1
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Babot M, Boulard Y, Agouda S, Pieri L, Fieulaine S, Bressanelli S, Gervais V. Oligomeric assembly of the C-terminal and transmembrane region of SARS-CoV-2 nsp3. J Virol 2024; 98:e0157523. [PMID: 38483167 PMCID: PMC11019948 DOI: 10.1128/jvi.01575-23] [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: 10/16/2023] [Accepted: 02/22/2024] [Indexed: 04/17/2024] Open
Abstract
As for all single-stranded, positive-sense RNA (+RNA) viruses, intracellular RNA synthesis relies on extensive remodeling of host cell membranes that leads to the formation of specialized structures. In the case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus causing COVID-19, endoplasmic reticulum membranes are modified, resulting in the formation of double-membrane vesicles (DMVs), which contain the viral dsRNA intermediate and constitute membrane-bound replication organelles. The non-structural and transmembrane protein nsp3 is a key player in the biogenesis of DMVs and, therefore, represents an interesting antiviral target. However, as an integral transmembrane protein, it is challenging to express for structural biology. The C-terminus of nsp3 encompasses all the membrane-spanning, -interacting, and -remodeling elements. By using a cell-free expression system, we successfully produced the C-terminal region of nsp3 (nsp3C) and reconstituted purified nsp3C into phospholipid nanodiscs, opening the way for structural studies. Negative-stain transmission electron microscopy revealed the presence of nsp3C oligomers very similar to the region abutting and spanning the membrane on the cytosolic side of DMVs in a recent subtomogram average of the SARS-CoV-2 nsp3-4 pore (1). AlphaFold-predicted structural models fit particularly well with our experimental data and support a pore-forming hexameric assembly. Altogether, our data give unprecedented clues to understand the structural organization of nsp3, the principal component that shapes the molecular pore that spans the DMVs and is required for the export of RNA in vivo. IMPORTANCE Membrane remodeling is at the heart of intracellular replication for single-stranded, positive-sense RNA viruses. In the case of coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), this leads to the formation of a network of double-membrane vesicles (DMVs). Targeting DMV biogenesis offers promising prospects for antiviral therapies. This requires a better understanding of the molecular mechanisms and proteins involved. Three non-structural proteins (nsp3, nsp4, and nsp6) direct the intracellular membrane rearrangements upon SARS-CoV-2 infection. All of them contain transmembrane helices. The nsp3 component, the largest and multi-functional protein of the virus, plays an essential role in this process. Aiming to understand its structural organization, we used a cell-free protein synthesis assay to produce and reconstitute the C-terminal part of nsp3 (nsp3C) including transmembrane domains into phospholipid nanodiscs. Our work reveals the oligomeric organization of one key player in the biogenesis of SARS-CoV-2 DMVs, providing basis for the design of future antiviral strategies.
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Affiliation(s)
- Marion Babot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Yves Boulard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Samira Agouda
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Laura Pieri
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Sonia Fieulaine
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Virginie Gervais
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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2
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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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3
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Denker L, Dixon AM. The cell edit: Looking at and beyond non-structural proteins to understand membrane rearrangement in coronaviruses. Arch Biochem Biophys 2024; 752:109856. [PMID: 38104958 DOI: 10.1016/j.abb.2023.109856] [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: 10/08/2023] [Revised: 11/24/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-stranded RNA virus that sits at the centre of the recent global pandemic. As a member of the coronaviridae family of viruses, it shares features such as a very large genome (>30 kb) that is replicated in a purpose-built replication organelle. Biogenesis of the replication organelle requires significant and concerted rearrangement of the endoplasmic reticulum membrane, a job that is carried out by a group of integral membrane non-structural proteins (NSP3, 4 and 6) expressed by the virus along with a host of viral replication enzymes and other factors that support transcription and replication. The primary sites for RNA replication within the replication organelle are double membrane vesicles (DMVs). The small size of DMVs requires generation of high membrane curvature, as well as stabilization of a double-membrane arrangement, but the mechanisms that underlie DMV formation remain elusive. In this review, we discuss recent breakthroughs in our understanding of the molecular basis for membrane rearrangements by coronaviruses. We incorporate established models of NSP3-4 protein-protein interactions to drive double membrane formation, and recent data highlighting the roles of lipid composition and host factor proteins (e.g. reticulons) that influence membrane curvature, to propose a revised model for DMV formation in SARS-CoV-2.
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Affiliation(s)
- Lea Denker
- Warwick Medical School, Biomedical Sciences, University of Warwick, Coventry, CV4 7AL, UK.
| | - Ann M Dixon
- Department of Chemistry, University of Warwick, Coventry, CV4 7SH, UK.
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4
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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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5
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Zimmermann L, Zhao X, Makroczyova J, Wachsmuth-Melm M, Prasad V, Hensel Z, Bartenschlager R, Chlanda P. SARS-CoV-2 nsp3 and nsp4 are minimal constituents of a pore spanning replication organelle. Nat Commun 2023; 14:7894. [PMID: 38036567 PMCID: PMC10689437 DOI: 10.1038/s41467-023-43666-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023] Open
Abstract
Coronavirus replication is associated with the remodeling of cellular membranes, resulting in the formation of double-membrane vesicles (DMVs). A DMV-spanning pore was identified as a putative portal for viral RNA. However, the exact components and the structure of the SARS-CoV-2 DMV pore remain to be determined. Here, we investigate the structure of the DMV pore by in situ cryo-electron tomography combined with subtomogram averaging. We identify non-structural protein (nsp) 3 and 4 as minimal components required for the formation of a DMV-spanning pore, which is dependent on nsp3-4 proteolytic cleavage. In addition, we show that Mac2-Mac3-DPUP-Ubl2 domains are critical for nsp3 oligomerization and crown integrity which influences membrane curvature required for biogenesis of DMVs. Altogether, SARS-CoV-2 nsp3-4 have a dual role by driving the biogenesis of replication organelles and assembly of DMV-spanning pores which we propose here to term replicopores.
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Affiliation(s)
- Liv Zimmermann
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Xiaohan Zhao
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Jana Makroczyova
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Moritz Wachsmuth-Melm
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Vibhu Prasad
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Zach Hensel
- ITQB NOVA, Universidade NOVA de Lisboa, 2780-157, Oeiras, Portugal
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120, Heidelberg, Germany
- Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg partner site, 69120, Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany.
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6
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Li P, Xue B, Schnicker NJ, Wong LYR, Meyerholz DK, Perlman S. Nsp3-N interactions are critical for SARS-CoV-2 fitness and virulence. Proc Natl Acad Sci U S A 2023; 120:e2305674120. [PMID: 37487098 PMCID: PMC10400999 DOI: 10.1073/pnas.2305674120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/22/2023] [Indexed: 07/26/2023] Open
Abstract
SARS-CoV-2, the causative agent of COVID-19 encodes at least 16 nonstructural proteins of variably understood function. Nsp3, the largest nonstructural protein contains several domains, including a SARS-unique domain (SUD), which occurs only in Sarbecovirus. The SUD has a role in preferentially enhancing viral translation. During isolation of mouse-adapted SARS-CoV-2, we isolated an attenuated virus that contained a single mutation in a linker region of nsp3 (nsp3-S676T). The S676T mutation decreased virus replication in cultured cells and primary human cells and in mice. Nsp3-S676T alleviated the SUD translational enhancing ability by decreasing the interaction between two translation factors, Paip1 and PABP1. We also identified a compensatory mutation in the nucleocapsid (N) protein (N-S194L) that restored the virulent phenotype, without directly binding to SUD. Together, these results reveal an aspect of nsp3-N interactions, which impact both SARS-CoV-2 replication and, consequently, pathogenesis.
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Affiliation(s)
- Pengfei Li
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242
| | - Biyun Xue
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242
| | | | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242
| | | | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242
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7
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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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8
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Ni X, Han Y, Zhou R, Zhou Y, Lei J. Structural insights into ribonucleoprotein dissociation by nucleocapsid protein interacting with non-structural protein 3 in SARS-CoV-2. Commun Biol 2023; 6:193. [PMID: 36806252 PMCID: PMC9938351 DOI: 10.1038/s42003-023-04570-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 02/09/2023] [Indexed: 02/20/2023] Open
Abstract
The coronavirus nucleocapsid (N) protein interacts with non-structural protein 3 (Nsp3) to facilitate viral RNA synthesis and stabilization. However, structural information on the N-Nsp3 complex is limited. Here, we report a 2.6 Å crystal structure of the N-terminal domain (NTD) of the N protein in complex with the ubiquitin-like domain 1 (Ubl1) of Nsp3 in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). One NTD and two Ubl1s formed a stable heterotrimer. We performed mutational analysis to reveal the key residues for this interaction. We confirmed the colocalization of SARS-CoV-2 N and Nsp3 in Huh-7 cells. N-Ubl1 interaction also exists in SARS-CoV and Middle East respiratory syndrome coronavirus. We found that SARS-CoV-2 Ubl1 competes with RNA to bind N protein in a dose-dependent manner. Based on our results, we propose a model for viral ribonucleoprotein dissociation through N protein binding to Ubl1 of Nsp3.
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Affiliation(s)
- Xincheng Ni
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yinze Han
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Renjie Zhou
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yanmei Zhou
- grid.412901.f0000 0004 1770 1022National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Jian Lei
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China. .,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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9
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Wu W, Cheng Y, Zhou H, Sun C, Zhang S. The SARS-CoV-2 nucleocapsid protein: its role in the viral life cycle, structure and functions, and use as a potential target in the development of vaccines and diagnostics. Virol J 2023; 20:6. [PMID: 36627683 PMCID: PMC9831023 DOI: 10.1186/s12985-023-01968-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) continues to take a heavy toll on personal health, healthcare systems, and economies around the globe. Scientists are expending tremendous effort to develop diagnostic technologies for detecting positive infections within the shortest possible time, and vaccines and drugs specifically for the prevention and treatment of COVID-19 disease. At the same time, emerging novel variants have raised serious concerns about vaccine efficacy. The SARS-CoV-2 nucleocapsid (N) protein plays an important role in the coronavirus life cycle, and participates in various vital activities after virus invasion. It has attracted a large amount of attention for vaccine and drug development. Here, we summarize the latest research of the N protein, including its role in the SARS-CoV-2 life cycle, structure and function, and post-translational modifications in addition to its involvement in liquid-liquid phase separation (LLPS) and use as a basis for the development of vaccines and diagnostic techniques.
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Affiliation(s)
- Wenbing Wu
- grid.410578.f0000 0001 1114 4286Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000 China
| | - Ying Cheng
- grid.410578.f0000 0001 1114 4286Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000 China
| | - Hong Zhou
- grid.410578.f0000 0001 1114 4286Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000 China
| | - Changzhen Sun
- grid.410578.f0000 0001 1114 4286Drug Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000 China
| | - Shujun Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China.
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10
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Carlson CR, Adly AN, Bi M, Howard CJ, Frost A, Cheng Y, Morgan DO. Reconstitution of the SARS-CoV-2 ribonucleosome provides insights into genomic RNA packaging and regulation by phosphorylation. J Biol Chem 2022; 298:102560. [PMID: 36202211 PMCID: PMC9529352 DOI: 10.1016/j.jbc.2022.102560] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/06/2022] Open
Abstract
The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 is responsible for compaction of the ∼30-kb RNA genome in the ∼90-nm virion. Previous studies suggest that each virion contains 35 to 40 viral ribonucleoprotein (vRNP) complexes, or ribonucleosomes, arrayed along the genome. There is, however, little mechanistic understanding of the vRNP complex. Here, we show that N protein, when combined in vitro with short fragments of the viral genome, forms 15-nm particles similar to the vRNP structures observed within virions. These vRNPs depend on regions of N protein that promote protein-RNA and protein-protein interactions. Phosphorylation of N protein in its disordered serine/arginine region weakens these interactions to generate less compact vRNPs. We propose that unmodified N protein binds structurally diverse regions in genomic RNA to form compact vRNPs within the nucleocapsid, while phosphorylation alters vRNP structure to support other N protein functions in viral transcription.
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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
| | - Conor J Howard
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Adam Frost
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, California, USA.
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11
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Johnson BA, Zhou Y, Lokugamage KG, Vu MN, Bopp N, Crocquet-Valdes PA, Kalveram B, Schindewolf C, Liu Y, Scharton D, Plante JA, Xie X, Aguilar P, Weaver SC, Shi PY, Walker DH, Routh AL, Plante KS, Menachery VD. Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. PLoS Pathog 2022; 18:e1010627. [PMID: 35728038 PMCID: PMC9275689 DOI: 10.1371/journal.ppat.1010627] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/12/2022] [Accepted: 05/30/2022] [Indexed: 12/27/2022] Open
Abstract
While SARS-CoV-2 continues to adapt for human infection and transmission, genetic variation outside of the spike gene remains largely unexplored. This study investigates a highly variable region at residues 203-205 in the SARS-CoV-2 nucleocapsid protein. Recreating a mutation found in the alpha and omicron variants in an early pandemic (WA-1) background, we find that the R203K+G204R mutation is sufficient to enhance replication, fitness, and pathogenesis of SARS-CoV-2. The R203K+G204R mutant corresponds with increased viral RNA and protein both in vitro and in vivo. Importantly, the R203K+G204R mutation increases nucleocapsid phosphorylation and confers resistance to inhibition of the GSK-3 kinase, providing a molecular basis for increased virus replication. Notably, analogous alanine substitutions at positions 203+204 also increase SARS-CoV-2 replication and augment phosphorylation, suggesting that infection is enhanced through ablation of the ancestral 'RG' motif. Overall, these results demonstrate that variant mutations outside spike are key components in SARS-CoV-2's continued adaptation to human infection.
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Affiliation(s)
- Bryan A Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yiyang Zhou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kumari G Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Michelle N Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Nathen Bopp
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | | | - Birte Kalveram
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Craig Schindewolf
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Dionna Scharton
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Patricia Aguilar
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Drug Discovery, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - David H Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
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12
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Carlson CR, Adly AN, Bi M, Cheng Y, Morgan DO. Reconstitution of the SARS-CoV-2 ribonucleosome provides insights into genomic RNA packaging and regulation by phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.05.23.493138. [PMID: 35664996 PMCID: PMC9164447 DOI: 10.1101/2022.05.23.493138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The nucleocapsid (N) protein of coronaviruses is responsible for compaction of the ∼30-kb RNA genome in the ∼100-nm virion. Cryo-electron tomography suggests that each virion contains 35-40 viral ribonucleoprotein (vRNP) complexes, or ribonucleosomes, arrayed along the genome. There is, however, little mechanistic understanding of the vRNP complex. Here, we show that N protein, when combined with viral RNA fragments in vitro, forms cylindrical 15-nm particles similar to the vRNP structures observed within coronavirus virions. These vRNPs form in the presence of stem-loop-containing RNA and depend on regions of N protein that promote protein-RNA and protein-protein interactions. Phosphorylation of N protein in its disordered serine/arginine (SR) region weakens these interactions and disrupts vRNP assembly. We propose that unmodified N binds stem-loop-rich regions in genomic RNA to form compact vRNP complexes within the nucleocapsid, while phosphorylated N maintains uncompacted viral RNA to promote the protein's transcriptional function.
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Affiliation(s)
| | - Armin N. Adly
- Department of Physiology, University of California, San Francisco CA 94143
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco CA 94143
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco CA 94143
| | - David O. Morgan
- Department of Physiology, University of California, San Francisco CA 94143
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13
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Nishikiori M, den Boon JA, Unchwaniwala N, Ahlquist P. Crowning Touches in Positive-Strand RNA Virus Genome Replication Complex Structure and Function. Annu Rev Virol 2022; 9:193-212. [PMID: 35610038 DOI: 10.1146/annurev-virology-092920-021307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Positive-strand RNA viruses, the largest genetic class of eukaryotic viruses, include coronaviruses and many other established and emerging pathogens. A major target for understanding and controlling these viruses is their genome replication, which occurs in virus-induced membrane vesicles that organize replication steps and protect double-stranded RNA intermediates from innate immune recognition. The structure of these complexes has been greatly illuminated by recent cryo-electron microscope tomography studies with several viruses. One key finding in diverse systems is the organization of crucial viral RNA replication factors in multimeric rings or crowns that among other functions serve as exit channels gating release of progeny genomes to the cytosol for translation and encapsidation. Emerging results suggest that these crowns serve additional important purposes in replication complex assembly, function, and interaction with downstream processes such as encapsidation. The findings provide insights into viral function and evolution and new bases for understanding, controlling, and engineering positive-strand RNA viruses. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Masaki Nishikiori
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Johan A den Boon
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nuruddin Unchwaniwala
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Current affiliation: Assembly Biosciences, Inc., South San Francisco, California, USA
| | - Paul Ahlquist
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Wisconsin, USA; .,Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
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14
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Zhao H, Nguyen A, Wu D, Li Y, Hassan SA, Chen J, Shroff H, Piszczek G, Schuck P. Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. PNAS NEXUS 2022; 1:pgac049. [PMID: 35783502 PMCID: PMC9235412 DOI: 10.1093/pnasnexus/pgac049] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/19/2022] [Indexed: 02/06/2023]
Abstract
Worldwide SARS-CoV-2 sequencing efforts track emerging mutations in its spike protein, as well as characteristic mutations in other viral proteins. Besides their epidemiological importance, the observed SARS-CoV-2 sequences present an ensemble of viable protein variants, and thereby a source of information on viral protein structure and function. Charting the mutational landscape of the nucleocapsid (N) protein that facilitates viral assembly, we observe variability exceeding that of the spike protein, with more than 86% of residues that can be substituted, on average by three to four different amino acids. However, mutations exhibit an uneven distribution that tracks known structural features but also reveals highly protected stretches of unknown function. One of these conserved regions is in the central disordered linker proximal to the N-G215C mutation that has become dominant in the Delta variant, outcompeting G215 variants without further spike or N-protein substitutions. Structural models suggest that the G215C mutation stabilizes conserved transient helices in the disordered linker serving as protein-protein interaction interfaces. Comparing Delta variant N-protein to its ancestral version in biophysical experiments, we find a significantly more compact and less disordered structure. N-G215C exhibits substantially stronger self-association, shifting the unliganded protein from a dimeric to a tetrameric oligomeric state, which leads to enhanced coassembly with nucleic acids. This suggests that the sequence variability of N-protein is mirrored by high plasticity of N-protein biophysical properties, which we hypothesize can be exploited by SARS-CoV-2 to achieve greater efficiency of viral assembly, and thereby enhanced infectivity.
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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
| | - Ai Nguyen
- 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
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, 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
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hari Shroff
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of High Resolution Optical Imaging, 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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15
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Zhao H, Nguyen A, Wu D, Li Y, Hassan SA, Chen J, Shroff H, Piszczek G, Schuck P. Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.08.479556. [PMID: 35169797 PMCID: PMC8845419 DOI: 10.1101/2022.02.08.479556] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Worldwide SARS-CoV-2 sequencing efforts track emerging mutations in its spike protein, as well as characteristic mutations in other viral proteins. Besides their epidemiological importance, the observed SARS-CoV-2 sequences present an ensemble of viable protein variants, and thereby a source of information on viral protein structure and function. Charting the mutational landscape of the nucleocapsid (N) protein that facilitates viral assembly, we observe variability exceeding that of the spike protein, with more than 86% of residues that can be substituted, on average by 3-4 different amino acids. However, mutations exhibit an uneven distribution that tracks known structural features but also reveals highly protected stretches of unknown function. One of these conserved regions is in the central disordered linker proximal to the N-G215C mutation that has become dominant in the Delta variant, outcompeting G215 variants without further spike or N-protein substitutions. Structural models suggest that the G215C mutation stabilizes conserved transient helices in the disordered linker serving as protein-protein interaction interfaces. Comparing Delta variant N-protein to its ancestral version in biophysical experiments, we find a significantly more compact and less disordered structure. N-G215C exhibits substantially stronger self-association, shifting the unliganded protein from a dimeric to a tetrameric oligomeric state, which leads to enhanced co-assembly with nucleic acids. This suggests that the sequence variability of N-protein is mirrored by high plasticity of N-protein biophysical properties, which we hypothesize can be exploited by SARS-CoV-2 to achieve greater efficiency of viral assembly, and thereby enhanced infectivity.
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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
| | - Ai Nguyen
- 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
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, 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
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hari Shroff
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of High Resolution Optical Imaging, 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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16
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Lindenbach BD. Reinventing positive-strand RNA virus reverse genetics. Adv Virus Res 2022; 112:1-29. [PMID: 35840179 PMCID: PMC9273853 DOI: 10.1016/bs.aivir.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Reverse genetics is the prospective analysis of how genotype determines phenotype. In a typical experiment, a researcher alters a viral genome, then observes the phenotypic outcome. Among RNA viruses, this approach was first applied to positive-strand RNA viruses in the mid-1970s and over nearly 50 years has become a powerful and widely used approach for dissecting the mechanisms of viral replication and pathogenesis. During this time the global health importance of two virus groups, flaviviruses (genus Flavivirus, family Flaviviridae) and betacoronaviruses (genus Betacoronavirus, subfamily Orthocoronavirinae, family Coronaviridae), have dramatically increased, yet these viruses have genomes that are technically challenging to manipulate. As a result, several new techniques have been developed to overcome these challenges. Here I briefly review key historical aspects of positive-strand RNA virus reverse genetics, describe some recent reverse genetic innovations, particularly as applied to flaviviruses and coronaviruses, and discuss their benefits and limitations within the larger context of rigorous genetic analysis.
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17
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Johnson BA, Zhou Y, Lokugamage KG, Vu MN, Bopp N, Crocquet-Valdes PA, Schindewolf C, Liu Y, Scharton D, Plante JA, Xie X, Aguilar P, Weaver SC, Shi PY, Walker DH, Routh AL, Plante KS, Menachery VD. Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34671771 PMCID: PMC8528077 DOI: 10.1101/2021.10.14.464390] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
While SARS-CoV-2 continues to adapt for human infection and transmission, genetic variation outside of the spike gene remains largely unexplored. This study investigates a highly variable region at residues 203–205 in the SARS-CoV-2 nucleocapsid protein. Recreating a mutation found in the alpha and omicron variants in an early pandemic (WA-1) background, we find that the R203K+G204R mutation is sufficient to enhance replication, fitness, and pathogenesis of SARS-CoV-2. The R203K+G204R mutant corresponds with increased viral RNA and protein both in vitro and in vivo. Importantly, the R203K+G204R mutation increases nucleocapsid phosphorylation and confers resistance to inhibition of the GSK-3 kinase, providing a molecular basis for increased virus replication. Notably, analogous alanine substitutions at positions 203+204 also increase SARS-CoV-2 replication and augment phosphorylation, suggesting that infection is enhanced through ablation of the ancestral ‘RG’ motif. Overall, these results demonstrate that variant mutations outside spike are key components in SARS-CoV-2’s continued adaptation to human infection.
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