation(s)
- Benjamin W Neuman
- School of Biological Sciences, University of Reading, Reading, Berkshire, UK.
| | - Megan M Angelini
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Michael J Buchmeier
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA; Department of Medicine, Division of Infectious Disease, University of California Irvine, Irvine, CA, USA
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