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Zhao H, Syed AM, Khalid MM, Nguyen A, Ciling A, Wu D, Yau WM, Srinivasan S, Esposito D, Doudna J, Piszczek G, Ott M, Schuck P. Assembly of SARS-CoV-2 nucleocapsid protein with nucleic acid. Nucleic Acids Res 2024; 52:6647-6661. [PMID: 38587193 PMCID: PMC11194069 DOI: 10.1093/nar/gkae256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/18/2024] [Accepted: 03/27/2024] [Indexed: 04/09/2024] Open
Abstract
The viral genome of SARS-CoV-2 is packaged by the nucleocapsid (N-)protein into ribonucleoprotein particles (RNPs), 38 ± 10 of which are contained in each virion. Their architecture has remained unclear due to the pleomorphism of RNPs, the high flexibility of N-protein intrinsically disordered regions, and highly multivalent interactions between viral RNA and N-protein binding sites in both N-terminal (NTD) and C-terminal domain (CTD). Here we explore critical interaction motifs of RNPs by applying a combination of biophysical techniques to ancestral and mutant proteins binding different nucleic acids in an in vitro assay for RNP formation, and by examining nucleocapsid protein variants in a viral assembly assay. We find that nucleic acid-bound N-protein dimers oligomerize via a recently described protein-protein interface presented by a transient helix in its long disordered linker region between NTD and CTD. The resulting hexameric complexes are stabilized by multivalent protein-nucleic acid interactions that establish crosslinks between dimeric subunits. Assemblies are stabilized by the dimeric CTD of N-protein offering more than one binding site for stem-loop RNA. Our study suggests a model for RNP assembly where N-protein scaffolding at high density on viral RNA is followed by cooperative multimerization through protein-protein interactions in the disordered linker.
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Affiliation(s)
- Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abdullah M Syed
- Gladstone Institutes, San Francisco, CA 94158, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Mir M Khalid
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alison Ciling
- Gladstone Institutes, San Francisco, CA 94158, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dominic Esposito
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jennifer A Doudna
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- HHMI, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
- Center for Biomedical Engineering Technology Acceleration, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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2
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Bally I, Drumont G, Rossi V, Guseva S, Botova M, Reiser JB, Thépaut M, Dergan Dylon S, Dumestre-Pérard C, Gaboriaud C, Fieschi F, Blackledge M, Poignard P, Thielens NM. Revisiting the interaction between complement lectin pathway protease MASP-2 and SARS-CoV-2 nucleoprotein. Front Immunol 2024; 15:1419165. [PMID: 38911852 PMCID: PMC11190312 DOI: 10.3389/fimmu.2024.1419165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 05/27/2024] [Indexed: 06/25/2024] Open
Abstract
Complement activation is considered to contribute to the pathogenesis of severe SARS-CoV-2 infection, mainly by generating potent immune effector mechanisms including a strong inflammatory response. Involvement of the lectin complement pathway, a major actor of the innate immune anti-viral defense, has been reported previously. It is initiated by recognition of the viral surface Spike glycoprotein by mannose-binding lectin (MBL), which induces activation of the MBL-associated protease MASP-2 and triggers the proteolytic complement cascade. A role for the viral nucleoprotein (N) has also been reported, through binding to MASP-2, leading to protease overactivation and potentiation of the lectin pathway. In the present study, we reinvestigated the interactions of the SARS-CoV-2 N protein, produced either in bacteria or secreted by mammalian cells, with full-length MASP-2 or its catalytic domain, in either active or proenzyme form. We could not confirm the interaction of the N protein with the catalytic domain of MASP-2 but observed N protein binding to proenzyme MASP-2. We did not find a role of the N protein in MBL-mediated activation of the lectin pathway. Finally, we showed that incubation of the N protein with MASP-2 results in proteolysis of the viral protein, an observation that requires further investigation to understand a potential functional significance in infected patients.
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Affiliation(s)
| | | | | | | | - Maiia Botova
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | | | | | | - Chantal Dumestre-Pérard
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- Laboratory of Immunology, Grenoble Alpes University Hospital, Grenoble, France
| | | | | | | | - Pascal Poignard
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- Laboratory of Virology, Grenoble Alpes University Hospital, Grenoble, France
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3
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Alston JJ, Soranno A, Holehouse AS. Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation. RESEARCH SQUARE 2024:rs.3.rs-4477977. [PMID: 38883712 PMCID: PMC11177979 DOI: 10.21203/rs.3.rs-4477977/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Intrinsically disordered regions (IDRs) are critical for cellular function yet often appear to lack sequence conservation when assessed by multiple sequence alignments. This raises the question of if and how function can be encoded and preserved in these regions despite massive sequence variation. To address this question, we have applied coarse-grained molecular dynamics simulations to investigate non-specific RNA binding of coronavirus nucleocapsid proteins. Coronavirus nucleocapsid proteins consist of multiple interspersed disordered and folded domains that bind RNA. Here, we focus on the first two domains of coronavirus nucleocapsid proteins: the disordered N-terminal domain (NTD) and the folded RNA binding domain (RBD). While the NTD is highly variable across evolution, the RBD is structurally conserved. This combination makes the NTD-RBD a convenient model system for exploring the interplay between an IDR adjacent to a folded domain and how changes in IDR sequence can influence molecular recognition of a partner. Our results reveal a surprising degree of sequence-specificity encoded by both the composition and the precise order of the amino acids in the NTD. The presence of an NTD can - depending on the sequence - either suppress or enhance RNA binding. Despite this sensitivity, large-scale variation in NTD sequences is possible while certain sequence features are retained. Consequently, a conformationally-conserved dynamic and disordered RNA:protein complex is found across nucleocapsid protein orthologs despite large-scale changes in both NTD sequence and RBD surface chemistry. Taken together, these insights shed light on the ability of disordered regions to preserve functional characteristics despite their sequence variability.
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Affiliation(s)
- Jhullian J. Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
- Present Address, Program In Cellular and Molecular Medicine (PCMM), Boston Children’s Hospital, Boston, MA, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
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4
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Cui L, Li T, Xue W, Zhang S, Wang H, Liu H, Gu Y, Xia N, Li S. Comprehensive Overview of Broadly Neutralizing Antibodies against SARS-CoV-2 Variants. Viruses 2024; 16:900. [PMID: 38932192 PMCID: PMC11209230 DOI: 10.3390/v16060900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Currently, SARS-CoV-2 has evolved into various variants, including the numerous highly mutated Omicron sub-lineages, significantly increasing immune evasion ability. The development raises concerns about the possibly diminished effectiveness of available vaccines and antibody-based therapeutics. Here, we describe those representative categories of broadly neutralizing antibodies (bnAbs) that retain prominent effectiveness against emerging variants including Omicron sub-lineages. The molecular characteristics, epitope conservation, and resistance mechanisms of these antibodies are further detailed, aiming to offer suggestion or direction for the development of therapeutic antibodies, and facilitate the design of vaccines with broad-spectrum potential.
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Affiliation(s)
- Lingyan Cui
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Tingting Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Wenhui Xue
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Sibo Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Hong Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Hongjing Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Ying Gu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Shaowei Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
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5
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Huang Y, Chen J, Chen S, Huang C, Li B, Li J, Jin Z, Zhang Q, Pan P, Du W, Liu L, Liu Z. Molecular characterization of SARS-CoV-2 nucleocapsid protein. Front Cell Infect Microbiol 2024; 14:1415885. [PMID: 38846351 PMCID: PMC11153676 DOI: 10.3389/fcimb.2024.1415885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/07/2024] [Indexed: 06/09/2024] Open
Abstract
Corona Virus Disease 2019 (COVID-19) is a highly prevalent and potent infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Until now, the world is still endeavoring to develop new ways to diagnose and treat COVID-19. At present, the clinical prevention and treatment of COVID-19 mainly targets the spike protein on the surface of SRAS-CoV-2. However, with the continuous emergence of SARS-CoV-2 Variants of concern (VOC), targeting the spike protein therapy shows a high degree of limitation. The Nucleocapsid Protein (N protein) of SARS-CoV-2 is highly conserved in virus evolution and is involved in the key process of viral infection and assembly. It is the most expressed viral structural protein after SARS-CoV-2 infection in humans and has high immunogenicity. Therefore, N protein as the key factor of virus infection and replication in basic research and clinical application has great potential research value. This article reviews the research progress on the structure and biological function of SARS-CoV-2 N protein, the diagnosis and drug research of targeting N protein, in order to promote researchers' further understanding of SARS-CoV-2 N protein, and lay a theoretical foundation for the possible outbreak of new and sudden coronavirus infectious diseases in the future.
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Affiliation(s)
- Yanping Huang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Junkai Chen
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Siwei Chen
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Congcong Huang
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
| | - Bei Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Jian Li
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Zhixiong Jin
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Qiwei Zhang
- Central Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Pan Pan
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Weixing Du
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Long Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
| | - Zhixin Liu
- Department of Infectious Diseases, Renmin Hospital, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan, China
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, China
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6
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Kathe NC, Novakovic M, Allain FHT. Buffer choice and pH strongly influence phase separation of SARS-CoV-2 nucleocapsid with RNA. Mol Biol Cell 2024; 35:ar73. [PMID: 38568799 PMCID: PMC11151101 DOI: 10.1091/mbc.e23-12-0500] [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: 12/22/2023] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is crucial for virus replication and genome packaging. N protein forms biomolecular condensates both in vitro and in vivo in a process known as liquid-liquid phase separation (LLPS), but the exact factors regulating LLPS of N protein are not fully understood. Here, we show that pH and buffer choice have a profound impact on LLPS of N protein. The degree of phase separation is highly dependent on the pH of the solution, which is correlated with histidine protonation in N protein. Specifically, we demonstrate that protonation of H356 is essential for LLPS in phosphate buffer. Moreover, electrostatic interactions of buffer molecules with specific amino acid residues are able to alter the net charge of N protein, thus influencing its ability to undergo phase separation in the presence of RNA. Overall, these findings reveal that even subtle changes in amino acid protonation or surface charge caused by the pH and buffer system can strongly influence the LLPS behavior, and point to electrostatic interactions as the main driving forces of N protein phase separation. Further, our findings emphasize the importance of these experimental parameters when studying phase separation of biomolecules, especially in the context of viral infections where the intracellular milieu undergoes drastic changes and intracellular pH normally decreases.
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Affiliation(s)
- Nina C. Kathe
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Mihajlo Novakovic
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
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7
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Dong W, Cheng Y, Zhou Y, Zhang J, Yu X, Guan H, Du J, Zhou X, Yang Y, Fang W, Wang X, Song H. The nucleocapsid protein facilitates p53 ubiquitination-dependent proteasomal degradation via recruiting host ubiquitin ligase COP1 in PEDV infection. J Biol Chem 2024; 300:107135. [PMID: 38447796 PMCID: PMC10998216 DOI: 10.1016/j.jbc.2024.107135] [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: 01/03/2024] [Revised: 01/30/2024] [Accepted: 02/13/2024] [Indexed: 03/08/2024] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric pathogen of the coronavirus family and caused severe economic losses to the global swine industry. Previous studies have established that p53 is a host restriction factor for PEDV infection, and p53 degradation occurs in PEDV-infected cells. However, the underlying molecular mechanisms through which PEDV viral proteins regulate p53 degradation remain unclear. In this study, we found that PEDV infection or expression of the nucleocapsid protein downregulates p53 through a post-translational mechanism: increasing the ubiquitination of p53 and preventing its nuclear translocation. We also show that the PEDV N protein functions by recruiting the E3 ubiquitin ligase COP1 and suppressing COP1 self-ubiquitination and protein degradation, thereby augmenting COP1-mediated degradation of p53. Additionally, COP1 knockdown compromises N-mediated p53 degradation. Functional mapping using truncation analysis showed that the N-terminal domains of N protein were responsible for interacting with COP1 and critical for COP1 stability and p53 degradation. The results presented here suggest the COP1-dependent mechanism for PEDV N protein to abolish p53 activity. This study significantly increases our understanding of PEDV in antagonizing the host antiviral factor p53 and will help initiate novel antiviral strategies against PEDV.
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Affiliation(s)
- Wanyu Dong
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Yahao Cheng
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Yingshan Zhou
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Jingmiao Zhang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Xinya Yu
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Haicun Guan
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Jing Du
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Xingdong Zhou
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Yang Yang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Weihuan Fang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
| | - Xiaodu Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China.
| | - Houhui Song
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China.
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8
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Hussein HAM, Thabet AA, Wardany AA, El-Adly AM, Ali M, Hassan MEA, Abdeldayem MAB, Mohamed ARMA, Sobhy A, El-Mokhtar MA, Afifi MM, Fathy SM, Sultan S. SARS-CoV-2 outbreak: role of viral proteins and genomic diversity in virus infection and COVID-19 progression. Virol J 2024; 21:75. [PMID: 38539202 PMCID: PMC10967059 DOI: 10.1186/s12985-024-02342-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 03/12/2024] [Indexed: 05/15/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is the cause of coronavirus disease 2019 (COVID-19); a severe respiratory distress that has emerged from the city of Wuhan, Hubei province, China during December 2019. COVID-19 is currently the major global health problem and the disease has now spread to most countries in the world. COVID-19 has profoundly impacted human health and activities worldwide. Genetic mutation is one of the essential characteristics of viruses. They do so to adapt to their host or to move to another one. Viral genetic mutations have a high potentiality to impact human health as these mutations grant viruses unique unpredicted characteristics. The difficulty in predicting viral genetic mutations is a significant obstacle in the field. Evidence indicates that SARS-CoV-2 has a variety of genetic mutations and genomic diversity with obvious clinical consequences and implications. In this review, we comprehensively summarized and discussed the currently available knowledge regarding SARS-CoV-2 outbreaks with a fundamental focus on the role of the viral proteins and their mutations in viral infection and COVID-19 progression. We also summarized the clinical implications of SARS-CoV-2 variants and how they affect the disease severity and hinder vaccine development. Finally, we provided a massive phylogenetic analysis of the spike gene of 214 SARS-CoV-2 isolates from different geographical regions all over the world and their associated clinical implications.
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Affiliation(s)
- Hosni A M Hussein
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt.
| | - Ali A Thabet
- Department of Zoology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Ahmed A Wardany
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Ahmed M El-Adly
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed Ali
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed E A Hassan
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed A B Abdeldayem
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | | | - Ali Sobhy
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed A El-Mokhtar
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos Campus, Lebanon
| | - Magdy M Afifi
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City 11884, Cairo, Egypt
| | - Samah M Fathy
- Department of Zoology, Faculty of Science, Fayoum University, Fayoum, Egypt.
| | - Serageldeen Sultan
- Department of Microbiology, Virology Division, Faculty of Veterinary medicine, South Valley University, 83523, Qena, Egypt.
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9
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Yang Z, Johnson BA, Meliopoulos VA, Ju X, Zhang P, Hughes MP, Wu J, Koreski KP, Clary JE, Chang TC, Wu G, Hixon J, Duffner J, Wong K, Lemieux R, Lokugamage KG, Alvarado RE, Crocquet-Valdes PA, Walker DH, Plante KS, Plante JA, Weaver SC, Kim HJ, Meyers R, Schultz-Cherry S, Ding Q, Menachery VD, Taylor JP. Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication and pathogenicity. Cell Rep 2024; 43:113965. [PMID: 38492217 PMCID: PMC11044841 DOI: 10.1016/j.celrep.2024.113965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/29/2024] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
G3BP1/2 are paralogous proteins that promote stress granule formation in response to cellular stresses, including viral infection. The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) inhibits stress granule assembly and interacts with G3BP1/2 via an ITFG motif, including residue F17, in the N protein. Prior studies examining the impact of the G3PB1-N interaction on SARS-CoV-2 replication have produced inconsistent findings, and the role of this interaction in pathogenesis is unknown. Here, we use structural and biochemical analyses to define the residues required for G3BP1-N interaction and structure-guided mutagenesis to selectively disrupt this interaction. We find that N-F17A mutation causes highly specific loss of interaction with G3BP1/2. SARS-CoV-2 N-F17A fails to inhibit stress granule assembly in cells, has decreased viral replication, and causes decreased pathology in vivo. Further mechanistic studies indicate that the N-F17-mediated G3BP1-N interaction promotes infection by limiting sequestration of viral genomic RNA (gRNA) into stress granules.
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Affiliation(s)
- Zemin Yang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Bryan A Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - Victoria A Meliopoulos
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaohui Ju
- School of Medicine, Tsinghua University, Beijing, China
| | - Peipei Zhang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael P Hughes
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinjun Wu
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kaitlin P Koreski
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jemma E Clary
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | | | | | | | - Kumari G Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - R Elias Alvarado
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | | | - David H Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qiang Ding
- School of Medicine, Tsinghua University, Beijing, China
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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10
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Kubinski HC, Despres HW, Johnson BA, Schmidt MM, Jaffrani SA, Mills MG, Lokugamage K, Dumas CM, Shirley DJ, Estes LK, Pekosz A, Crothers JW, Roychoudhury P, Greninger AL, Jerome KR, Di Genova BM, Walker DH, Ballif BA, Ladinsky MS, Bjorkman PJ, Menachery VD, Bruce EA. Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584120. [PMID: 38559000 PMCID: PMC10979914 DOI: 10.1101/2024.03.08.584120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The evolution of SARS-CoV-2 variants and their respective phenotypes represents an important set of tools to understand basic coronavirus biology as well as the public health implications of individual mutations in variants of concern. While mutations outside of Spike are not well studied, the entire viral genome is undergoing evolutionary selection, particularly the central disordered linker region of the nucleocapsid (N) protein. Here, we identify a mutation (G215C), characteristic of the Delta variant, that introduces a novel cysteine into this linker domain, which results in the formation of a disulfide bond and a stable N-N dimer. Using reverse genetics, we determined that this cysteine residue is necessary and sufficient for stable dimer formation in a WA1 SARS-CoV-2 background, where it results in significantly increased viral growth both in vitro and in vivo. Finally, we demonstrate that the N:G215C virus packages more nucleocapsid per virion and that individual virions are larger, with elongated morphologies.
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Affiliation(s)
- Hannah C. Kubinski
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Hannah W. Despres
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Bryan A. Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - Madaline M. Schmidt
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Sara A. Jaffrani
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Margaret G. Mills
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
| | - Kumari Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Caroline M. Dumas
- Department of Biology, University of Vermont 109 Carrigan Drive, 120A Marsh Life Sciences, Burlington VT 05404, USA
| | - David J. Shirley
- Faraday, Inc. Data Science Department. Burlington VT, 05405, USA
| | - Leah K. Estes
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jessica W. Crothers
- Department of Pathology and Laboratory Medicine, Robert Larner, MD College of Medicine, University of Vermont, Burlington, VT, USA
| | - Pavitra Roychoudhury
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
| | - Alexander L. Greninger
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA
| | - Keith R. Jerome
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA
| | - Bruno Martorelli Di Genova
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - David H. Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Bryan A. Ballif
- Department of Biology, University of Vermont 109 Carrigan Drive, 120A Marsh Life Sciences, Burlington VT 05404, USA
| | - Mark S. Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA. 91125, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA. 91125, USA
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA
| | - Emily A. Bruce
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
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11
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Eltayeb A, Al-Sarraj F, Alharbi M, Albiheyri R, Mattar E, Abu Zeid IM, Bouback TA, Bamagoos A, Aljohny BO, Uversky VN, Redwan EM. Overview of the SARS-CoV-2 nucleocapsid protein. Int J Biol Macromol 2024; 260:129523. [PMID: 38232879 DOI: 10.1016/j.ijbiomac.2024.129523] [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: 06/04/2023] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 01/19/2024]
Abstract
Since the emergence of SARS-CoV in 2003, researchers worldwide have been toiling away at deciphering this virus's biological intricacies. In line with other known coronaviruses, the nucleocapsid (N) protein is an important structural component of SARS-CoV. As a result, much emphasis has been placed on characterizing this protein. Independent research conducted by a variety of laboratories has clearly demonstrated the primary function of this protein, which is to encapsidate the viral genome. Furthermore, various accounts indicate that this particular protein disrupts diverse intracellular pathways. Such observations imply its vital role in regulating the virus as well. The opening segment of this review will expound upon these distinct characteristics succinctly exhibited by the N protein. Additionally, it has been suggested that the N protein possesses diagnostic and vaccine capabilities when dealing with SARS-CoV. In light of this fact, we will be reviewing some recent headway in the use cases for N protein toward clinical purposes within this article's concluding segments. This forward movement pertains to both developments of COVID-19-oriented therapeutic targets as well as diagnostic measures. The strides made by medical researchers offer encouragement, knowing they are heading toward a brighter future combating global pandemic situations such as these.
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Affiliation(s)
- Ahmed Eltayeb
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Faisal Al-Sarraj
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Raed Albiheyri
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ehab Mattar
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Isam M Abu Zeid
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, P.O. Box 80200, Jeddah, Saudi Arabia
| | - Thamer A Bouback
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Princess Dr. Najla Bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, P.O. Box 80200, Jeddah, Saudi Arabia
| | - Atif Bamagoos
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Bassam O Aljohny
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Elrashdy M Redwan
- Department of Biological Science, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, 21934 Alexandria, Egypt.
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12
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Wan L, Li Y, Liao W, Lei L, Zhao M, Zeng J, Zhao Z, Tang J. Synergistic inhibition effects of andrographolide and baicalin on coronavirus mechanisms by downregulation of ACE2 protein level. Sci Rep 2024; 14:4287. [PMID: 38383655 PMCID: PMC10882053 DOI: 10.1038/s41598-024-54722-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/15/2024] [Indexed: 02/23/2024] Open
Abstract
The SARS-CoV-2 virus, belonging to the Coronavirus genus, which poses a threat to human health worldwide. Current therapies focus on inhibiting viral replication or using anti-inflammatory/immunomodulatory compounds to enhance host immunity. This makes the active ingredients of traditional Chinese medicine compounds ideal therapies due to their proven safety and minimal toxicity. Previous research suggests that andrographolide and baicalin inhibit coronaviruses; however, their synergistic effects remain unclear. Here, we studied the antiviral mechanisms of their synergistic use in vitro and in vivo. We selected the SARS-CoV-2 pseudovirus for viral studies and found that synergistic andrographolide and baicalein significantly reduced angiotensin-converting enzyme 2 protein level and viral entry of SARS-CoV-2 into cells compared to singal compound individually and inhibited the major protease activity of SARS-CoV-2. This mechanism is essential to reduce the pathogenesis of SARS-CoV-2. In addition, their synergistic use in vivo also inhibited the elevation of pro-inflammatory cytokines, including IL-6 and TNF-α-the primary cytokines in the development of acute respiratory distress syndrome (the main cause of COVID-19 deaths). In conclusion, this study shows that synergistic andrographolide and baicalein treatment acts as potent inhibitors of coronavirus mechanisms in vitro and in vivo-and is more effective together than in isolation.
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Affiliation(s)
- Lina Wan
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Yuchen Li
- Laboratory Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Wenhao Liao
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Lizhen Lei
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Maoyuan Zhao
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Jinhao Zeng
- TCM Regulating Metabolic Diseases Key Laboratory of Si Chuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China.
- Department of Digestive, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China.
| | - Ziyi Zhao
- TCM Regulating Metabolic Diseases Key Laboratory of Si Chuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China.
| | - Jianyuan Tang
- TCM Regulating Metabolic Diseases Key Laboratory of Si Chuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China.
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13
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Hong JY, Lin SC, Kehn-Hall K, Zhang KM, Luo SY, Wu HY, Chang SY, Hou MH. Targeting protein-protein interaction interfaces with antiviral N protein inhibitor in SARS-CoV-2. Biophys J 2024; 123:478-488. [PMID: 38234090 PMCID: PMC10912909 DOI: 10.1016/j.bpj.2024.01.013] [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: 08/24/2023] [Revised: 11/27/2023] [Accepted: 01/11/2024] [Indexed: 01/19/2024] Open
Abstract
Coronaviruses not only pose significant global public health threats but also cause extensive damage to livestock-based industries. Previous studies have shown that 5-benzyloxygramine (P3) targets the Middle East respiratory syndrome coronavirus (MERS-CoV) nucleocapsid (N) protein N-terminal domain (N-NTD), inducing non-native protein-protein interactions (PPIs) that impair N protein function. Moreover, P3 exhibits broad-spectrum antiviral activity against CoVs. The sequence similarity of N proteins is relatively low among CoVs, further exhibiting notable variations in the hydrophobic residue responsible for non-native PPIs in the N-NTD. Therefore, to ascertain the mechanism by which P3 demonstrates broad-spectrum anti-CoV activity, we determined the crystal structure of the SARS-CoV-2 N-NTD:P3 complex. We found that P3 was positioned in the dimeric N-NTD via hydrophobic contacts. Compared with the interfaces in MERS-CoV N-NTD, P3 had a reversed orientation in SARS-CoV-2 N-NTD. The Phe residue in the MERS-CoV N-NTD:P3 complex stabilized both P3 moieties. However, in the SARS-CoV-2 N-NTD:P3 complex, the Ile residue formed only one interaction with the P3 benzene ring. Moreover, the pocket in the SARS-CoV-2 N-NTD:P3 complex was more hydrophobic, favoring the insertion of the P3 benzene ring into the complex. Nevertheless, hydrophobic interactions remained the primary stabilizing force in both complexes. These findings suggested that despite the differences in the sequence, P3 can accommodate a hydrophobic pocket in N-NTD to mediate a non-native PPI, enabling its effectiveness against various CoVs.
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Affiliation(s)
- Jhen-Yi Hong
- Institute of Genomics and Bioinformatics and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Shih-Chao Lin
- Bachelor Degree Program in Marine Biotechnology, College of Life Sciences, National Taiwan Ocean University, Keelung, Taiwan
| | - Kylene Kehn-Hall
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | - Kai-Min Zhang
- Department of Chemistry, National Chung Hsing University, Taichung, Taiwan
| | - Shun-Yuan Luo
- Department of Chemistry, National Chung Hsing University, Taichung, Taiwan
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University. Taichung, Taiwan
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan; PhD Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan; Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
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14
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Chilmi S, Kesuma TA, Wibawa PA, Susianti H, Iskandar A, Wulanda IA, Wahono CS, Handono K. The Long-Term Serological Profile of CoronaVac Vaccine Based on Comorbidities and History of SARS-CoV-2 Infection in Indonesia. Jpn J Infect Dis 2024; 77:40-46. [PMID: 37914294 DOI: 10.7883/yoken.jjid.2023.061] [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: 11/03/2023]
Abstract
CoronaVac is one of the most widely administered COVID-19 vaccines in Indonesia. Previous studies have documented its effectiveness in protecting against COVID-19 in several countries. This study aimed to assess the long-term immunogenicity of CoronaVac in individuals with comorbidities or a history of SARS-CoV-2 infection. The total anti-N Ig and anti-S-RBD Ig levels at 7 and 26 weeks after the second dose of vaccine were documented in 194 health workers. The participants were divided into groups based on their comorbidities and history of SARS-CoV-2 infection. The antibody titers did not differ according to comorbidity status or history of SARS-CoV-2 infection. The total anti-nucleocapsid Ig and total anti-S-RBD Ig levels were significantly lower in individuals without a history of SARS-CoV-2 infection. These results indicate that CoronaVac induces a lower specific antibody response than natural infection and less long-term immunogenicity.
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Affiliation(s)
- Syahrul Chilmi
- Department of Clinical Pathology, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
| | - Tanti Adelia Kesuma
- Residency of Clinical Pathology, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
| | - Purwa Adrianta Wibawa
- Residency of Clinical Pathology, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
| | - Hani Susianti
- Department of Clinical Pathology, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
| | - Agustin Iskandar
- Department of Clinical Pathology, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
| | - Indah Adhita Wulanda
- Department of Clinical Pathology, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
| | - Caesarius Singgih Wahono
- Department of Internal Medicine, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
| | - Kusworini Handono
- Department of Clinical Pathology, Faculty of Medicine, Brawijaya University / RSUD Dr. Saiful Anwar, Indonesia
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15
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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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16
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Chatterjee S, Zaia J. Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples. MASS SPECTROMETRY REVIEWS 2024; 43:193-229. [PMID: 36177493 PMCID: PMC9538640 DOI: 10.1002/mas.21813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 05/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the on-going global pandemic of coronavirus disease 2019 (COVID-19) that continues to pose a significant threat to public health worldwide. SARS-CoV-2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin-converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high-throughput technique. Alternate strategies such as proteomics and glycoproteomics-based mass spectrometry enable a more detailed and holistic view of the viral proteins and host-pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS-CoV-2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS-CoV-2 from biological complex matrices to identify potential COVID-19 markers.
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Affiliation(s)
- Sayantani Chatterjee
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
- Bioinformatics ProgramBoston University School of MedicineBostonMassachusettsUSA
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17
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Adly AN, Bi M, Carlson CR, Syed AM, Ciling A, Doudna JA, Cheng Y, Morgan DO. Assembly of SARS-CoV-2 ribonucleosomes by truncated N ∗ variant of the nucleocapsid protein. J Biol Chem 2023; 299:105362. [PMID: 37863261 PMCID: PMC10665939 DOI: 10.1016/j.jbc.2023.105362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compacts the RNA genome into viral ribonucleoprotein (vRNP) complexes within virions. Assembly of vRNPs is inhibited by phosphorylation of the N protein serine/arginine (SR) region. Several SARS-CoV-2 variants of concern carry N protein mutations that reduce phosphorylation and enhance the efficiency of viral packaging. Variants of the dominant B.1.1 viral lineage also encode a truncated N protein, termed N∗ or Δ(1-209), that mediates genome packaging despite lacking the N-terminal RNA-binding domain and SR region. Here, we use mass photometry and negative stain electron microscopy to show that purified Δ(1-209) and viral RNA assemble into vRNPs that are remarkably similar in size and shape to those formed with full-length N protein. We show that assembly of Δ(1-209) vRNPs requires the leucine-rich helix of the central disordered region and that this helix promotes N protein oligomerization. We also find that fusion of a phosphomimetic SR region to Δ(1-209) inhibits RNA binding and vRNP assembly. Our results provide new insights into the mechanisms by which RNA binding promotes N protein self-association and vRNP assembly, and how this process is modulated by phosphorylation.
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Affiliation(s)
- Armin N Adly
- Department of Physiology, University of California, San Francisco, California, USA
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | | | - Abdullah M Syed
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Alison Ciling
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Jennifer A Doudna
- J. David Gladstone Institutes, San Francisco, California, USA; Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA; Innovative Genomics Institute, University of California, Berkeley, California, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA; Howard Hughes Medical Institute, University of California, San Francisco, California, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, California, USA.
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18
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Zhou Z, Ali A, Walelign E, Demissie GF, El Masry I, Abayneh T, Getachew B, Krishnan P, Ng DY, Gardner E, Makonnen Y, Miguel E, Chevalier V, Chu DK, So RTY, Von Dobschuetz S, Mamo G, Poon LLM, Peiris M. Genetic diversity and molecular epidemiology of Middle East Respiratory Syndrome Coronavirus in dromedaries in Ethiopia, 2017-2020. Emerg Microbes Infect 2023; 12:e2164218. [PMID: 36620913 PMCID: PMC9888459 DOI: 10.1080/22221751.2022.2164218] [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] [Indexed: 01/10/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is enzootic in dromedary camels and causes zoonotic infection and disease in humans. Although over 80% of the global population of infected dromedary camels are found in Africa, zoonotic disease had only been reported in the Arabia Peninsula and travel-associated disease has been reported elsewhere. In this study, genetic diversity and molecular epidemiology of MERS-CoV in dromedary camels in Ethiopia were investigated during 2017-2020. Of 1766 nasal swab samples collected, 61 (3.5%) were detected positive for MERS-CoV RNA. Of 484 turbinate swab samples collected, 10 (2.1%) were detected positive for MERS-CoV RNA. Twenty-five whole genome sequences were obtained from these MERS-CoV positive samples. Phylogenetically, these Ethiopian camel-originated MERS-CoV belonged to clade C2, clustering with other East African camel strains. Virus sequences from camel herds clustered geographically while in an abattoir, two distinct phylogenetic clusters of MERS-CoVs were observed in two sequential sampling collections, which indicates the greater genetic diversity of MERS-CoV in abattoirs. In contrast to clade A and B viruses from the Arabian Peninsula, clade C camel-originated MERS-CoV from Ethiopia had various nucleotide insertions and deletions in non-structural gene nsp3, accessory genes ORF3 and ORF5 and structural gene N. This study demonstrates the genetic instability of MERS-CoV in dromedaries in East Africa, which indicates that the virus is still actively adapting to its camel host. The impact of the observed nucleotide insertions and deletions on virus evolution, viral fitness, and zoonotic potential deserves further study.
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Affiliation(s)
- Ziqi Zhou
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Abraham Ali
- Bacterial, Parasitic and Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia,Department of Veterinary Microbiology, Immunology and Public Health, College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia
| | - Elias Walelign
- Food and Agriculture Organization, Emergency Centre for Transboundary Animal Diseases, Addis Ababa, Ethiopia
| | - Getnet F. Demissie
- College of Veterinary Medicine, Department of Veterinary Epidemiology, Microbiology and Public Health, Haramaya University, Haramaya, Ethiopia
| | - Ihab El Masry
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | | | | | - Pavithra Krishnan
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Daisy Y.M. Ng
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Emma Gardner
- Food and Agriculture Organization of the United Nations, Rome, Italy
| | - Yilma Makonnen
- Food and Agriculture Organization, Subregional Office for Eastern Africa, Addis Ababa, Ethiopia
| | - Eve Miguel
- Animal, Santé, Territoires, Risques et Ecosystèmes, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut National de la Recherche Agronomique, Université de Montpellier, Montpellier, France,Maladies Infectieuses et Vecteurs: Ecologie Genetique, Evolution et Controle, L’Institut de Recherche pour le Developpment, CNRS, Montpellier, France
| | - Véronique Chevalier
- International Center of Research in Agriculture for Development (CIRAD), UMR ASTRE, Montpellier, France,CIRAD, UMR ASTRE, Antananarivo, Madagascar,Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Daniel K. Chu
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China,UK Health Security Agency, London, UK
| | - Ray T. Y. So
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | | | - Gezahegne Mamo
- Department of Veterinary Microbiology, Immunology and Public Health, College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia
| | - Leo L. M. Poon
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Malik Peiris
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China, Malik Peiris
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19
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Dong H, Zhang H, Jalin J, He Z, Wang R, Huang L, Liu Z, Zhang S, Dai B, Li D. Nucleocapsid proteins from human coronaviruses possess phase separation capabilities and promote FUS pathological aggregation. Protein Sci 2023; 32:e4826. [PMID: 37906538 PMCID: PMC10659942 DOI: 10.1002/pro.4826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/16/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023]
Abstract
The nucleocapsid (N) protein is an essential structural component necessary for genomic packaging and replication in various human coronaviruses (HCoVs), such as SARS-CoV-2 and MERS-CoV. Recent studies have revealed that the SARS-CoV-2 N protein exhibits a high capacity for liquid-liquid phase separation (LLPS), which plays multiple roles in viral infection and replication. In this study, we systematically investigate the LLPS capabilities of seven homologous N proteins from different HCoVs using a high-throughput protein phase separation assay. We found that LLPS is a shared intrinsic property among these N proteins. However, the phase separation profiles of the various N protein homologs differ, and they undergo phase separation under distinct in vitro conditions. Moreover, we demonstrate that N protein homologs can co-phase separate with FUS, a SG-containing protein, and accelerate its liquid-to-solid phase transition and amyloid aggregation, which is closely related to amyotrophic lateral sclerosis. Further study shows that N protein homologs can directly bind to the low complexity domain of FUS. Together, our work demonstrates that N proteins of different HCoVs possess phase separation capabilities, which may contribute to promoting pathological aggregation of host proteins and disrupting SG homeostasis during the infection and replication of various HCoVs.
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Affiliation(s)
- Hui Dong
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Present address:
Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic Chemistry, Chinese Academy of SciencesShanghaiChina
| | - Hong Zhang
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Julie Jalin
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ziqi He
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
| | - Runhan Wang
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Leqi Huang
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zibo Liu
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Shenqing Zhang
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
- Zhangjiang Institute for Advanced StudyShanghai Jiao Tong UniversityShanghaiChina
| | - Bin Dai
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Dan Li
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
- Zhangjiang Institute for Advanced StudyShanghai Jiao Tong UniversityShanghaiChina
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20
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Zhao H, Syed AM, Khalid MM, Nguyen A, Ciling A, Wu D, Yau WM, Srinivasan S, Esposito D, Doudna JA, Piszczek G, Ott M, Schuck P. Assembly reactions of SARS-CoV-2 nucleocapsid protein with nucleic acid. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568361. [PMID: 38045338 PMCID: PMC10690241 DOI: 10.1101/2023.11.22.568361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The viral genome of SARS-CoV-2 is packaged by the nucleocapsid (N-) protein into ribonucleoprotein particles (RNPs), 38±10 of which are contained in each virion. Their architecture has remained unclear due to the pleomorphism of RNPs, the high flexibility of N-protein intrinsically disordered regions, and highly multivalent interactions between viral RNA and N-protein binding sites in both N-terminal (NTD) and C-terminal domain (CTD). Here we explore critical interaction motifs of RNPs by applying a combination of biophysical techniques to mutant proteins binding different nucleic acids in an in vitro assay for RNP formation, and by examining mutant proteins in a viral assembly assay. We find that nucleic acid-bound N-protein dimers oligomerize via a recently described protein-protein interface presented by a transient helix in its long disordered linker region between NTD and CTD. The resulting hexameric complexes are stabilized by multi-valent protein-nucleic acid interactions that establish crosslinks between dimeric subunits. Assemblies are stabilized by the dimeric CTD of N-protein offering more than one binding site for stem-loop RNA. Our study suggests a model for RNP assembly where N-protein scaffolding at high density on viral RNA is followed by cooperative multimerization through protein-protein interactions in the disordered linker.
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Affiliation(s)
- Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| | - Abdullah M. Syed
- Gladstone Institutes, San Francisco, CA 94158
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
| | | | - Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| | - Alison Ciling
- Gladstone Institutes, San Francisco, CA 94158
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| | - Dominic Esposito
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Jennifer A. Doudna
- Gladstone Institutes, San Francisco, CA 94158
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- HHMI, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158
- Department of Medicine, University of California, San Francisco, CA 94143
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
- Center for Biomedical Engineering Technology Acceleration, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
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21
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Zhou K, Chen D. Conventional Understanding of SARS-CoV-2 M pro and Common Strategies for Developing Its Inhibitors. Chembiochem 2023; 24:e202300301. [PMID: 37577869 DOI: 10.1002/cbic.202300301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
The Coronavirus Disease 2019 (COVID-19) pandemic has brought a widespread influence on the world, especially in the face of sudden coronavirus infections, and there is still an urgent need for specific small molecule therapies to cope with possible future pandemics. The pathogen responsible for this pandemic is Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and understanding its structure and lifecycle is beneficial for designing specific drugs of treatment for COVID-19. The main protease (Mpro ) which has conservative and specific advantages is essential for viral replication and transcription. It is regarded as one of the most potential targets for anti-SARS-CoV-2 drug development. This review introduces the popular knowledge of SARS-CoV-2 Mpro in drug development and lists a series of design principles and relevant activities of advanced Mpro inhibitors, hoping to provide some new directions and ideas for researchers.
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Affiliation(s)
- Kun Zhou
- School of Pharmacy, Yantai University, Yantai, Shandong, RT 264005, P. R. China
| | - Daquan Chen
- School of Pharmacy, Yantai University, Yantai, Shandong, RT 264005, P. R. China
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22
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Lao T, Farnos O, Bueno A, Alvarez A, Rodríguez E, Palacios J, de la Luz KR, Kamen A, Carpio Y, Estrada MP. Transient Expression in HEK-293 Cells in Suspension Culture as a Rapid and Powerful Tool: SARS-CoV-2 N and Chimeric SARS-CoV-2N-CD154 Proteins as a Case Study. Biomedicines 2023; 11:3050. [PMID: 38002050 PMCID: PMC10669214 DOI: 10.3390/biomedicines11113050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
In a previous work, we proposed a vaccine chimeric antigen based on the fusion of the SARS-CoV-2 N protein to the extracellular domain of the human CD40 ligand (CD154). This vaccine antigen was named N-CD protein and its expression was carried out in HEK-293 stably transfected cells, grown in adherent conditions and serum-supplemented medium. The chimeric protein obtained in these conditions presented a consistent pattern of degradation. The immunization of mice and monkeys with this chimeric protein was able to induce a high N-specific IgG response with only two doses in pre-clinical experiments. In order to explore ways to diminish protein degradation, in the present work, the N and N-CD proteins were produced in suspension cultures and serum-free media following transient transfection of the HEK-293 clone 3F6, at different scales, including stirred-tank controlled bioreactors. The results showed negligible or no degradation of the target proteins. Further, clones stably expressing N-CD were obtained and adapted to suspension culture, obtaining similar results to those observed in the transient expression experiments in HEK-293-3F6. The evidence supports transient protein expression in suspension cultures and serum-free media as a powerful tool to produce in a short period of time high levels of complex proteins susceptible to degradation, such as the SARS-CoV-2 N protein.
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Affiliation(s)
- Thailin Lao
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana 10600, Cuba; (T.L.)
| | - Omar Farnos
- Department of Bioengineering, McGill University, Montreal, QC H3A 0E9, Canada; (O.F.); (A.K.)
| | - Alexi Bueno
- Process Development Department, Center of Molecular Immunology, Havana 11600, Cuba (J.P.); (K.R.d.l.L.)
| | - Anays Alvarez
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana 10600, Cuba; (T.L.)
| | - Elsa Rodríguez
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana 10600, Cuba; (T.L.)
| | - Julio Palacios
- Process Development Department, Center of Molecular Immunology, Havana 11600, Cuba (J.P.); (K.R.d.l.L.)
| | - Kathya Rashida de la Luz
- Process Development Department, Center of Molecular Immunology, Havana 11600, Cuba (J.P.); (K.R.d.l.L.)
| | - Amine Kamen
- Department of Bioengineering, McGill University, Montreal, QC H3A 0E9, Canada; (O.F.); (A.K.)
| | - Yamila Carpio
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana 10600, Cuba; (T.L.)
| | - Mario Pablo Estrada
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana 10600, Cuba; (T.L.)
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23
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Hsu CJ, Chen CH, Chen WT, Liu PC, Chang TY, Lin MH, Chen CC, Chen HY, Huang CH, Cheng YH, Sun JR. Development of an EBOV MiniG plus system as an advanced tool for anti-Ebola virus drug screening. Heliyon 2023; 9:e22138. [PMID: 38045158 PMCID: PMC10692823 DOI: 10.1016/j.heliyon.2023.e22138] [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: 08/03/2023] [Revised: 10/21/2023] [Accepted: 11/05/2023] [Indexed: 12/05/2023] Open
Abstract
The incidence of zoonotic diseases, such as coronavirus disease 2019 and Ebola virus disease, is increasing worldwide. However, drug and vaccine development for zoonotic diseases has been hampered because the experiments involving live viruses are limited to high-containment laboratories. The Ebola virus minigenome system enables researchers to study the Ebola virus under BSL-2 conditions. Here, we found that the addition of the nucleocapsid protein of human coronaviruses, such as severe acute respiratory syndrome coronavirus 2, can increase the ratio of green fluorescent protein-positive cells by 1.5-2 folds in the Ebola virus minigenome system. Further analysis showed that the nucleocapsid protein acts as an activator of the Ebola virus minigenome system. Here, we developed an EBOV MiniG Plus system based on the Ebola virus minigenome system by adding the SARS-CoV-2 nucleocapsid protein. By evaluating the antiviral effect of remdesivir and rupintrivir, we demonstrated that compared to that of the traditional Ebola virus minigenome system, significant concentration-dependent activity was observed in the EBOV MiniG Plus system. Taken together, these results demonstrate the utility of adding nucleocapsid protein to the Ebola virus minigenome system to create a powerful platform for screening antiviral drugs against the Ebola virus.
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Affiliation(s)
- Chi-Ju Hsu
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Cheng-Hsiu Chen
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Wen-Ting Chen
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Ping-Cheng Liu
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taiwan
| | - Tein-Yao Chang
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan
- Department of Pathology and Graduate Institute of Pathology and Parasitology, Tri-Service General Hospital, National Defense Medical Center, Taiwan
| | - Meng-He Lin
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Cheng-Cheung Chen
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Hsing-Yu Chen
- Department of Medical Techniques, Taipei City Hospital Ren-Ai Branch, Taiwan
| | - Chih-Heng Huang
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Yun-Hsiang Cheng
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan
- Department of Physiology and Biophysics, Graduate Institute of Physiology, National Defense Medical Center, Taiwan
| | - Jun-Ren Sun
- Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
- Department of Physiology and Biophysics, Graduate Institute of Physiology, National Defense Medical Center, Taiwan
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taiwan
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24
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Boniardi I, Corona A, Basquin J, Basquin C, Milia J, Nagy I, Tramontano E, Zinzula L. Suramin inhibits SARS-CoV-2 nucleocapsid phosphoprotein genome packaging function. Virus Res 2023; 336:199221. [PMID: 37704176 PMCID: PMC10514558 DOI: 10.1016/j.virusres.2023.199221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/27/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is fading, however its etiologic agent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues posing - despite the availability of licensed vaccines - a global health threat, due to the potential emergence of vaccine-resistant SARS-CoV-2 variants. This makes the development of new drugs against COVID-19 a persistent urgency and sets as research priority the validation of novel therapeutic targets within the SARS-CoV-2 proteome. Among these, a promising one is the SARS-CoV-2 nucleocapsid (N) phosphoprotein, a major structural component of the virion with indispensable role in packaging the viral genome into a ribonucleoprotein (RNP) complex, which also contributes to SARS-CoV-2 innate immune evasion by inhibiting the host cell type-I interferon (IFN-I) response. By combining miniaturized differential scanning fluorimetry with microscale thermophoresis, we found that the 100-year-old drug Suramin interacts with SARS-CoV-2 N-terminal domain (NTD) and C-terminal domain (CTD), thereby inhibiting their single-stranded RNA (ssRNA) binding function with low-micromolar Kd and IC50 values. Molecular docking suggests that Suramin interacts with basic NTD cleft and CTD dimer interface groove, highlighting three potentially druggable ssRNA binding sites. Electron microscopy shows that Suramin inhibits the formation in vitro of RNP complex-like condensates by SARS-CoV-2 N with a synthetic ssRNA. In a dose-dependent manner, Suramin also reduced SARS-CoV-2-induced cytopathic effect on Vero E6 and Calu-3 cells, partially reverting the SARS-CoV-2 N-inhibited IFN-I production in 293T cells. Our findings indicate that Suramin inhibits SARS-CoV-2 replication by hampering viral genome packaging, thereby representing a starting model for design of new COVID-19 antivirals.
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Affiliation(s)
- Irene Boniardi
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato 09042, Italy
| | - Jerome Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Claire Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Jessica Milia
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato 09042, Italy
| | - István Nagy
- Center of Research and Development, Eszterházy Károly Catholic University, Eger 3300, Hungary
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato 09042, Italy.
| | - Luca Zinzula
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.
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25
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Liu Y, Ye Q. The Key Site Variation and Immune Challenges in SARS-CoV-2 Evolution. Vaccines (Basel) 2023; 11:1472. [PMID: 37766148 PMCID: PMC10537874 DOI: 10.3390/vaccines11091472] [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: 08/07/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a worldwide public health and economic threat, and virus variation amplifies the difficulty in epidemic prevention and control. The structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been studied extensively and is now well defined. The S protein is the most distinguishing feature in terms of infection and immunity, mediating virus entrance and inducing neutralizing antibodies. The S protein and its essential components are also the most promising target to develop vaccines and antibody-based drugs. Therefore, the key site mutation in the S gene is of high interest. Among them, RBD, NTD, and furin cleavage sites are the most mutable regions with the most mutation sites and the most serious consequences for SARS-CoV-2 biological characteristics, including infectivity, pathogenicity, natural immunity, vaccine efficacy, and antibody therapeutics. We are also aware that this outbreak may not be the last. Therefore, in this narrative review, we summarized viral variation and prevalence condition, discussed specific amino acid replacement and associated immune challenges and attempted to sum up some prevention and control strategies by reviewing the literature on previously published research about SARS-CoV-2 variation to assist in clarifying the mutation pathway and consequences of SARS-CoV-2 for developing countermeasures against such viruses as soon as possible.
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Affiliation(s)
| | - Qing Ye
- Department of ‘A’, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China;
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26
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Khan SS, Ullah A. Comparative genomics of spike, envelope, and nucleocapsid protein of severe acute respiratory syndrome coronavirus 2. Afr Health Sci 2023; 23:384-399. [PMID: 38357143 PMCID: PMC10862604 DOI: 10.4314/ahs.v23i3.45] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Background Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) upsurge sprang up in Wuhan, China, in late December 2019. Objectives Due to the exceptionally high mutation frequency, comparative genomics of viruses isolated throughout time and in various geographical locations are crucial. To better understand how SARS-CoV-2 heterogeneity has changed around the globe, this research was conducted. Methods Nucleotide and protein sequences of SARS-CoV-2, SARS-CoV, and bat SARS-like CoV were extracted from the NCBI Virus database. The Wuhan SARS-CoV-2 variant was used as a reference. Molecular Evolutionary Genetics Study performed the phylogenetic analysis, while the Genome Detective Coronavirus Typing Tool performed the mutational analysis. Results The evolutionary research has revealed that bats are the primary host for coronavirus evolution and the origin of the formation of SARS-CoV and SARS-CoV-2. Numerous mutations have been discovered in the spike, envelope, and nucleocapsid protein. Conclusions The current research findings may have an implication that facilitates the development of prospective immunization candidates/small pharmacological compounds targeting COVID-19.
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Affiliation(s)
- Sufyan Sohail Khan
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Anwar Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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27
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Higgins CA, Nilsson-Payant BE, Bonaventure B, Kurland AP, Ye C, Yaron TM, Johnson JL, Adhikary P, Golynker I, Panis M, Danziger O, Rosenberg BR, Cantley LC, Martínez-Sobrido L, tenOever B, Johnson JR. SARS-CoV-2 hijacks p38β/MAPK11 to promote virus replication. mBio 2023; 14:e0100723. [PMID: 37345956 PMCID: PMC10470746 DOI: 10.1128/mbio.01007-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/08/2023] [Indexed: 06/23/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic, drastically modifies infected cells to optimize virus replication. One such modification is the activation of the host p38 mitogen-activated protein kinase (MAPK) pathway, which plays a major role in inflammatory cytokine production, a hallmark of severe COVID-19. We previously demonstrated that inhibition of p38/MAPK activity in SARS-CoV-2-infected cells reduced both cytokine production and viral replication. Here, we combined quantitative genetic screening, genomics, proteomics, and phosphoproteomics to better understand mechanisms underlying the dependence of SARS-CoV-2 on the p38 pathway. We found that p38β is a critical host factor for SARS-CoV-2 replication in multiple relevant cell lines and that it functions at a step after viral mRNA expression. We identified putative host and viral p38β substrates in the context of SARS-CoV-2 infection and found that most host substrates have intrinsic antiviral activities. Taken together, this study reveals a unique proviral function for p38β and supports exploring p38β inhibitor development as a strategy toward creating a new class of COVID-19 therapies. IMPORTANCE SARS-CoV-2 is the causative agent of the COVID-19 pandemic that has claimed millions of lives since its emergence in 2019. SARS-CoV-2 infection of human cells requires the activity of several cellular pathways for successful replication. One such pathway, the p38 MAPK pathway, is required for virus replication and disease pathogenesis. Here, we applied systems biology approaches to understand how MAPK pathways benefit SARS-CoV-2 replication to inform the development of novel COVID-19 drug therapies.
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Affiliation(s)
- Christina A Higgins
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Department of Microbiology, New York University Langone Health , New York, New York, USA
- Vilcek Graduate School for Biomedical Sciences, New York University Langone Health , New York, New York, USA
| | | | - Boris Bonaventure
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Andrew P Kurland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute , San Antonio, Texas, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine , New York, New York, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine Weill Cornell Medicine , New York, New York, USA
- Columbia University Vagelos College of Physicians and Surgeons , New York, New York, USA
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine , New York, New York, USA
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Harvard Medical School , Boston, Massachusetts, USA
| | - Prithy Adhikary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Ilona Golynker
- Department of Microbiology, New York University Langone Health , New York, New York, USA
| | - Maryline Panis
- Department of Microbiology, New York University Langone Health , New York, New York, USA
| | - Oded Danziger
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Brad R Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine , New York, New York, USA
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Harvard Medical School , Boston, Massachusetts, USA
| | | | - Benjamin tenOever
- Department of Microbiology, New York University Langone Health , New York, New York, USA
| | - Jeffrey R Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York, New York, USA
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28
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Alston JJ, Soranno A, Holehouse AS. Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.06.552128. [PMID: 37609146 PMCID: PMC10441348 DOI: 10.1101/2023.08.06.552128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Intrinsically disordered regions (IDRs) are critical for cellular function, yet often appear to lack sequence conservation when assessed by multiple sequence alignments. This raises the question of if and how function can be encoded and preserved in these regions despite massive sequence variation. To address this question, we have applied coarse-grained molecular dynamics simulations to investigate non-specific RNA binding of coronavirus nucleocapsid proteins. Coronavirus nucleocapsid proteins consist of multiple interspersed disordered and folded domains that bind RNA. We focussed here on the first two domains of coronavirus nucleocapsid proteins, the disordered N-terminal domain (NTD) followed by the folded RNA binding domain (RBD). While the NTD is highly variable across evolution, the RBD is structurally conserved. This combination makes the NTD-RBD a convenient model system to explore the interplay between an IDR adjacent to a folded domain, and how changes in IDR sequence can influence molecular recognition of a partner. Our results reveal a surprising degree of sequence-specificity encoded by both the composition and the precise order of the amino acids in the NTD. The presence of an NTD can - depending on the sequence - either suppress or enhance RNA binding. Despite this sensitivity, large-scale variation in NTD sequences is possible while certain sequence features are retained. Consequently, a conformationally-conserved fuzzy RNA:protein complex is found across nucleocapsid protein orthologs, despite large-scale changes in both NTD sequence and RBD surface chemistry. Taken together, these insights shed light on the ability of disordered regions to preserve functional characteristics despite their sequence variability.
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29
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Aloise C, Schipper JG, van Vliet A, Oymans J, Donselaar T, Hurdiss DL, de Groot RJ, van Kuppeveld FJM. SARS-CoV-2 nucleocapsid protein inhibits the PKR-mediated integrated stress response through RNA-binding domain N2b. PLoS Pathog 2023; 19:e1011582. [PMID: 37607209 PMCID: PMC10473545 DOI: 10.1371/journal.ppat.1011582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 09/01/2023] [Accepted: 07/27/2023] [Indexed: 08/24/2023] Open
Abstract
The nucleocapsid protein N of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enwraps and condenses the viral genome for packaging but is also an antagonist of the innate antiviral defense. It suppresses the integrated stress response (ISR), purportedly by interacting with stress granule (SG) assembly factors G3BP1 and 2, and inhibits type I interferon responses. To elucidate its mode of action, we systematically deleted and over-expressed distinct regions and domains. We show that N via domain N2b blocks PKR-mediated ISR activation, as measured by suppression of ISR-induced translational arrest and SG formation. N2b mutations that prevent dsRNA binding abrogate these activities also when introduced in the intact N protein. Substitutions reported to block post-translation modifications of N or its interaction with G3BP1/2 did not have a detectable additive effect. In an encephalomyocarditis virus-based infection model, N2b - but not a derivative defective in RNA binding-prevented PKR activation, inhibited β-interferon expression and promoted virus replication. Apparently, SARS-CoV-2 N inhibits innate immunity by sequestering dsRNA to prevent activation of PKR and RIG-I-like receptors. Similar observations were made for the N protein of human coronavirus 229E, suggesting that this may be a general trait conserved among members of other orthocoronavirus (sub)genera.
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Affiliation(s)
- Chiara Aloise
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jelle G. Schipper
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Arno van Vliet
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Judith Oymans
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Tim Donselaar
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Daniel L. Hurdiss
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Raoul J. de Groot
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Frank J. M. van Kuppeveld
- Virology Section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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30
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Madahar V, Dang R, Zhang Q, Liu C, Rodgers VGJ, Liao J. Human Post-Translational SUMOylation Modification of SARS-CoV-2 Nucleocapsid Protein Enhances Its Interaction Affinity with Itself and Plays a Critical Role in Its Nuclear Translocation. Viruses 2023; 15:1600. [PMID: 37515286 PMCID: PMC10384427 DOI: 10.3390/v15071600] [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: 04/11/2023] [Revised: 06/25/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
Viruses, such as Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), infect hosts and take advantage of host cellular machinery for genome replication and new virion production. Identifying and elucidating host pathways for viral infection is critical for understanding the development of the viral life cycle and novel therapeutics. The SARS-CoV-2 N protein is critical for viral RNA (vRNA) genome packaging in new virion formation. Using our quantitative Förster energy transfer/Mass spectrometry (qFRET/MS) coupled method and immunofluorescence imaging, we identified three SUMOylation sites of the SARS-CoV-2 N protein. We found that (1) Small Ubiquitin-like modifier (SUMO) modification in Nucleocapsid (N) protein interaction affinity increased, leading to enhanced oligomerization of the N protein; (2) one of the identified SUMOylation sites, K65, is critical for its nuclear translocation. These results suggest that the host human SUMOylation pathway may be critical for N protein functions in viral replication and pathology in vivo. Thus, blocking essential host pathways could provide a novel strategy for future anti-viral therapeutics development, such as for SARS-CoV-2 and other viruses.
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Affiliation(s)
- Vipul Madahar
- Department of Bioengineering, College of Engineering, Bourns College of Engineering, University of California at Riverside, Riverside, CA 92521, USA
| | - Runrui Dang
- Department of Bioengineering, College of Engineering, Bourns College of Engineering, University of California at Riverside, Riverside, CA 92521, USA
| | - Quanqing Zhang
- Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA 92521, USA
- Department of Botany, College of Natural & Agricultural Sciences, University of California at Riverside, Riverside, CA 92521, USA
| | - Chuchu Liu
- Department of Bioengineering, College of Engineering, Bourns College of Engineering, University of California at Riverside, Riverside, CA 92521, USA
| | - Victor G J Rodgers
- Department of Bioengineering, College of Engineering, Bourns College of Engineering, University of California at Riverside, Riverside, CA 92521, USA
- Biomedical Science, School of Medicine, University of California at Riverside, Riverside, CA 92521, USA
| | - Jiayu Liao
- Department of Bioengineering, College of Engineering, Bourns College of Engineering, University of California at Riverside, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA 92521, USA
- Biomedical Science, School of Medicine, University of California at Riverside, Riverside, CA 92521, USA
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31
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Segovia-de los Santos P, Padula-Roca C, Simon X, Echaides C, Lassabe G, Gonzalez-Sapienza G. A highly sensitive nanobody-based immunoassay detecting SARS-CoV-2 nucleocapsid protein using all-recombinant reagents. Front Immunol 2023; 14:1220477. [PMID: 37497229 PMCID: PMC10367427 DOI: 10.3389/fimmu.2023.1220477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023] Open
Abstract
Antigen tests have been crucial for managing the COVID-19 pandemic by identifying individuals infected with SARS-CoV-2. This remains true even after immunity has been widely attained through natural infection and vaccination, since it only provides moderate protection against transmission and is highly permeable to the emergence of new virus variants. For this reason, the widespread availability of diagnostic methods is essential for health systems to manage outbreaks effectively. In this work, we generated nanobodies to the virus nucleocapsid protein (NP) and after an affinity-guided selection identified a nanobody pair that allowed the detection of NP at sub-ng/mL levels in a colorimetric two-site ELISA, demonstrating high diagnostic value with clinical samples. We further modified the assay by using a nanobody-NanoLuc luciferase chimeric tracer, resulting in increased sensitivity (detection limit = 61 pg/mL) and remarkable improvement in diagnostic performance. The luminescent assay was finally evaluated using 115 nasopharyngeal swab samples. Receiver Operating Characteristic (ROC) curve analysis revealed a sensitivity of 78.7% (95% confidence interval: 64.3%-89.3%) and specificity of 100.0% (95% confidence interval: 94.7%-100.0%). The test allows the parallel analysis of a large number of untreated samples, and fulfills our goal of producing a recombinant reagent-based test that can be reproduced at low cost by other laboratories with recombinant expression capabilities, aiding to build diagnostic capacity.
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Affiliation(s)
- Paula Segovia-de los Santos
- Cátedra de Inmunología, Departamento de Biociencias (DEPBIO), Facultad de Química, Instituto de Higiene, Montevideo, Uruguay
| | - Carolina Padula-Roca
- Cátedra de Inmunología, Departamento de Biociencias (DEPBIO), Facultad de Química, Instituto de Higiene, Montevideo, Uruguay
| | | | - Cesar Echaides
- Parque Lecocq, Intendencia Municipal de Montevideo (IMM), Montevideo, Uruguay
| | - Gabriel Lassabe
- Cátedra de Inmunología, Departamento de Biociencias (DEPBIO), Facultad de Química, Instituto de Higiene, Montevideo, Uruguay
| | - Gualberto Gonzalez-Sapienza
- Cátedra de Inmunología, Departamento de Biociencias (DEPBIO), Facultad de Química, Instituto de Higiene, Montevideo, Uruguay
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32
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Min YQ, Huang M, Feng K, Jia Y, Sun X, Ning YJ. A New Cellular Interactome of SARS-CoV-2 Nucleocapsid Protein and Its Biological Implications. Mol Cell Proteomics 2023; 22:100579. [PMID: 37211047 PMCID: PMC10198743 DOI: 10.1016/j.mcpro.2023.100579] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023] Open
Abstract
There is still much to uncover regarding the molecular details of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. As the most abundant protein, coronavirus nucleocapsid (N) protein encapsidates viral RNAs, serving as the structural component of ribonucleoprotein and virion, and participates in transcription, replication, and host regulations. Virus-host interaction might give clues to better understand how the virus affects or is affected by its host during infection and identify promising therapeutic candidates. Considering the critical roles of N, we here established a new cellular interactome of SARS-CoV-2 N by using a high-specific affinity purification (S-pulldown) assay coupled with quantitative mass spectrometry and immunoblotting validations, uncovering many N-interacting host proteins unreported previously. Bioinformatics analysis revealed that these host factors are mainly involved in translation regulations, viral transcription, RNA processes, stress responses, protein folding and modification, and inflammatory/immune signaling pathways, in line with the supposed actions of N in viral infection. Existing pharmacological cellular targets and the directing drugs were then mined, generating a drug-host protein network. Accordingly, we experimentally identified several small-molecule compounds as novel inhibitors against SARS-CoV-2 replication. Furthermore, a newly identified host factor, DDX1, was verified to interact and colocalize with N mainly by binding to the N-terminal domain of the viral protein. Importantly, loss/gain/reconstitution-of-function experiments showed that DDX1 acts as a potent anti-SARS-CoV-2 host factor, inhibiting the viral replication and protein expression. The N-targeting and anti-SARS-CoV-2 abilities of DDX1 are consistently independent of its ATPase/helicase activity. Further mechanism studies revealed that DDX1 impedes multiple activities of N, including the N-N interaction, N oligomerization, and N-viral RNA binding, thus likely inhibiting viral propagation. These data provide new clues to better depiction of the N-cell interactions and SARS-CoV-2 infection and may help inform the development of new therapeutic candidates.
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Affiliation(s)
- Yuan-Qin Min
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Mengzhuo Huang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China; State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Kuan Feng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China; State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yajie Jia
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xiulian Sun
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
| | - Yun-Jia Ning
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China; State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China; Hubei Jiangxia Laboratory, Wuhan, China.
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Yang Z, Johnson BA, Meliopoulos VA, Ju X, Zhang P, Hughes MP, Wu J, Koreski KP, Chang TC, Wu G, Hixon J, Duffner J, Wong K, Lemieux R, Lokugamage KG, Alvardo RE, Crocquet-Valdes PA, Walker DH, Plante KS, Plante JA, Weaver SC, Kim HJ, Meyers R, Schultz-Cherry S, Ding Q, Menachery VD, Taylor JP. Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.546885. [PMID: 37425880 PMCID: PMC10327126 DOI: 10.1101/2023.06.29.546885] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
G3BP1/2 are paralogous proteins that promote stress granule formation in response to cellular stresses, including viral infection. G3BP1/2 are prominent interactors of the nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the functional consequences of the G3BP1-N interaction in the context of viral infection remain unclear. Here we used structural and biochemical analyses to define the residues required for G3BP1-N interaction, followed by structure-guided mutagenesis of G3BP1 and N to selectively and reciprocally disrupt their interaction. We found that mutation of F17 within the N protein led to selective loss of interaction with G3BP1 and consequent failure of the N protein to disrupt stress granule assembly. Introduction of SARS-CoV-2 bearing an F17A mutation resulted in a significant decrease in viral replication and pathogenesis in vivo, indicating that the G3BP1-N interaction promotes infection by suppressing the ability of G3BP1 to form stress granules.
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Affiliation(s)
- Zemin Yang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bryan A Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Victoria A Meliopoulos
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaohui Ju
- School of Medicine, Tsinghua University, Beijing, China
| | - Peipei Zhang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael P Hughes
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinjun Wu
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kaitlin P Koreski
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | | | | | | | - Kumari G Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Rojelio E Alvardo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | | | - David H Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Jessica A Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qiang Ding
- School of Medicine, Tsinghua University, Beijing, China
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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34
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Vandervaart JP, Inniss NL, Ling-Hu T, Minasov G, Wiersum G, Rosas-Lemus M, Shuvalova L, Achenbach CJ, Hultquist JF, Satchell KJF, Bachta KER. Serodominant SARS-CoV-2 Nucleocapsid Peptides Map to Unstructured Protein Regions. Microbiol Spectr 2023; 11:e0032423. [PMID: 37191546 PMCID: PMC10269789 DOI: 10.1128/spectrum.00324-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is highly immunogenic, and anti-N antibodies are commonly used as markers for prior infection. While several studies have examined or predicted the antigenic regions of N, these have lacked consensus and structural context. Using COVID-19 patient sera to probe an overlapping peptide array, we identified six public and four private epitope regions across N, some of which are unique to this study. We further report the first deposited X-ray structure of the stable dimerization domain at 2.05 Å as similar to all other reported structures. Structural mapping revealed that most epitopes are derived from surface-exposed loops on the stable domains or from the unstructured linker regions. An antibody response to an epitope in the stable RNA binding domain was found more frequently in sera from patients requiring intensive care. Since emerging amino acid variations in N map to immunogenic peptides, N protein variation could impact detection of seroconversion for variants of concern. IMPORTANCE As SARS-CoV-2 continues to evolve, a structural and genetic understanding of key viral epitopes will be essential to the development of next-generation diagnostics and vaccines. This study uses structural biology and epitope mapping to define the antigenic regions of the viral nucleocapsid protein in sera from a cohort of COVID-19 patients with diverse clinical outcomes. These results are interpreted in the context of prior structural and epitope mapping studies as well as in the context of emergent viral variants. This report serves as a resource for synthesizing the current state of the field toward improving strategies for future diagnostic and therapeutic design.
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Affiliation(s)
- Jacob P. Vandervaart
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Nicole L. Inniss
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Ted Ling-Hu
- Department of Medicine, Division of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - George Minasov
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Grant Wiersum
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Monica Rosas-Lemus
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Ludmilla Shuvalova
- Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Chad J. Achenbach
- Department of Medicine, Division of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Judd F. Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Karla J. F. Satchell
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kelly E. R. Bachta
- Department of Medicine, Division of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
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LeBlanc K, Lynch J, Layne C, Vendramelli R, Sloan A, Tailor N, Deschambault Y, Zhang F, Kobasa D, Safronetz D, Xiang Y, Cao J. The Nucleocapsid Proteins of SARS-CoV-2 and Its Close Relative Bat Coronavirus RaTG13 Are Capable of Inhibiting PKR- and RNase L-Mediated Antiviral Pathways. Microbiol Spectr 2023; 11:e0099423. [PMID: 37154717 PMCID: PMC10269842 DOI: 10.1128/spectrum.00994-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/11/2023] [Indexed: 05/10/2023] Open
Abstract
Coronaviruses (CoVs), including severe acute respiratory syndrome CoV (SARS-CoV), Middle East respiratory syndrome CoV (MERS-CoV), and SARS-CoV-2, produce double-stranded RNA (dsRNA) that activates antiviral pathways such as PKR and OAS/RNase L. To successfully replicate in hosts, viruses must evade such antiviral pathways. Currently, the mechanism of how SARS-CoV-2 antagonizes dsRNA-activated antiviral pathways is unknown. In this study, we demonstrate that the SARS-CoV-2 nucleocapsid (N) protein, the most abundant viral structural protein, is capable of binding to dsRNA and phosphorylated PKR, inhibiting both the PKR and OAS/RNase L pathways. The N protein of the bat coronavirus (bat-CoV) RaTG13, the closest relative of SARS-CoV-2, has a similar ability to inhibit the human PKR and RNase L antiviral pathways. Via mutagenic analysis, we found that the C-terminal domain (CTD) of the N protein is sufficient for binding dsRNA and inhibiting RNase L activity. Interestingly, while the CTD is also sufficient for binding phosphorylated PKR, the inhibition of PKR antiviral activity requires not only the CTD but also the central linker region (LKR). Thus, our findings demonstrate that the SARS-CoV-2 N protein is capable of antagonizing the two critical antiviral pathways activated by viral dsRNA and that its inhibition of PKR activities requires more than dsRNA binding mediated by the CTD. IMPORTANCE The high transmissibility of SARS-CoV-2 is an important viral factor defining the coronavirus disease 2019 (COVID-19) pandemic. To transmit efficiently, SARS-CoV-2 must be capable of disarming the innate immune response of its host efficiently. Here, we describe that the nucleocapsid protein of SARS-CoV-2 is capable of inhibiting two critical innate antiviral pathways, PKR and OAS/RNase L. Moreover, the counterpart of the closest animal coronavirus relative of SARS-CoV-2, bat-CoV RaTG13, can also inhibit human PKR and OAS/RNase L antiviral activities. Thus, the importance of our discovery for understanding the COVID-19 pandemic is 2-fold. First, the ability of SARS-CoV-2 N to inhibit innate antiviral activity is likely a factor contributing to the transmissibility and pathogenicity of the virus. Second, the bat relative of SARS-CoV-2 has the capacity to inhibit human innate immunity, which thus likely contributed to the establishment of infection in humans. The findings described in this study are valuable for developing novel antivirals and vaccines.
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Affiliation(s)
- Kyle LeBlanc
- Poxviruses and Vaccine Design, Division of Viral Diseases, Directorate of Science Reference and Surveillance, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jessie Lynch
- Poxviruses and Vaccine Design, Division of Viral Diseases, Directorate of Science Reference and Surveillance, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Christine Layne
- Poxviruses and Vaccine Design, Division of Viral Diseases, Directorate of Science Reference and Surveillance, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Robert Vendramelli
- Special Pathogens, Division of Health Security and Response, Directorate of Scientific Operations and Response, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Angela Sloan
- Special Pathogens, Division of Health Security and Response, Directorate of Scientific Operations and Response, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Nikesh Tailor
- Special Pathogens, Division of Health Security and Response, Directorate of Scientific Operations and Response, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Yvon Deschambault
- Special Pathogens, Division of Health Security and Response, Directorate of Scientific Operations and Response, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Fushun Zhang
- Department of Microbiology and Immunology, The University of Texas Health Science Center, San Antonio, Texas, USA
| | - Darwyn Kobasa
- Special Pathogens, Division of Health Security and Response, Directorate of Scientific Operations and Response, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - David Safronetz
- Special Pathogens, Division of Health Security and Response, Directorate of Scientific Operations and Response, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Yan Xiang
- Department of Microbiology and Immunology, The University of Texas Health Science Center, San Antonio, Texas, USA
| | - Jingxin Cao
- Poxviruses and Vaccine Design, Division of Viral Diseases, Directorate of Science Reference and Surveillance, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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Khamjan NA, Lohani M, Khan MF, Khan S, Algaissi A. Immunoinformatics Strategy to Develop a Novel Universal Multiple Epitope-Based COVID-19 Vaccine. Vaccines (Basel) 2023; 11:1090. [PMID: 37376479 DOI: 10.3390/vaccines11061090] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 06/29/2023] Open
Abstract
Currently available COVID vaccines are effective in reducing mortality and severity but do not prevent transmission of the virus or reinfection by the emerging SARS-CoV-2 variants. There is an obvious need for better and longer-lasting effective vaccines for various prevailing strains and the evolving SARS-CoV-2 virus, necessitating the development of a broad-spectrum vaccine that can be used to prevent infection by reducing both the transmission rate and re-infection. During the initial phases of SARS-CoV-2 infection, the nucleocapsid (N) protein is one of the most abundantly expressed proteins. Additionally, it has been identified as the most immunogenic protein of SARS-CoV-2. In this study, state-of-the-art bioinformatics techniques have been exploited to design novel multiple epitope vaccines using conserved regions of N proteins from prevalent strains of SARS-CoV-2 for the prediction of B- and T-cell epitopes. These epitopes were sorted based on their immunogenicity, antigenicity score, and toxicity. The most effective multi-epitope construct with possible immunogenic properties was created using epitope combinations. EAAAK, AAY, and GPGPG were used as linkers to connect epitopes. The developed vaccines have shown positive results in terms of overall population coverage and stimulation of the immune response. Potential expression of the chimeric protein construct was detected after it was cloned into the Pet28a/Cas9-cys vector for expression screening in Escherichia coli. The developed vaccine performed well in computer-based immune response simulation and covered a diverse allelic population worldwide. These computational findings are very encouraging for the further testing of our candidate vaccine, which could eventually aid in the control and prevention of SARS-CoV-2 infections globally.
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Affiliation(s)
- Nizar A Khamjan
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Mohtashim Lohani
- Department of Emergency Medical Services, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
- Medical Research Centre, Jazan University, Jazan 45142, Saudi Arabia
| | - Mohammad Faheem Khan
- Department of Biotechnology, K.C.M.T., M. J. P. Rohilkhand University, Bareilly 243006, India
| | - Saif Khan
- Department of Basic Dental and Medical Sciences, College of Dentistry, Hail University, Hail 2440, Saudi Arabia
| | - Abdullah Algaissi
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
- Medical Research Centre, Jazan University, Jazan 45142, Saudi Arabia
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Ignatz RM, Zirkenbach VA, Kaya M, Stroikova V, Öttl R, Frey N, Kaya Z. No Evidence for Myocarditis or Other Organ Affection by Induction of an Immune Response against Critical SARS-CoV-2 Protein Epitopes in a Mouse Model Susceptible for Autoimmunity. Int J Mol Sci 2023; 24:9873. [PMID: 37373021 DOI: 10.3390/ijms24129873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
After Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) developed into a global pandemic, not only the infection itself but also several immune-mediated side effects led to additional consequences. Immune reactions such as epitope spreading and cross-reactivity may also play a role in the development of long-COVID, although the exact pathomechanisms have not yet been elucidated. Infection with SARS-CoV-2 can not only cause direct damage to the lungs but can also lead to secondary indirect organ damage (e.g., myocardial involvement), which is often associated with high mortality. To investigate whether an immune reaction against the viral peptides can lead to organ affection, a mouse strain known to be susceptible to the development of autoimmune diseases, such as experimental autoimmune myocarditis (EAM), was used. First, the mice were immunized with single or pooled peptide sequences of the virus's spike (SP), membrane (MP), nucleocapsid (NP), and envelope protein (EP), then the heart and other organs such as the liver, kidney, lung, intestine, and muscle were examined for signs of inflammation or other damage. Our results showed no significant inflammation or signs of pathology in any of these organs as a result of the immunization with these different viral protein sequences. In summary, immunization with different SARS-CoV-2 spike-, membrane-, nucleocapsid-, and envelope-protein peptides does not significantly affect the heart or other organ systems adversely, even when using a highly susceptible mouse strain for experimental autoimmune diseases. This suggests that inducing an immune reaction against these peptides of the SARS-CoV-2 virus alone is not sufficient to cause inflammation and/or dysfunction of the myocardium or other studied organs.
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Affiliation(s)
| | | | - Mansur Kaya
- Department of Cardiology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Vera Stroikova
- Department of Cardiology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Renate Öttl
- Department of Cardiology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Norbert Frey
- Department of Cardiology, University of Heidelberg, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, University of Heidelberg, 69120 Heidelberg, Germany
| | - Ziya Kaya
- Department of Cardiology, University of Heidelberg, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, University of Heidelberg, 69120 Heidelberg, Germany
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38
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Abstract
There are over 100 computational predictors of intrinsic disorder. These methods predict amino acid-level propensities for disorder directly from protein sequences. The propensities can be used to annotate putative disordered residues and regions. This unit provides a practical and holistic introduction to the sequence-based intrinsic disorder prediction. We define intrinsic disorder, explain the format of computational prediction of disorder, and identify and describe several accurate predictors. We also introduce recently released databases of intrinsic disorder predictions and use an illustrative example to provide insights into how predictions should be interpreted and combined. Lastly, we summarize key experimental methods that can be used to validate computational predictions. © 2023 Wiley Periodicals LLC.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, Virginia
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Lekshmi VS, Asha K, Sanicas M, Asi A, Arya UM, Kumar B. PI3K/Akt/Nrf2 mediated cellular signaling and virus-host interactions: latest updates on the potential therapeutic management of SARS-CoV-2 infection. Front Mol Biosci 2023; 10:1158133. [PMID: 37325475 PMCID: PMC10267462 DOI: 10.3389/fmolb.2023.1158133] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
The emergence and re-emergence of viral diseases, which cause significant global mortality and morbidity, are the major concerns of this decade. Of these, current research is focused majorly on the etiological agent of the COVID-19 pandemic, SARS-CoV-2. Understanding the host response and metabolic changes during viral infection may provide better therapeutic targets for the proper management of pathophysiological conditions associated with SARS-CoV-2 infection. We have achieved control over most emerging viral diseases; however, a lack of understanding of the underlying molecular events prevents us from exploring novel therapeutic targets, leaving us forced to witness re-emerging viral infections. SARS-CoV-2 infection is usually accompanied by oxidative stress, which leads to an overactive immune response, the release of inflammatory cytokines, increasing lipid production, and also alterations in the endothelial and mitochondrial functions. PI3K/Akt signaling pathway confers protection against oxidative injury by various cell survival mechanisms including Nrf2-ARE mediated antioxidant transcriptional response. SARS-CoV-2 is also reported to hijack this pathway for its survival within host and few studies have suggested the role of antioxidants in modulating the Nrf2 pathway to manage disease severity. This review highlights the interrelated pathophysiological conditions associated with SARS-CoV-2 infection and the host survival mechanisms mediated by PI3K/Akt/Nrf2 signaling pathways that can help ameliorate the severity of the disease and provide effective antiviral targets against SARS-CoV-2.
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Affiliation(s)
- V S Lekshmi
- Department of Antiviral Research, Institute of Advanced Virology, Thiruvananthapuram, Kerala, India
| | - Kumari Asha
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
| | | | - Abhila Asi
- Department of Antiviral Research, Institute of Advanced Virology, Thiruvananthapuram, Kerala, India
| | - U M Arya
- Department of Antiviral Research, Institute of Advanced Virology, Thiruvananthapuram, Kerala, India
| | - Binod Kumar
- Department of Antiviral Research, Institute of Advanced Virology, Thiruvananthapuram, Kerala, India
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40
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Srinivasan Rajsri K, McRae MP, Christodoulides NJ, Dapkins I, Simmons GW, Matz H, Dooley H, Fenyö D, McDevitt JT. Simultaneous Quantitative SARS-CoV-2 Antigen and Host Antibody Detection and Pre-Screening Strategy at the Point of Care. Bioengineering (Basel) 2023; 10:670. [PMID: 37370601 PMCID: PMC10295356 DOI: 10.3390/bioengineering10060670] [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: 04/26/2023] [Revised: 05/16/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
As COVID-19 pandemic public health measures are easing globally, the emergence of new SARS-CoV-2 strains continue to present high risk for vulnerable populations. The antibody-mediated protection acquired from vaccination and/or infection is seen to wane over time and the immunocompromised populations can no longer expect benefit from monoclonal antibody prophylaxis. Hence, there is a need to monitor new variants and its effect on vaccine performance. In this context, surveillance of new SARS-CoV-2 infections and serology testing are gaining consensus for use as screening methods, especially for at-risk groups. Here, we described an improved COVID-19 screening strategy, comprising predictive algorithms and concurrent, rapid, accurate, and quantitative SARS-CoV-2 antigen and host antibody testing strategy, at point of care (POC). We conducted a retrospective analysis of 2553 pre- and asymptomatic patients who were tested for SARS-CoV-2 by RT-PCR. The pre-screening model had an AUC (CI) of 0.76 (0.73-0.78). Despite being the default method for screening, body temperature had lower AUC (0.52 [0.49-0.55]) compared to case incidence rate (0.65 [0.62-0.68]). POC assays for SARS-CoV-2 nucleocapsid protein (NP) and spike (S) receptor binding domain (RBD) IgG antibody showed promising preliminary results, demonstrating a convenient, rapid (<20 min), quantitative, and sensitive (ng/mL) antigen/antibody assay. This integrated pre-screening model and simultaneous antigen/antibody approach may significantly improve accuracy of COVID-19 infection and host immunity screening, helping address unmet needs for monitoring vaccine effectiveness and severe disease surveillance.
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Affiliation(s)
- Kritika Srinivasan Rajsri
- Division of Biomaterials, Department of Molecular Pathobiology, New York University School of Dentistry, New York, NY 10010, USA; (K.S.R.); (M.P.M.); (N.J.C.); (G.W.S.)
- Department of Pathology, Vilcek Institute of Graduate Biomedical Sciences, New York University School of Medicine, New York, NY 10010, USA
| | - Michael P. McRae
- Division of Biomaterials, Department of Molecular Pathobiology, New York University School of Dentistry, New York, NY 10010, USA; (K.S.R.); (M.P.M.); (N.J.C.); (G.W.S.)
| | - Nicolaos J. Christodoulides
- Division of Biomaterials, Department of Molecular Pathobiology, New York University School of Dentistry, New York, NY 10010, USA; (K.S.R.); (M.P.M.); (N.J.C.); (G.W.S.)
| | - Isaac Dapkins
- Departments of Population Health and Medicine, New York University School of Medicine, New York, NY 10010, USA;
| | - Glennon W. Simmons
- Division of Biomaterials, Department of Molecular Pathobiology, New York University School of Dentistry, New York, NY 10010, USA; (K.S.R.); (M.P.M.); (N.J.C.); (G.W.S.)
| | - Hanover Matz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (H.M.); (H.D.)
| | - Helen Dooley
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (H.M.); (H.D.)
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10010, USA;
| | - John T. McDevitt
- Division of Biomaterials, Department of Molecular Pathobiology, New York University School of Dentistry, New York, NY 10010, USA; (K.S.R.); (M.P.M.); (N.J.C.); (G.W.S.)
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Wang Y, Ling X, Zhang C, Zou J, Luo B, Luo Y, Jia X, Jia G, Zhang M, Hu J, Liu T, Wang Y, Lu K, Li D, Ma J, Liu C, Su Z. Modular characterization of SARS-CoV-2 nucleocapsid protein domain functions in nucleocapsid-like assembly. MOLECULAR BIOMEDICINE 2023; 4:16. [PMID: 37211575 DOI: 10.1186/s43556-023-00129-z] [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: 01/13/2023] [Accepted: 04/09/2023] [Indexed: 05/23/2023] Open
Abstract
SARS-CoV-2 and its variants, with the Omicron subvariant XBB currently prevailing the global infections, continue to pose threats on public health worldwide. This non-segmented positive-stranded RNA virus encodes the multi-functional nucleocapsid protein (N) that plays key roles in viral infection, replication, genome packaging and budding. N protein consists of two structural domains, NTD and CTD, and three intrinsically disordered regions (IDRs) including the NIDR, the serine/arginine rich motif (SRIDR), and the CIDR. Previous studies revealed functions of N protein in RNA binding, oligomerization, and liquid-liquid phase separation (LLPS), however, characterizations of individual domains and their dissected contributions to N protein functions remain incomplete. In particular, little is known about N protein assembly that may play essential roles in viral replication and genome packing. Here, we present a modular approach to dissect functional roles of individual domains in SARS-CoV-2 N protein that reveals inhibitory or augmented modulations of protein assembly and LLPS in the presence of viral RNAs. Intriguingly, full-length N protein (NFL) assembles into ring-like architecture whereas the truncated SRIDR-CTD-CIDR (N182-419) promotes filamentous assembly. Moreover, LLPS droplets of NFL and N182-419 are significantly enlarged in the presence of viral RNAs, and we observed filamentous structures in the N182-419 droplets using correlative light and electron microscopy (CLEM), suggesting that the formation of LLPS droplets may promote higher-order assembly of N protein for transcription, replication and packaging. Together this study expands our understanding of the multiple functions of N protein in SARS-CoV-2.
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Affiliation(s)
- Yan Wang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Xiaobin Ling
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chong Zhang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Jian Zou
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Bingnan Luo
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Yongbo Luo
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Xinyu Jia
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Guowen Jia
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Minghua Zhang
- College of Polymer Science and Engineering, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Junchao Hu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Ting Liu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Yuanfeiyi Wang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Kefeng Lu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Cong Liu
- Interdisciplinary Research Center On Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China.
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Bonam SR, Hu H. Next-Generation Vaccines Against COVID-19 Variants: Beyond the Spike Protein. ZOONOSES (BURLINGTON, MASS.) 2023; 3:10.15212/zoonoses-2023-0003. [PMID: 38031548 PMCID: PMC10686570 DOI: 10.15212/zoonoses-2023-0003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Vaccines are among the most effective medical countermeasures against infectious diseases. The current Coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spurred the scientific strategies to fight against the disease. Since 2020, a great number of vaccines based on different platforms have been in development in response to the pandemic, among which mRNA, adenoviral vector, and subunit vaccines have been clinically approved for use in humans. These first-generation COVID-19 vaccines largely target the viral spike (S) protein and aim for eliciting potent neutralizing antibodies. With the emergence of SARS-CoV-2 variants, especially the highly transmissible Omicron strains, the S-based vaccine strategies have been faced constant challenges due to strong immune escape by the variants. The coronavirus nucleocapsid (N) is one of the viral proteins that induces strong T-cell immunity and is more conserved across different SARS-CoV-2 variants. Inclusion of N in the development of COVID-19 vaccines has been reported. Here, we briefly reviewed and discussed COVID-19 disease, current S-based vaccine strategies, and focused on the immunobiology of N protein in SARS-CoV-2 host immunity, as well as the next-generation vaccine strategies involving N protein, to combat current and emerging SARS-CoV-2 variants.
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Affiliation(s)
- Srinivasa Reddy Bonam
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA 77555
| | - Haitao Hu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA 77555
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA 77555
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA 77555
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Zhao H, Wu D, Hassan SA, Nguyen A, Chen J, Piszczek G, Schuck P. A conserved oligomerization domain in the disordered linker of coronavirus nucleocapsid proteins. SCIENCE ADVANCES 2023; 9:eadg6473. [PMID: 37018390 PMCID: PMC10075959 DOI: 10.1126/sciadv.adg6473] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/07/2023] [Indexed: 06/01/2023]
Abstract
The nucleocapsid (N-)protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a key role in viral assembly and scaffolding of the viral RNA. It promotes liquid-liquid phase separation (LLPS), forming dense droplets that support the assembly of ribonucleoprotein particles with as-of-yet unknown macromolecular architecture. Combining biophysical experiments, molecular dynamics simulations, and analysis of the mutational landscape, we describe a heretofore unknown oligomerization site that contributes to LLPS, is required for the assembly of higher-order protein-nucleic acid complexes, and is coupled to large-scale conformational changes of N-protein upon nucleic acid binding. The self-association interface is located in a leucine-rich sequence of the intrinsically disordered linker between N-protein folded domains and formed by transient helices assembling into trimeric coiled-coils. Critical residues stabilizing hydrophobic and electrostatic interactions between adjacent helices are highly protected against mutations in viable SARS-CoV-2 genomes, and the oligomerization motif is conserved across related coronaviruses, thus presenting a target for antiviral therapeutics.
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Affiliation(s)
- Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergio A. Hassan
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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Parker JE, Rodriguez RA. Development of a charged model of the SARS-CoV-2 viral surface. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184136. [PMID: 36746311 PMCID: PMC9898061 DOI: 10.1016/j.bbamem.2023.184136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/12/2023] [Accepted: 01/31/2023] [Indexed: 02/06/2023]
Abstract
A recent study provided experimental evidence of inactivation of viral activity after radio-frequency (RF) exposures in the 6-12 GHz band that was hypothesized to be caused by vibrations of an acoustic dipole mode in the virus that excited the viral membrane to failure. Here, we develop an atomic-scale molecular dynamics (MD) model of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral surface to estimate the electric fields necessary to rupture the viral membrane via dipole shaking of the virus. We computed the absorption spectrum of the system via unbiased MD simulations and found no particular strong absorption in the GHz band. We investigated the mechanical resiliency of the viral membrane by introducing uniaxial strains in the system and observed no pore formation in the membrane for strains up to 50%. Because the computed absorption spectrum was found to be essentially flat, and the strain required to break the viral membrane was >0.5, the field strength associated with rupture of the virus was greater than the dielectric breakdown value of air. Thus, RF disinfection of enveloped viruses would occur only once sufficient heat was transferred to the virus via a thermal mechanism and not by direct action (shaking) of the RF field oscillations on the viral membrane.
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Affiliation(s)
- James E Parker
- General Dynamics Information Technology, 4141 Petroleum Road, JBSA Fort Sam Houston, TX, 78234-2644, United States.
| | - Roberto A Rodriguez
- General Dynamics Information Technology, 4141 Petroleum Road, JBSA Fort Sam Houston, TX, 78234-2644, United States.
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Lee E, Redzic JS, Saviola AJ, Li X, Ebmeier CC, Kutateladze T, Hansen KC, Zhao R, Ahn N, Sluchanko NN, Eisenmesser E. Molecular insight into the specific interactions of the SARS-Coronavirus-2 nucleocapsid with RNA and host protein. Protein Sci 2023; 32:e4603. [PMID: 36807437 PMCID: PMC10019451 DOI: 10.1002/pro.4603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/23/2023]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) nucleocapsid protein is the most abundantly expressed viral protein during infection where it targets both RNA and host proteins. However, identifying how a single viral protein interacts with so many different targets remains a challenge, providing the impetus here for identifying the interaction sites through multiple methods. Through a combination of nuclear magnetic resonance (NMR), electron microscopy, and biochemical methods, we have characterized nucleocapsid interactions with RNA and with three host proteins, which include human cyclophilin-A, Pin1, and 14-3-3τ. Regarding RNA interactions, the nucleocapsid protein N-terminal folded domain preferentially interacts with smaller RNA fragments relative to the C-terminal region, suggesting an initial RNA engagement is largely dictated by this N-terminal region followed by weaker interactions to the C-terminal region. The nucleocapsid protein forms 10 nm ribonuclear complexes with larger RNA fragments that include 200 and 354 nucleic acids, revealing its potential diversity in sequestering different viral genomic regions during viral packaging. Regarding host protein interactions, while the nucleocapsid targets all three host proteins through its serine-arginine-rich region, unstructured termini of the nucleocapsid protein also engage host cyclophilin-A and host 14-3-3τ. Considering these host proteins play roles in innate immunity, the SARS-CoV-2 nucleocapsid protein may block the host response by competing interactions. Finally, phosphorylation of the nucleocapsid protein quenches an inherent dynamic exchange process within its serine-arginine-rich region. Our studies identify many of the diverse interactions that may be important for SARS-CoV-2 pathology during infection.
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Affiliation(s)
- Eunjeong Lee
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - Jasmina S. Redzic
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - Anthony J. Saviola
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | | | - Tatiana Kutateladze
- Department of PharmacologySchool of Medicine, University of Colorado DenverAuroraColoradoUSA
| | - Kirk Charles Hansen
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
| | - Natalie Ahn
- Department of BiochemistryUniversity of Colorado BoulderBoulderColoradoUSA
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of SciencesMoscowRussia
| | - Elan Eisenmesser
- Department of Biochemistry and Molecular Genetics, School of MedicineUniversity of Colorado DenverAuroraColoradoUSA
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Mao S, Cai X, Niu S, Wei J, Jiang N, Deng H, Wang W, Zhang J, Shen S, Ma Y, Wu X, Peng Q, Huang A, Wang D. TRIM21 promotes ubiquitination of SARS-CoV-2 nucleocapsid protein to regulate innate immunity. J Med Virol 2023; 95:e28719. [PMID: 37185839 DOI: 10.1002/jmv.28719] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 05/17/2023]
Abstract
The innate immune response is the first line of host defense against viral infections, but its role in immunity against SARS-CoV-2 remains unclear. By using immunoprecipitation coupled with mass spectroscopy, we observed that the E3 ubiquitin ligase TRIM21 interacted with the SARS-CoV-2 nucleocapsid (N) protein and ubiquitinated it at Lys375 . Upon determining the topology of the TRIM21-mediated polyubiquitination chain on N protein, we then found that polyubiquitination led to tagging of the N protein for degradation by the host cell proteasome. Furthermore, TRIM21 also ubiquitinated the N proteins of SARS-CoV-2 variants of concern, including Alpha, Beta, Gamma, Delta, and Omicron together with SARS-CoV and MERS-CoV variants. Herein, we propose that ubiquitylation and degradation of the SARS-CoV-2 N protein inhibited SARS-CoV-2 viral particle assembly, by which it probably involved in preventing cytokine storm. Eventually, our study has fully revealed the association between the host innate immune system and SARS-CoV-2 N protein, which may aid in developing novel SARS-CoV-2 treatment strategies.
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Affiliation(s)
- Shenglan Mao
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xuefei Cai
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Siqiang Niu
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Wei
- Department of Clinical Laboratory, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai, Guangdong, China
| | - Ning Jiang
- School of Basic Medical Science, Chongqing Medical University, Chongqing, China
| | - Haijun Deng
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Wen Wang
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Jing Zhang
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Shimei Shen
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yuanyan Ma
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xiaoli Wu
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Qiling Peng
- School of Basic Medical Science, Chongqing Medical University, Chongqing, China
| | - Ailong Huang
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Deqiang Wang
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
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Ong'era EM, Mohammed KS, Makori TO, Bejon P, Ocholla-Oyier LI, Nokes DJ, Agoti CN, Githinji G. High-throughput sequencing approaches applied to SARS-CoV-2. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18701.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
High-throughput sequencing is crucial for surveillance and control of viral outbreaks. During the ongoing coronavirus disease 2019 (COVID-19) pandemic, advances in the high-throughput sequencing technology resources have enhanced diagnosis, surveillance, and vaccine discovery. From the onset of the pandemic in December 2019, several genome-sequencing approaches have been developed and supported across the major sequencing platforms such as Illumina, Oxford Nanopore, PacBio, MGI DNBSEQTM and Ion Torrent. Here, we share insights from the sequencing approaches developed for sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between December 2019 and October 2022.
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Vidal LEL, Figueira-Mansur J, Jurgilas PB, Argondizzo APC, Pestana CP, Martins FO, da Silva Junior HC, Miguez M, Loureiro BO, Marques CDFS, Trinta KS, da Silva LBR, de Mello MB, da Silva ED, Bastos RC, Esteves G. Process development and characterization of recombinant nucleocapsid protein for its application on COVID-19 diagnosis. Protein Expr Purif 2023; 207:106263. [PMID: 36921810 PMCID: PMC10012136 DOI: 10.1016/j.pep.2023.106263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/10/2023] [Indexed: 03/15/2023]
Abstract
COVID-19 pandemic was caused by the severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2). The nucleocapsid (N) protein from Sars-CoV-2 is a highly immunogenic antigen and responsible for genome packing. Serological assays are important tools to detect previous exposure to SARS-CoV-2, complement epidemiological studies, vaccine evaluation and also in COVID-19 surveillance. SARS-CoV-2 N (r2N) protein was produced in Escherichia coli, characterized, and the immunological performance was evaluated by enzyme-linked immunosorbent assay (ELISA) and beads-based array immunoassay. r2N protein oligomers were evidenced when it is associated to nucleic acid. Benzonase treatment reduced host nucleic acid associated to r2N protein, but crosslinking assay still demonstrates the presence of higher-order oligomers. Nevertheless, after RNase treatment the higher-order oligomers reduced, and dimer form increased, suggesting RNA contributes to the oligomer formation. Structural analysis revealed nucleic acid did not interfere with the thermal stability of the recombinant protein. Interestingly, nucleic acid was able to prevent r2N protein aggregation even with increasing temperature while the protein benzonase treated begin aggregation process above 55 °C. In immunological characterization, ELISA performed with 233 serum samples presented a sensitivity of 97.44% (95% Confidence Interval, CI, 91.04%, 99.69%) and a specificity of 98.71% (95% CI, 95.42%, 99.84%) while beads-based array immunoassay carried out with 217 samples showed 100% sensitivity and 98.6% specificity. The results exhibited an excellent immunological performance of r2N protein in serologic assays showing that, even in presence of nucleic acid, it can be used as a component of an immunoassay for the sensitive and specific detection of SARS-CoV-2 antibodies.
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Affiliation(s)
- Luãnna Elisa Liebscher Vidal
- Macromolecules Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil.
| | - Janaina Figueira-Mansur
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Patrícia Barbosa Jurgilas
- Macromolecules Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Ana Paula Correa Argondizzo
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Cristiane Pinheiro Pestana
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Fernanda Otaviano Martins
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Haroldo Cid da Silva Junior
- Immunological Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Mariana Miguez
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Bernardo Oliveira Loureiro
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Christiane de Fátima Silva Marques
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Karen Soares Trinta
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Leila Botelho Rodrigues da Silva
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Marcelle Bral de Mello
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Edimilson Domingos da Silva
- Diagnostic Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Renata Chagas Bastos
- Macromolecules Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Gabriela Esteves
- Recombinant Technology Laboratory, Institute of Technology in Immunobiologicals (Bio-Manguinhos), Fundação Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
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49
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Suramin Disturbs the Association of the N-Terminal Domain of SARS-CoV-2 Nucleocapsid Protein with RNA. Molecules 2023; 28:molecules28062534. [PMID: 36985506 PMCID: PMC10051649 DOI: 10.3390/molecules28062534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Suramin was originally used as an antiparasitic drug in clinics. Here, we demonstrate that suramin can bind to the N-terminal domain of SARS-CoV-2 nucleocapsid protein (N-NTD) and disturb its interaction with RNA. The BLI experiments showed that N-NTD interacts suramin with a dissociate constant (Kd = 2.74 μM) stronger than that of N-NTD with ssRNA-16 (Kd = 8.37 μM). Furthermore, both NMR titration experiments and molecular docking analysis suggested that suramin mainly binds to the positively charged cavity between the finger and the palm subdomains of N-NTD, and residues R88, R92, R93, I94, R95, K102 and A156 are crucial for N-NTD capturing suramin. Besides, NMR dynamics experiments showed that suramin-bound N-NTD adopts a more rigid structure, and the loop between β2-β3 exhibits fast motion on the ps-ns timescale, potentially facilitating suramin binding. Our findings not only reveal the molecular basis of suramin disturbing the association of SARS-CoV-2 N-NTD with RNA but also provide valuable structural information for the development of drugs against SARS-CoV-2.
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50
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Ma P, Gu K, Wen R, Li C, Zhou C, Zhao Y, Li H, Lei C, Yang X, Wang H. Guanylate-binding protein 1 restricts avian coronavirus infectious bronchitis virus-infected HD11 cells. Poult Sci 2023; 102:102398. [PMID: 36580763 PMCID: PMC9731647 DOI: 10.1016/j.psj.2022.102398] [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: 08/17/2022] [Revised: 10/23/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
The Infectious Bronchitis Virus (IBV), a coronavirus, is a key avian pathogen that causes acute and highly infectious viral respiratory diseases. IBV is an enveloped, positive-sense RNA virus, and the host factors that restrict infection and replication of the virus remain poorly understood. Guanylate-binding protein 1 (GBP1), an interferon-gamma (IFN-γ)-inducible guanosine triphosphatase (GTPase), is a major player in host immunity and provides defense against viral replication. However, the role of chicken GBP1 (chGBP1) in the IBV-life cycle is not well understood. Therefore, this study aimed to reveal the potential role of IFN-γ-induced chGBP1 in mediating host anti-IBV infection responses. We identified the host restriction factor, chGBP1, in IBV-infected chicken macrophages HD11 cell lines. We showed that chGBP1 was upregulated by treatment with both IFN-γ and IBV in HD11 cells. chGBP1 inhibited IBV replication in a dose-dependent manner and enhanced IFN-γ anti-IBV activity. Importantly, the GTPase domain of chGBP1 played a pivotal role in its anti-IBV activity. Furthermore, chGBP1 interacts with IBV Nucleocapsids protein to degrade IBV-N protein through the autophagy pathway. Taken together, our results demonstrate a critical role of chGBP1 in anti-IBV in macrophages HD11 cells.
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Affiliation(s)
- Peng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Kui Gu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Renqiao Wen
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Changyu Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Yu Zhao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Hao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Xin Yang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China.
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