1
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Hardy K, Lutz M, Takimoto T. Human coronavirus NL63 nsp1 induces degradation of RNA polymerase II to inhibit host protein synthesis. PLoS Pathog 2024; 20:e1012329. [PMID: 38900816 PMCID: PMC11218958 DOI: 10.1371/journal.ppat.1012329] [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: 02/14/2024] [Revised: 07/02/2024] [Accepted: 06/09/2024] [Indexed: 06/22/2024] Open
Abstract
Coronavirus (CoV) nonstructural protein 1 (nsp1) is considered a pathogenic factor due to its ability to inhibit host antiviral responses by inducing general shutoff of host protein synthesis. Nsp1 is expressed by α- and β-CoVs, but its functions and strategies to induce host shutoff are not fully elucidated. We compared the nsp1s from two β-CoVs (SARS-CoV and SARS-CoV-2) and two α-CoVs (NL63 and 229E) and found that NL63 nsp1 has the strongest shutoff activity. Unlike SARS-CoV nsp1s, which bind to 40S ribosomes and block translation of cellular mRNA, NL63 nsp1 did not inhibit translation of mRNAs transfected into cells. Instead, NL63 nsp1 localized to the nucleus and specifically inhibited transcription of genes under an RNA polymerase II (RNAPII) promoter. Further analysis revealed that NL63 nsp1 induces degradation of the largest subunit of RNAPII, Rpb1. This degradation was detected regardless of the phosphorylation state of Rpb1 and was blocked by the proteasome inhibitor MG132. We also found that Rpb1 was ubiquitinated in NL63-infected cells, and inhibition of ubiquitination by a ubiquitin activating enzyme inhibitor (TAK243) prevented degradation of Rpb1 in virus-infected cells. These data reveal an unrecognized strategy of host shutoff by human α-CoV NL63: targeting host transcription by inducing Rpb1 degradation to prevent host protein expression. Our study indicates that viruses within the same family can use completely distinct mechanisms to regulate host antiviral responses.
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Affiliation(s)
- Kala Hardy
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Michael Lutz
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Toru Takimoto
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
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2
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Shehata SI, Watkins JM, Burke JM, Parker R. Mechanisms and consequences of mRNA destabilization during viral infections. Virol J 2024; 21:38. [PMID: 38321453 PMCID: PMC10848536 DOI: 10.1186/s12985-024-02305-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
During viral infection there is dynamic interplay between the virus and the host to regulate gene expression. In many cases, the host induces the expression of antiviral genes to combat infection, while the virus uses "host shut-off" systems to better compete for cellular resources and to limit the induction of the host antiviral response. Viral mechanisms for host shut-off involve targeting translation, altering host RNA processing, and/or inducing the degradation of host mRNAs. In this review, we discuss the diverse mechanisms viruses use to degrade host mRNAs. In addition, the widespread degradation of host mRNAs can have common consequences including the accumulation of RNA binding proteins in the nucleus, which leads to altered RNA processing, mRNA export, and changes to transcription.
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Affiliation(s)
- Soraya I Shehata
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J Monty Watkins
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, USA
| | - James M Burke
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
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3
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Karousis ED, Schubert K, Ban N. Coronavirus takeover of host cell translation and intracellular antiviral response: a molecular perspective. EMBO J 2024; 43:151-167. [PMID: 38200146 PMCID: PMC10897431 DOI: 10.1038/s44318-023-00019-8] [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: 06/01/2023] [Revised: 11/01/2023] [Accepted: 11/24/2023] [Indexed: 01/12/2024] Open
Abstract
Coronaviruses are a group of related RNA viruses that cause respiratory diseases in humans and animals. Understanding the mechanisms of translation regulation during coronaviral infections is critical for developing antiviral therapies and preventing viral spread. Translation of the viral single-stranded RNA genome in the host cell cytoplasm is an essential step in the life cycle of coronaviruses, which affects the cellular mRNA translation landscape in many ways. Here we discuss various viral strategies of translation control, including how members of the Betacoronavirus genus shut down host cell translation and suppress host innate immune functions, as well as the role of the viral non-structural protein 1 (Nsp1) in the process. We also outline the fate of viral RNA, considering stress response mechanisms triggered in infected cells, and describe how unique viral RNA features contribute to programmed ribosomal -1 frameshifting, RNA editing, and translation shutdown evasion.
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Affiliation(s)
- Evangelos D Karousis
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Katharina Schubert
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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4
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Devarkar SC, Vetick M, Balaji S, Lomakin IB, Yang L, Jin D, Gilbert WV, Chen S, Xiong Y. Structural basis for translation inhibition by MERS-CoV Nsp1 reveals a conserved mechanism for betacoronaviruses. Cell Rep 2023; 42:113156. [PMID: 37733586 DOI: 10.1016/j.celrep.2023.113156] [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: 06/16/2023] [Revised: 08/13/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023] Open
Abstract
All betacoronaviruses (β-CoVs) encode non-structural protein 1 (Nsp1), an essential pathogenicity factor that potently restricts host gene expression. Among the β-CoV family, MERS-CoV is the most distantly related member to SARS-CoV-2, and the mechanism for host translation inhibition by MERS-CoV Nsp1 remains controversial. Herein, we show that MERS-CoV Nsp1 directly interacts with the 40S ribosomal subunit. Using cryogenic electron microscopy (cryo-EM), we report a 2.6-Å structure of the MERS-CoV Nsp1 bound to the human 40S ribosomal subunit. The extensive interactions between C-terminal domain of MERS-CoV Nsp1 and the mRNA entry channel of the 40S ribosomal subunit are critical for its translation inhibition function. This mechanism of MERS-CoV Nsp1 is strikingly similar to SARS-CoV and SARS-CoV-2 Nsp1, despite modest sequence conservation. Our results reveal that the mechanism of host translation inhibition is conserved across β-CoVs and highlight a potential therapeutic target for the development of antivirals that broadly restrict β-CoVs.
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Affiliation(s)
- Swapnil C Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Michael Vetick
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Shravani Balaji
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Ivan B Lomakin
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Luojia Yang
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Danni Jin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Wendy V Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Sidi Chen
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
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5
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Maurina SF, O'Sullivan JP, Sharma G, Pineda Rodriguez DC, MacFadden A, Cendali F, Henen MA, Vögeli B, Kieft JS, Glasgow A, Steckelberg AL. An Evolutionarily Conserved Strategy for Ribosome Binding and Host Translation Inhibition by β-coronavirus Non-structural Protein 1. J Mol Biol 2023; 435:168259. [PMID: 37660941 PMCID: PMC10543557 DOI: 10.1016/j.jmb.2023.168259] [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: 06/12/2023] [Revised: 08/15/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
An important pathogenicity factor of SARS-CoV-2 and related coronaviruses is Non-structural protein 1 (Nsp1), which suppresses host gene expression and stunts antiviral signaling. SARS-CoV-2 Nsp1 binds the ribosome to inhibit translation through mRNA displacement and induces degradation of host mRNAs. Here we show that Nsp1-dependent host shutoff is conserved in diverse coronaviruses, but only Nsp1 from β-Coronaviruses (β-CoV) inhibits translation through ribosome binding. The C-terminal domain (CTD) of all β-CoV Nsp1s confers high-affinity ribosome binding despite low sequence conservation. Modeling of interactions of four Nsp1s with the ribosome identified the few absolutely conserved amino acids that, together with an overall conservation in surface charge, form the β-CoV Nsp1 ribosome-binding domain. Contrary to previous models, the Nsp1 ribosome-binding domain is an inefficient translation inhibitor. Instead, the Nsp1-CTD likely functions by recruiting Nsp1's N-terminal "effector" domain. Finally, we show that a cis-acting viral RNA element has co-evolved to fine-tune SARS-CoV-2 Nsp1 function, but does not provide similar protection against Nsp1 from related viruses. Together, our work provides new insight into the diversity and conservation of ribosome-dependent host-shutoff functions of Nsp1, knowledge that could aid future efforts in pharmacological targeting of Nsp1 from SARS-CoV-2 and related human-pathogenic β-CoVs. Our study also exemplifies how comparing highly divergent Nsp1 variants can help to dissect the different modalities of this multi-functional viral protein.
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Affiliation(s)
- Stephanie F Maurina
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - John P O'Sullivan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Geetika Sharma
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Francesca Cendali
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA; RNA BioScience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Anum Glasgow
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Anna-Lena Steckelberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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6
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Schubert K, Karousis ED, Ban I, Lapointe CP, Leibundgut M, Bäumlin E, Kummerant E, Scaiola A, Schönhut T, Ziegelmüller J, Puglisi JD, Mühlemann O, Ban N. Universal features of Nsp1-mediated translational shutdown by coronaviruses. Mol Cell 2023; 83:3546-3557.e8. [PMID: 37802027 PMCID: PMC10575594 DOI: 10.1016/j.molcel.2023.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/16/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
Nonstructural protein 1 (Nsp1) produced by coronaviruses inhibits host protein synthesis. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Nsp1 C-terminal domain was shown to bind the ribosomal mRNA channel to inhibit translation, but it is unclear whether this mechanism is broadly used by coronaviruses, whether the Nsp1 N-terminal domain binds the ribosome, or how Nsp1 allows viral RNAs to be translated. Here, we investigated Nsp1 from SARS-CoV-2, Middle East respiratory syndrome coronavirus (MERS-CoV), and Bat-Hp-CoV coronaviruses using structural, biophysical, and biochemical experiments, revealing a conserved role for the C-terminal domain. Additionally, the N-terminal domain of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit, where it would prevent mRNA and eIF1A accommodation. Structure-based experiments demonstrated the importance of decoding center interactions in all three coronaviruses and showed that the same regions of Nsp1 are necessary for the selective translation of viral RNAs. Our results provide a mechanistic framework to understand how Nsp1 controls preferential translation of viral RNAs.
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Affiliation(s)
- Katharina Schubert
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8049, Switzerland
| | - Evangelos D Karousis
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland; Multidisciplinary Center for Infectious Diseases, University of Bern, Bern 3012, Switzerland.
| | - Ivo Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8049, Switzerland
| | - Christopher P Lapointe
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8049, Switzerland
| | - Emilie Bäumlin
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland; Multidisciplinary Center for Infectious Diseases, University of Bern, Bern 3012, Switzerland
| | - Eric Kummerant
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8049, Switzerland
| | - Alain Scaiola
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8049, Switzerland
| | - Tanja Schönhut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8049, Switzerland
| | - Jana Ziegelmüller
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8049, Switzerland.
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7
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Tamayo-Ordóñez MC, Rosas-García NM, Ayil-Gutiérrez BA, Bello-López JM, Tamayo-Ordóñez FA, Anguebes-Franseschi F, Damas-Damas S, Tamayo-Ordóñez YDJ. Non-Structural Proteins (Nsp): A Marker for Detection of Human Coronavirus Families. Pathogens 2023; 12:1185. [PMID: 37764993 PMCID: PMC10537875 DOI: 10.3390/pathogens12091185] [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: 07/29/2023] [Revised: 09/06/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
SARS-CoV-2 was the cause of the global pandemic that caused a total of 14.9 million deaths during the years 2020 and 2021, according to the WHO. The virus presents a mutation rate between 10-5 and 10-3 substitutions per nucleotide site per cell infection (s/n/c). Due to this, studies aimed at knowing the evolution of this virus could help us to foresee (through the future development of new detection strategies and vaccines that prevent the infection of this virus in human hosts) that a pandemic caused by this virus will be generated again. In this research, we performed a functional annotation and identification of changes in Nsp (non-structural proteins) domains in the coronavirus genome. The comparison of the 13 selected coronavirus pangenomes demonstrated a total of 69 protein families and 57 functions associated with the structural domain's differentials between genomes. A marked evolutionary conservation of non-structural proteins was observed. This allowed us to identify and classify highly pathogenic human coronaviruses into alpha, beta, gamma, and delta groups. The designed Nsp cluster provides insight into the trajectory of SARS-CoV-2, demonstrating that it continues to evolve rapidly. An evolutionary marker allows us to discriminate between phylogenetically divergent groups, viral genotypes, and variants between the alpha and betacoronavirus genera. These types of evolutionary studies provide a window of opportunity to use these Nsp as targets of viral therapies.
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Affiliation(s)
- María Concepción Tamayo-Ordóñez
- Laboratorio de Ingeniería Genética, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Saltillo 25280, Coahuila, Mexico;
| | - Ninfa María Rosas-García
- Laboratorio de Biotecnología Ambiental del Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Tamaulipas, Mexico
| | - Benjamín Abraham Ayil-Gutiérrez
- CONAHCYT-Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Biotecnología Vegetal, Reynosa 88710, Tamaulipas, Mexico
| | - Juan Manuel Bello-López
- División de Investigación, Hospital Juárez de México, Ciudad de México 07760, Campeche, Mexico
| | - Francisco Alberto Tamayo-Ordóñez
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico (S.D.-D.)
| | - Francisco Anguebes-Franseschi
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico (S.D.-D.)
| | - Siprian Damas-Damas
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico (S.D.-D.)
| | - Yahaira de Jesús Tamayo-Ordóñez
- Laboratorio de Biotecnología Ambiental del Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Tamaulipas, Mexico
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8
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Abaeva IS, Arhab Y, Miścicka A, Hellen CUT, Pestova TV. In vitro reconstitution of SARS-CoV-2 Nsp1-induced mRNA cleavage reveals the key roles of the N-terminal domain of Nsp1 and the RRM domain of eIF3g. Genes Dev 2023; 37:844-860. [PMID: 37821106 PMCID: PMC10620056 DOI: 10.1101/gad.350829.123] [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: 05/25/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023]
Abstract
SARS CoV-2 nonstructural protein 1 (Nsp1) is the major pathogenesis factor that inhibits host translation using a dual strategy of impairing initiation and inducing endonucleolytic cleavage of cellular mRNAs. To investigate the mechanism of cleavage, we reconstituted it in vitro on β-globin, EMCV IRES, and CrPV IRES mRNAs that use unrelated initiation mechanisms. In all instances, cleavage required Nsp1 and only canonical translational components (40S subunits and initiation factors), arguing against involvement of a putative cellular RNA endonuclease. Requirements for initiation factors differed for these mRNAs, reflecting their requirements for ribosomal attachment. Cleavage of CrPV IRES mRNA was supported by a minimal set of components consisting of 40S subunits and eIF3g's RRM domain. The cleavage site was located in the coding region 18 nt downstream from the mRNA entrance, indicating that cleavage occurs on the solvent side of the 40S subunit. Mutational analysis identified a positively charged surface on Nsp1's N-terminal domain (NTD) and a surface above the mRNA-binding channel on eIF3g's RRM domain that contain residues essential for cleavage. These residues were required for cleavage on all three mRNAs, highlighting general roles of the Nsp1 NTD and eIF3g's RRM domain in cleavage per se, irrespective of the mode of ribosomal attachment.
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Affiliation(s)
- Irina S Abaeva
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Yani Arhab
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Anna Miścicka
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
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9
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Maurina SF, O’Sullivan JP, Sharma G, Pineda Rodriguez DC, MacFadden A, Cendali F, Henen MA, Kieft JS, Glasgow A, Steckelberg AL. An evolutionarily conserved strategy for ribosome binding and inhibition by β-coronavirus non-structural protein 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544141. [PMID: 37333070 PMCID: PMC10274807 DOI: 10.1101/2023.06.07.544141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
An important pathogenicity factor of SARS-CoV-2 and related coronaviruses is Nsp1, which suppresses host gene expression and stunts antiviral signaling. SARS-CoV-2 Nsp1 binds the ribosome to inhibit translation through mRNA displacement and induces degradation of host mRNAs through an unknown mechanism. Here we show that Nsp1-dependent host shutoff is conserved in diverse coronaviruses, but only Nsp1 from β-CoV inhibits translation through ribosome binding. The C-terminal domain of all β-CoV Nsp1s confers high-affinity ribosome-binding despite low sequence conservation. Modeling of interactions of four Nsp1s to the ribosome identified few absolutely conserved amino acids that, together with an overall conservation in surface charge, form the β-CoV Nsp1 ribosome-binding domain. Contrary to previous models, the Nsp1 ribosome-binding domain is an inefficient translation inhibitor. Instead, the Nsp1-CTD likely functions by recruiting Nsp1's N-terminal "effector" domain. Finally, we show that a viral cis -acting RNA element has co-evolved to fine-tune SARS-CoV-2 Nsp1 function, but does not provide similar protection against Nsp1 from related viruses. Together, our work provides new insight into the diversity and conservation of ribosome-dependent host-shutoff functions of Nsp1, knowledge that could aide future efforts in pharmacological targeting of Nsp1 from SARS-CoV-2, but also related human-pathogenic β-coronaviruses. Our study also exemplifies how comparing highly divergent Nsp1 variants can help to dissect the different modalities of this multi-functional viral protein.
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Affiliation(s)
- Stephanie F. Maurina
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - John P. O’Sullivan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Geetika Sharma
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Francesca Cendali
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Morkos A. Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jeffrey S. Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA BioScience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
- Current address: New York Structural Biology Center, New York, NY, USA
| | - Anum Glasgow
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Anna-Lena Steckelberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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10
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Mishra N, Kant R, Leung DW, Gross ML, Amarasinghe GK. Biochemical and HDX Mass Spectral Characterization of the SARS-CoV-2 Nsp1 Protein. Biochemistry 2023; 62:1744-1754. [PMID: 37205707 PMCID: PMC10228561 DOI: 10.1021/acs.biochem.3c00035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/29/2023] [Indexed: 05/21/2023]
Abstract
A major challenge in defining the pathophysiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is to better understand virally encoded multifunctional proteins and their interactions with host factors. Among the many proteins encoded by the positive-sense, single-stranded RNA genome, nonstructural protein 1 (Nsp1) stands out due to its impact on several stages of the viral replication cycle. Nsp1 is the major virulence factor that inhibits mRNA translation. Nsp1 also promotes host mRNA cleavage to modulate host and viral protein expression and to suppress host immune functions. To better define how this multifunctional protein can facilitate distinct functions, we characterize SARS-CoV-2 Nsp1 by using a combination of biophysical techniques, including light scattering, circular dichroism, hydrogen/deuterium exchange mass spectrometry (HDX-MS), and temperature-dependent HDX-MS. Our results reveal that the SARS-CoV-2 Nsp1 N- and C-terminus are unstructured in solution, and in the absence of other proteins, the C-terminus has an increased propensity to adopt a helical conformation. In addition, our data indicate that a short helix exists near the C-terminus and adjoins the region that binds the ribosome. Together, these findings provide insights into the dynamic nature of Nsp1 that impacts its functions during infection. Furthermore, our results will inform efforts to understand SARS-CoV-2 infection and antiviral development.
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Affiliation(s)
- Nawneet Mishra
- Department
of Pathology and Immunology, Washington
University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
| | - Ravi Kant
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Daisy W. Leung
- Department
of Pathology and Immunology, Washington
University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
- Department
of Medicine, Washington University School
of Medicine, St. Louis, Missouri 63110, United States
| | - Michael L. Gross
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Gaya K. Amarasinghe
- Department
of Pathology and Immunology, Washington
University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
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11
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Dyson HJ. Vital for Viruses: Intrinsically Disordered Proteins. J Mol Biol 2023; 435:167860. [PMID: 37330280 PMCID: PMC10656058 DOI: 10.1016/j.jmb.2022.167860] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 06/19/2023]
Abstract
Viruses infect all kingdoms of life; their genomes vary from DNA to RNA and in size from 2kB to 1 MB or more. Viruses frequently employ disordered proteins, that is, protein products of virus genes that do not themselves fold into independent three-dimensional structures, but rather, constitute a versatile molecular toolkit to accomplish a range of functions necessary for viral infection, assembly, and proliferation. Interestingly, disordered proteins have been discovered in almost all viruses so far studied, whether the viral genome consists of DNA or RNA, and whatever the configuration of the viral capsid or other outer covering. In this review, I present a wide-ranging set of stories illustrating the range of functions of IDPs in viruses. The field is rapidly expanding, and I have not tried to include everything. What is included is meant to be a survey of the variety of tasks that viruses accomplish using disordered proteins.
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Affiliation(s)
- H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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12
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Schubert K, Karousis ED, Ban I, Lapointe CP, Leibundgut M, Bäumlin E, Kummerant E, Scaiola A, Schönhut T, Ziegelmüller J, Puglisi JD, Mühlemann O, Ban N. Universal features of Nsp1-mediated translational shutdown by coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543022. [PMID: 37398176 PMCID: PMC10312502 DOI: 10.1101/2023.05.31.543022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Nonstructural protein 1 (Nsp1) produced by coronaviruses shuts down host protein synthesis in infected cells. The C-terminal domain of SARS-CoV-2 Nsp1 was shown to bind to the small ribosomal subunit to inhibit translation, but it is not clear whether this mechanism is broadly used by coronaviruses, whether the N-terminal domain of Nsp1 binds the ribosome, or how Nsp1 specifically permits translation of viral mRNAs. Here, we investigated Nsp1 from three representative Betacoronaviruses - SARS-CoV-2, MERS-CoV, and Bat-Hp-CoV - using structural, biophysical, and biochemical assays. We revealed a conserved mechanism of host translational shutdown across the three coronaviruses. We further demonstrated that the N-terminal domain of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit, where it would prevent mRNA and eIF1A binding. Structure-based biochemical experiments identified a conserved role of these inhibitory interactions in all three coronaviruses and showed that the same regions of Nsp1 are responsible for the preferential translation of viral mRNAs. Our results provide a mechanistic framework to understand how Betacoronaviruses overcome translational inhibition to produce viral proteins.
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Affiliation(s)
- Katharina Schubert
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Evangelos D Karousis
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Ivo Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Christopher P Lapointe
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Emilie Bäumlin
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Eric Kummerant
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Alain Scaiola
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Tanja Schönhut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Jana Ziegelmüller
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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13
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Abaeva IS, Arhab Y, Miścicka A, Hellen CUT, Pestova TV. In vitro reconstitution of SARS CoV-2 Nsp1-induced mRNA cleavage reveals the key roles of the N-terminal domain of Nsp1 and the RRM domain of eIF3g. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542379. [PMID: 37292671 PMCID: PMC10245999 DOI: 10.1101/2023.05.25.542379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
SARS CoV-2 nonstructural protein 1 (Nsp1) is the major pathogenesis factor that inhibits host translation using a dual strategy of impairing initiation and inducing endonucleolytic cleavage of cellular mRNAs. To investigate the mechanism of cleavage, we reconstituted it in vitro on β-globin, EMCV IRES and CrPV IRES mRNAs that use unrelated initiation mechanisms. In all instances, cleavage required Nsp1 and only canonical translational components (40S subunits and initiation factors), arguing against involvement of a putative cellular RNA endonuclease. Requirements for initiation factors differed for these mRNAs, reflecting their requirements for ribosomal attachment. Cleavage of CrPV IRES mRNA was supported by a minimal set of components consisting of 40S subunits and eIF3g's RRM domain. The cleavage site was located in the coding region 18 nucleotides downstream from the mRNA entrance indicating that cleavage occurs on the solvent side of the 40S subunit. Mutational analysis identified a positively charged surface on Nsp1's N-terminal domain (NTD) and a surface above the mRNA-binding channel on eIF3g's RRM domain that contain residues essential for cleavage. These residues were required for cleavage on all three mRNAs, highlighting general roles of Nsp1-NTD and eIF3g's RRM domain in cleavage per se, irrespective of the mode of ribosomal attachment.
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Affiliation(s)
- Irina S. Abaeva
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Yani Arhab
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Anna Miścicka
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | | | - Tatyana V. Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
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14
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Kandwal S, Fayne D. Genetic conservation across SARS-CoV-2 non-structural proteins - Insights into possible targets for treatment of future viral outbreaks. Virology 2023; 581:97-115. [PMID: 36940641 PMCID: PMC9999249 DOI: 10.1016/j.virol.2023.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/10/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023]
Abstract
The majority of SARS-CoV-2 therapeutic development work has focussed on targeting the spike protein, viral polymerase and proteases. As the pandemic progressed, many studies reported that these proteins are prone to high levels of mutation and can become drug resistant. Thus, it is necessary to not only target other viral proteins such as the non-structural proteins (NSPs) but to also target the most conserved residues of these proteins. In order to understand the level of conservation among these viruses, in this review, we have focussed on the conservation across RNA viruses, conservation across the coronaviruses and then narrowed our focus to conservation of NSPs across coronaviruses. We have also discussed the various treatment options for SARS-CoV-2 infection. A synergistic melding of bioinformatics, computer-aided drug-design and in vitro/vivo studies can feed into better understanding of the virus and therefore help in the development of small molecule inhibitors against the viral proteins.
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Affiliation(s)
- Shubhangi Kandwal
- Molecular Design Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse Street, Dublin, 2, Ireland
| | - Darren Fayne
- Molecular Design Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse Street, Dublin, 2, Ireland.
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15
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All Domains of SARS-CoV-2 nsp1 Determine Translational Shutoff and Cytotoxicity of the Protein. J Virol 2023; 97:e0186522. [PMID: 36847528 PMCID: PMC10062135 DOI: 10.1128/jvi.01865-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Replication of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strongly affects cellular metabolism and results in rapid development of the cytopathic effect (CPE). The hallmarks of virus-induced modifications are inhibition of translation of cellular mRNAs and redirection of the cellular translational machinery to the synthesis of virus-specific proteins. The multifunctional nonstructural protein 1 (nsp1) of SARS-CoV-2 is a major virulence factor and a key contributor to the development of translational shutoff. In this study, we applied a wide range of virological and structural approaches to further analyze nsp1 functions. The expression of this protein alone was found to be sufficient to cause CPE. However, we selected several nsp1 mutants exhibiting noncytopathic phenotypes. The attenuating mutations were detected in three clusters, located in the C-terminal helices, in one of the loops of the structured domain and in the junction of the disordered and structured fragment of nsp1. NMR-based analysis of the wild type nsp1 and its mutants did not confirm the existence of a stable β5-strand that was proposed by the X-ray structure. In solution, this protein appears to be present in a dynamic conformation, which is required for its functions in CPE development and viral replication. The NMR data also suggest a dynamic interaction between the N-terminal and C-terminal domains. The identified nsp1 mutations make this protein noncytotoxic and incapable of inducing translational shutoff, but they do not result in deleterious effects on viral cytopathogenicity. IMPORTANCE The nsp1 of SARS-CoV-2 is a multifunctional protein that modifies the intracellular environment for the needs of viral replication. It is responsible for the development of translational shutoff, and its expression alone is sufficient to cause a cytopathic effect (CPE). In this study, we selected a wide range of nsp1 mutants exhibiting noncytopathic phenotypes. The attenuating mutations, clustered in three different fragments of nsp1, were extensively characterized via virological and structural methods. Our data strongly suggest interactions between the nsp1 domains, which are required for the protein's functions in CPE development. Most of the mutations made nsp1 noncytotoxic and incapable of inducing translational shutoff. Most of them did not affect the viability of the viruses, but they did decrease the rates of replication in cells competent in type I IFN induction and signaling. These mutations, and their combinations, in particular, can be used for the development of SARS-CoV-2 variants with attenuated phenotypes.
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16
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Structural insights into the activity regulation of full-length non-structural protein 1 from SARS-CoV-2. Structure 2023; 31:128-137.e5. [PMID: 36610391 PMCID: PMC9817231 DOI: 10.1016/j.str.2022.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/17/2022] [Accepted: 12/05/2022] [Indexed: 01/09/2023]
Abstract
Non-structural protein 1 (Nsp1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major virulence factor and thus an attractive drug target. The last 33 amino acids of Nsp1 have been shown to bind within the mRNA entry tunnel of the 40S ribosomal subunit, shutting off host gene expression. Here, we report the solution-state structure of full-length Nsp1, which features an α/β fold formed by a six-stranded, capped β-barrel-like globular domain (N-terminal domain [NTD]), flanked by short N-terminal and long C-terminal flexible tails. The NTD has been found to be critical for 40S-mediated viral mRNA recognition and promotion of viral gene expression. We find that in free Nsp1, the NTD mRNA-binding surface is occluded by interactions with the acidic C-terminal tail, suggesting a mechanism of activity regulation based on the interplay between the folded NTD and the disordered C-terminal region. These results are relevant for drug-design efforts targeting Nsp1.
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17
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Jahirul Islam M, Nawal Islam N, Siddik Alom M, Kabir M, Halim MA. A review on structural, non-structural, and accessory proteins of SARS-CoV-2: Highlighting drug target sites. Immunobiology 2023; 228:152302. [PMID: 36434912 PMCID: PMC9663145 DOI: 10.1016/j.imbio.2022.152302] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 10/30/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is a highly transmittable and pathogenic human coronavirus that first emerged in China in December 2019. The unprecedented outbreak of SARS-CoV-2 devastated human health within a short time leading to a global public health emergency. A detailed understanding of the viral proteins including their structural characteristics and virulence mechanism on human health is very crucial for developing vaccines and therapeutics. To date, over 1800 structures of non-structural, structural, and accessory proteins of SARS-CoV-2 are determined by cryo-electron microscopy, X-ray crystallography, and NMR spectroscopy. Designing therapeutics to target the viral proteins has several benefits since they could be highly specific against the virus while maintaining minimal detrimental effects on humans. However, for ongoing and future research on SARS-CoV-2, summarizing all the viral proteins and their detailed structural information is crucial. In this review, we compile comprehensive information on viral structural, non-structural, and accessory proteins structures with their binding and catalytic sites, different domain and motifs, and potential drug target sites to assist chemists, biologists, and clinicians finding necessary details for fundamental and therapeutic research.
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Affiliation(s)
- Md. Jahirul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, 16 Tejkunipara, Tejgaon, Dhaka 1215, Bangladesh
| | - Nafisa Nawal Islam
- Department of Biotechnology and Genetic Engineering, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Md. Siddik Alom
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Mahmuda Kabir
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Mohammad A. Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, 370 Paulding Avenue NW, Kennesaw, GA 30144, USA,Corresponding author
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18
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Abstract
Many viruses induce shutoff of host gene expression (host shutoff) as a strategy to take over cellular machinery and evade host immunity. Without host shutoff activity, these viruses generally replicate poorly in vivo, attesting to the importance of this antiviral strategy. In this review, we discuss one particularly advantageous way for viruses to induce host shutoff: triggering widespread host messenger RNA (mRNA) decay. Viruses can trigger increased mRNA destruction either directly, by encoding RNA cleaving or decapping enzymes, or indirectly, by activating cellular RNA degradation pathways. We review what is known about the mechanism of action of several viral RNA degradation factors. We then discuss the consequences of widespread RNA degradation on host gene expression and on the mechanisms of immune evasion, highlighting open questions. Answering these questions is critical to understanding how viral RNA degradation factors regulate host gene expression and how this process helps viruses evade host responses and replicate.
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Affiliation(s)
- Léa Gaucherand
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, and Graduate Program in Molecular Microbiology, Tufts Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, USA;
| | - Marta Maria Gaglia
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, and Graduate Program in Molecular Microbiology, Tufts Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, USA;
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19
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Jeevanandam J, Paramasivam E, Palanisamy A, Ragavendran S, Thangavel SN. Molecular insights on bioactive compounds againstCovid-19: A Network pharmacological and computational study. Curr Comput Aided Drug Des 2022; 18:CAD-EPUB-126303. [PMID: 36111763 DOI: 10.2174/1573409918666220914092145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/04/2022] [Accepted: 07/20/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Network pharmacology based identification of phytochemicals in the form of cocktails against off-targets can play a significant role in inhibition of SARS_CoV2 viral entry and its propagation. This study includes network pharmacology, virtual screening, docking and molecular dynamics to investigate the distinct antiviral mechanisms of effective phytochemicals against SARS_CoV2. METHODS SARS_CoV2 human-protein interaction network was explored from the BioGRID database and analysed using Cytoscape. Further analysis was performed to explore biological function, protein-phytochemical/drugs network and up-down regulation of pathological host target proteins. This lead to understand the antiviral mechanism of phytochemicals against SARS_CoV2. The network was explored through g:Profiler, EnrichR, CTD, SwissTarget, STITCH, DrugBank, BindingDB, STRING and SuperPred. Virtual screening of phytochemicals against potential antiviral targets such as M-Pro, NSP1, Receptor binding domain, RNA binding domain, and ACE2 discloses the effective interaction between them. Further, the binding energy calculations through simulation of the docked complex explains the efficiency and stability of the interactions. RESULTS The network analysis identified quercetin, genistein, luteolin, eugenol, berberine, isorhamnetin and cinnamaldehyde to be interacting with host proteins ACE2, DPP4, COMT, TUBGCP3, CENPF, BRD2 and HMOX1 which are involved in antiviral mechanisms such as viral entry, viral replication, host immune response, and antioxidant activity. Thus indicating that herbal cocktails can effectively tackle the viral hijacking of the crucial biological functions of human host. Further exploration through Virtual screening, docking and molecular dynamics recognizes the effective interaction of phytochemicals such as punicalagin, scutellarin, and solamargine with their respective potential targets. CONCLUSION This work illustrates probable strategy for identification of phytochemical based cocktails and off-targets which are effective against SARS_CoV 2.
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Affiliation(s)
- Jayanth Jeevanandam
- Molecular Biophysics lab, School of Chemical and Biotechnology, SASTRA Deemed to- be University, Thanjavur-613401, Tamilnadu, India
| | - Esackimuthu Paramasivam
- Molecular Biophysics lab, School of Chemical and Biotechnology, SASTRA Deemed to- be University, Thanjavur-613401, Tamilnadu, India
| | | | - Srikanth Ragavendran
- TATA-Realty Data science lab, School of Humanity and Science, SASTRA Deemed to-be University, Thanjavur-613401, Tamilnadu, India
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20
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Low ZY, Zabidi NZ, Yip AJW, Puniyamurti A, Chow VTK, Lal SK. SARS-CoV-2 Non-Structural Proteins and Their Roles in Host Immune Evasion. Viruses 2022; 14:v14091991. [PMID: 36146796 PMCID: PMC9506350 DOI: 10.3390/v14091991] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 12/02/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has caused an unprecedented global crisis and continues to threaten public health. The etiological agent of this devastating pandemic outbreak is the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). COVID-19 is characterized by delayed immune responses, followed by exaggerated inflammatory responses. It is well-established that the interferon (IFN) and JAK/STAT signaling pathways constitute the first line of defense against viral and bacterial infections. To achieve viral replication, numerous viruses are able to antagonize or hijack these signaling pathways to attain productive infection, including SARS-CoV-2. Multiple studies document the roles of several non-structural proteins (NSPs) of SARS-CoV-2 that facilitate the establishment of viral replication in host cells via immune escape. In this review, we summarize and highlight the functions and characteristics of SARS-CoV-2 NSPs that confer host immune evasion. The molecular mechanisms mediating immune evasion and the related potential therapeutic strategies for controlling the COVID-19 pandemic are also discussed.
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Affiliation(s)
- Zheng Yao Low
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Nur Zawanah Zabidi
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Ashley Jia Wen Yip
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Ashwini Puniyamurti
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Vincent T. K. Chow
- Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Kent Ridge, Singapore 117545, Singapore
- Correspondence: (V.T.K.C.); (S.K.L.)
| | - Sunil K. Lal
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
- Tropical Medicine & Biology Platform, Monash University, Subang Jaya 47500, Malaysia
- Correspondence: (V.T.K.C.); (S.K.L.)
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21
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Lou Z, Rao Z. The Life of SARS-CoV-2 Inside Cells: Replication-Transcription Complex Assembly and Function. Annu Rev Biochem 2022; 91:381-401. [PMID: 35729072 DOI: 10.1146/annurev-biochem-052521-115653] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The persistence of the coronavirus disease 2019 (COVID-19) pandemic has resulted in increasingly disruptive impacts, and it has become the most devastating challenge to global health in a century. The rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants challenges the currently available therapeutics for clinical application. Nonstructural proteins (also known as replicase proteins) with versatile biological functions play central roles in viral replication and transcription inside the host cells, and they are the most conserved target proteins among the SARS-CoV-2 variants. Specifically, they constitute the replication-transcription complexes (RTCs) dominating the synthesis of viral RNA. Knowledge of themolecular mechanisms of nonstructural proteins and their assembly into RTCs will benefit the development of antivirals targeting them against existing or potentially emerging variants. In this review, we summarize current knowledge of the structures and functions of coronavirus nonstructural proteins as well as the assembly and functions of RTCs in the life cycle of the virus.
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Affiliation(s)
- Zhiyong Lou
- Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; ,
| | - Zihe Rao
- Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; , .,Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,School of Life Sciences, Tsinghua University, Beijing, China.,State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Guangzhou Laboratory, Guangzhou, China
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22
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Synergistic interactions of repurposed drugs that inhibit Nsp1, a major virulence factor for COVID-19. Sci Rep 2022; 12:10174. [PMID: 35715434 PMCID: PMC9204075 DOI: 10.1038/s41598-022-14194-x] [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] [Received: 02/15/2022] [Accepted: 06/02/2022] [Indexed: 11/25/2022] Open
Abstract
Nsp1 is one of the first proteins expressed from the SARS-CoV-2 genome and is a major virulence factor for COVID-19. A rapid multiplexed assay for detecting the action of Nsp1 was developed in cultured lung cells. The assay is based on the acute cytopathic effects induced by Nsp1. Virtual screening was used to stratify compounds that interact with two functional Nsp1 sites: the RNA-binding groove and C-terminal helix-loop-helix region. Experimental screening focused on compounds that could be readily repurposed to treat COVID-19. Multiple synergistic combinations of compounds that significantly inhibited Nsp1 action were identified. Among the most promising combinations are Ponatinib, Rilpivirine, and Montelukast, which together, reversed the toxic effects of Nsp1 to the same extent as null mutations in the Nsp1 gene.
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23
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The impact of the suppression of highly connected protein interactions on the corona virus infection. Sci Rep 2022; 12:9188. [PMID: 35654986 PMCID: PMC9160517 DOI: 10.1038/s41598-022-13373-0] [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] [Received: 11/20/2021] [Accepted: 05/09/2022] [Indexed: 11/28/2022] Open
Abstract
Several highly effective Covid-19 vaccines are in emergency use, although more-infectious coronavirus strains, could delay the end of the pandemic even further. Because of this, it is highly desirable to develop fast antiviral drug treatments to accelerate the lasting immunity against the virus. From a theoretical perspective, computational approaches are useful tools for antiviral drug development based on the data analysis of gene expression, chemical structure, molecular pathway, and protein interaction mapping. This work studies the structural stability of virus–host interactome networks based on the graphical representation of virus–host protein interactions as vertices or nodes connected by commonly shared proteins. These graphical network visualization methods are analogous to those use in the design of artificial neural networks in neuromorphic computing. In standard protein-node-based network representation, virus–host interaction merges with virus–protein and host–protein networks, introducing redundant links associated with the internal virus and host networks. On the contrary, our approach provides a direct geometrical representation of viral infection structure and allows the effective and fast detection of the structural robustness of the virus–host network through proteins removal. This method was validated by applying it to H1N1 and HIV viruses, in which we were able to pinpoint the changes in the Interactome Network produced by known vaccines. The application of this method to the SARS-CoV-2 virus–host protein interactome implies that nonstructural proteins nsp4, nsp12, nsp16, the nuclear pore membrane glycoprotein NUP210, and ubiquitin specific peptidase USP54 play a crucial role in the viral infection, and their removal may provide an efficient therapy. This method may be extended to any new mutations or other viruses for which the Interactome Network is experimentally determined. Since time is of the essence, because of the impact of more-infectious strains on controlling the spread of the virus, this method may be a useful tool for novel antiviral therapies.
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24
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Rezaei S, Pereira F, Uversky VN, Sefidbakht Y. Molecular dynamics and intrinsic disorder analysis of the SARS-CoV-2 Nsp1 structural changes caused by substitution and deletion mutations. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2075546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Shokouh Rezaei
- Protein Research Center, Shahid Beheshti University, G.C., Tehran, Iran
| | - Filipe Pereira
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- IDENTIFICA genetic testing, Maia, Portugal
| | - Vladimir N. Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
| | - Yahya Sefidbakht
- Protein Research Center, Shahid Beheshti University, G.C., Tehran, Iran
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25
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Sosnowski P, Tidu A, Eriani G, Westhof E, Martin F. Correlated sequence signatures are present within the genomic 5'UTR RNA and NSP1 protein in coronaviruses. RNA (NEW YORK, N.Y.) 2022; 28:729-741. [PMID: 35236777 PMCID: PMC9014872 DOI: 10.1261/rna.078972.121] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
The 5'UTR part of coronavirus genomes plays key roles in the viral replication cycle and translation of viral mRNAs. The first 75-80 nt, also called the leader sequence, are identical for genomic mRNA and subgenomic mRNAs. Recently, it was shown that cooperative actions of a 5'UTR segment and the nonstructural protein NSP1 are essential for both the inhibition of host mRNAs and for specific translation of viral mRNAs. Here, sequence analyses of both the 5'UTR RNA segment and the NSP1 protein have been done for several coronaviruses, with special attention to the betacoronaviruses. The conclusions are: (i) precise specific molecular signatures can be found in both the RNA and the NSP1 protein; (ii) both types of signatures correlate between each other. Indeed, definite sequence motifs in the RNA correlate with sequence motifs in the protein, indicating a coevolution between the 5'UTR and NSP1 in betacoronaviruses. Experimental mutational data on 5'UTR and NSP1 from SARS-CoV-2 using cell-free translation extracts support these conclusions and show that some conserved key residues in the amino-terminal half of the NSP1 protein are essential for evasion to the inhibitory effect of NSP1 on translation.
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Affiliation(s)
- Piotr Sosnowski
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, F-67084 Strasbourg, France
| | - Antonin Tidu
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, F-67084 Strasbourg, France
| | - Gilbert Eriani
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, F-67084 Strasbourg, France
| | - Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, F-67084 Strasbourg, France
| | - Franck Martin
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR9002, F-67084 Strasbourg, France
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26
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Kumar P, Schexnaydre E, Rafie K, Kurata T, Terenin I, Hauryliuk V, Carlson LA. Clinically observed deletions in SARS-CoV-2 Nsp1 affect its stability and ability to inhibit translation. FEBS Lett 2022; 596:1203-1213. [PMID: 35434785 PMCID: PMC9081967 DOI: 10.1002/1873-3468.14354] [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: 11/17/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 11/11/2022]
Abstract
Nonstructural protein 1 (Nsp1) of SARS‐CoV‐2 inhibits host cell translation through an interaction between its C‐terminal domain and the 40S ribosome. The N‐terminal domain (NTD) of Nsp1 is a target of recurring deletions, some of which are associated with altered COVID‐19 disease progression. Here, we characterize the efficiency of translational inhibition by clinically observed Nsp1 deletion variants. We show that a frequent deletion of residues 79–89 severely reduces the ability of Nsp1 to inhibit translation while not abrogating Nsp1 binding to the 40S. Notably, while the SARS‐CoV‐2 5′ untranslated region enhances translation of mRNA, it does not protect from Nsp1‐mediated inhibition. Finally, thermal stability measurements and structure predictions reveal a correlation between stability of the NTD and the efficiency of translation inhibition.
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Affiliation(s)
- Pravin Kumar
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 87, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87, Umeå, Sweden
| | - Erin Schexnaydre
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 87, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87, Umeå, Sweden
| | - Karim Rafie
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 87, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87, Umeå, Sweden
| | - Tatsuaki Kurata
- Department of Experimental Medicine, University of Lund, 221 84, Lund, Sweden
| | - Ilya Terenin
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Leninskie Gory 1, Bldg. 40, Moscow, 119992, Russia
| | - Vasili Hauryliuk
- Department of Experimental Medicine, University of Lund, 221 84, Lund, Sweden.,Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden.,University of Tartu, Institute of Technology, 50411, Tartu, Estonia
| | - Lars-Anders Carlson
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 87, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87, Umeå, Sweden
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27
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Eriani G, Martin F. Viral and cellular translation during SARS‐CoV‐2 infection. FEBS Open Bio 2022; 12:1584-1601. [PMID: 35429230 PMCID: PMC9110871 DOI: 10.1002/2211-5463.13413] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/30/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022] Open
Abstract
SARS‐CoV‐2 is a betacoronavirus that emerged in China in December 2019 and which is the causative agent of the Covid‐19 pandemic. This enveloped virus contains a large positive‐sense single‐stranded RNA genome. In this review, we summarize the current knowledge on the molecular mechanisms for the translation of both viral transcripts and cellular messenger RNAs. Non‐structural proteins are encoded by the genomic RNA and are produced in the early steps of infection. In contrast, the structural proteins are produced from subgenomic RNAs that are translated in the late phase of the infectious program. Non‐structural protein 1 (NSP1) is a key molecule that regulates both viral and cellular translation. In addition, NSP1 interferes with multiple steps of the interferon I pathway and thereby blocks host antiviral responses. Therefore, NSP1 is a drug target of choice for the development of antiviral therapies.
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Affiliation(s)
- Gilbert Eriani
- Université de Strasbourg Institut de Biologie Moléculaire et Cellulaire Architecture et Réactivité de l’ARN CNRS UPR9002 2, allée Konrad Roentgen F‐67084 Strasbourg France
| | - Franck Martin
- Université de Strasbourg Institut de Biologie Moléculaire et Cellulaire Architecture et Réactivité de l’ARN CNRS UPR9002 2, allée Konrad Roentgen F‐67084 Strasbourg France
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28
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Zhang D, Zhu L, Wang Y, Li P, Gao Y. Translational Control of COVID-19 and Its Therapeutic Implication. Front Immunol 2022; 13:857490. [PMID: 35422818 PMCID: PMC9002053 DOI: 10.3389/fimmu.2022.857490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/07/2022] [Indexed: 12/19/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19, which has broken out worldwide for more than two years. However, due to limited treatment, new cases of infection are still rising. Therefore, there is an urgent need to understand the basic molecular biology of SARS-CoV-2 to control this virus. SARS-CoV-2 replication and spread depend on the recruitment of host ribosomes to translate viral messenger RNA (mRNA). To ensure the translation of their own mRNAs, the SARS-CoV-2 has developed multiple strategies to globally inhibit the translation of host mRNAs and block the cellular innate immune response. This review provides a comprehensive picture of recent advancements in our understanding of the molecular basis and complexity of SARS-CoV-2 protein translation. Specifically, we summarize how this viral infection inhibits host mRNA translation to better utilize translation elements for translation of its own mRNA. Finally, we discuss the potential of translational components as targets for therapeutic interventions.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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29
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Chan WKB, Olson KM, Wotring JW, Sexton JZ, Carlson HA, Traynor JR. In silico analysis of SARS-CoV-2 proteins as targets for clinically available drugs. Sci Rep 2022; 12:5320. [PMID: 35351926 PMCID: PMC8963407 DOI: 10.1038/s41598-022-08320-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/02/2022] [Indexed: 12/20/2022] Open
Abstract
The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires treatments with rapid clinical translatability. Here we develop a multi-target and multi-ligand virtual screening method to identify FDA-approved drugs with potential activity against SARS-CoV-2 at traditional and understudied viral targets. 1,268 FDA-approved small molecule drugs were docked to 47 putative binding sites across 23 SARS-CoV-2 proteins. We compared drugs between binding sites and filtered out compounds that had no reported activity in an in vitro screen against SARS-CoV-2 infection of human liver (Huh-7) cells. This identified 17 "high-confidence", and 97 "medium-confidence" drug-site pairs. The "high-confidence" group was subjected to molecular dynamics simulations to yield six compounds with stable binding poses at their optimal target proteins. Three drugs-amprenavir, levomefolic acid, and calcipotriol-were predicted to bind to 3 different sites on the spike protein, domperidone to the Mac1 domain of the non-structural protein (Nsp) 3, avanafil to Nsp15, and nintedanib to the nucleocapsid protein involved in packaging the viral RNA. Our "two-way" virtual docking screen also provides a framework to prioritize drugs for testing in future emergencies requiring rapidly available clinical drugs and/or treating diseases where a moderate number of targets are known.
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Affiliation(s)
- Wallace K B Chan
- Department of Pharmacology, University of Michigan, 2301 MSRBIII, 1150 W Medical Center Dr, Ann Arbor, MI, 48190-5606, USA
- Edward F Domino Research Center, University of Michigan, Ann Arbor, MI, 48190, USA
| | - Keith M Olson
- Department of Pharmacology, University of Michigan, 2301 MSRBIII, 1150 W Medical Center Dr, Ann Arbor, MI, 48190-5606, USA
- Edward F Domino Research Center, University of Michigan, Ann Arbor, MI, 48190, USA
| | - Jesse W Wotring
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48190, USA
| | - Jonathan Z Sexton
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48190, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48190, USA
| | - Heather A Carlson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48190, USA
| | - John R Traynor
- Department of Pharmacology, University of Michigan, 2301 MSRBIII, 1150 W Medical Center Dr, Ann Arbor, MI, 48190-5606, USA.
- Edward F Domino Research Center, University of Michigan, Ann Arbor, MI, 48190, USA.
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48190, USA.
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30
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Kilkenny ML, Veale CE, Guppy A, Hardwick SW, Chirgadze DY, Rzechorzek NJ, Maman JD, Pellegrini L. Structural basis for the interaction of SARS-CoV-2 virulence factor nsp1 with DNA polymerase α-primase. Protein Sci 2022; 31:333-344. [PMID: 34719824 PMCID: PMC8661717 DOI: 10.1002/pro.4220] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 11/21/2022]
Abstract
The molecular mechanisms that drive the infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-the causative agent of coronavirus disease 2019 (COVID-19)-are under intense current scrutiny to understand how the virus operates and to uncover ways in which the disease can be prevented or alleviated. Recent proteomic screens of the interactions between viral and host proteins have identified the human proteins targeted by SARS-CoV-2. The DNA polymerase α (Pol α)-primase complex or primosome-responsible for initiating DNA synthesis during genomic duplication-was identified as a target of nonstructural protein 1 (nsp1), a major virulence factor in the SARS-CoV-2 infection. Here, we validate the published reports of the interaction of nsp1 with the primosome by demonstrating direct binding with purified recombinant components and providing a biochemical characterization of their interaction. Furthermore, we provide a structural basis for the interaction by elucidating the cryo-electron microscopy structure of nsp1 bound to the primosome. Our findings provide biochemical evidence for the reported targeting of Pol α by the virulence factor nsp1 and suggest that SARS-CoV-2 interferes with Pol α's putative role in the immune response during the viral infection.
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Affiliation(s)
| | | | - Amir Guppy
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1GAUK
| | | | | | - Neil J. Rzechorzek
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1GAUK
- Present address:
The Francis Crick InstituteLondonNW1 1ATUK
| | - Joseph D. Maman
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1GAUK
| | - Luca Pellegrini
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1GAUK
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31
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Pizzato M, Baraldi C, Boscato Sopetto G, Finozzi D, Gentile C, Gentile MD, Marconi R, Paladino D, Raoss A, Riedmiller I, Ur Rehman H, Santini A, Succetti V, Volpini L. SARS-CoV-2 and the Host Cell: A Tale of Interactions. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2021.815388] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The ability of a virus to spread between individuals, its replication capacity and the clinical course of the infection are macroscopic consequences of a multifaceted molecular interaction of viral components with the host cell. The heavy impact of COVID-19 on the world population, economics and sanitary systems calls for therapeutic and prophylactic solutions that require a deep characterization of the interactions occurring between virus and host cells. Unveiling how SARS-CoV-2 engages with host factors throughout its life cycle is therefore fundamental to understand the pathogenic mechanisms underlying the viral infection and to design antiviral therapies and prophylactic strategies. Two years into the SARS-CoV-2 pandemic, this review provides an overview of the interplay between SARS-CoV-2 and the host cell, with focus on the machinery and compartments pivotal for virus replication and the antiviral cellular response. Starting with the interaction with the cell surface, following the virus replicative cycle through the characterization of the entry pathways, the survival and replication in the cytoplasm, to the mechanisms of egress from the infected cell, this review unravels the complex network of interactions between SARS-CoV-2 and the host cell, highlighting the knowledge that has the potential to set the basis for the development of innovative antiviral strategies.
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32
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Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex. PLoS Comput Biol 2022; 18:e1009804. [PMID: 35045069 PMCID: PMC8803185 DOI: 10.1371/journal.pcbi.1009804] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 01/31/2022] [Accepted: 01/04/2022] [Indexed: 11/19/2022] Open
Abstract
Nonstructural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a 180-residue protein that blocks translation of host mRNAs in SARS-CoV-2-infected cells. Although it is known that SARS-CoV-2’s own RNA evades nsp1’s host translation shutoff, the molecular mechanism underlying the evasion was poorly understood. We performed an extended ensemble molecular dynamics simulation to investigate the mechanism of the viral RNA evasion. Simulation results suggested that the stem loop structure of the SARS-CoV-2 RNA 5’-untranslated region (SL1) binds to both nsp1’s N-terminal globular region and intrinsically disordered region. The consistency of the results was assessed by modeling nsp1-40S ribosome structure based on reported nsp1 experiments, including the X-ray crystallographic structure analysis, the cryo-EM electron density map, and cross-linking experiments. The SL1 binding region predicted from the simulation was open to the solvent, yet the ribosome could interact with SL1. Cluster analysis of the binding mode and detailed analysis of the binding poses suggest residues Arg124, Lys47, Arg43, and Asn126 may be involved in the SL1 recognition mechanism, consistent with the existing mutational analysis. The pandemic of COVID-19 is still rampant all over the world as of 2021 June. SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causative pathogen of COVID-19, encodes a protein called nsp1 (nonstructural protein 1), which modulates and hijacks the ribosome of the infected host cells. With nsp1, infected human cells selectively translate SARS-CoV-2’s RNA, which increases the virus reproduction efficiency while evading the host immunity. Though it has been known that nsp1 recognizes characteristic stem-loop structure at 5’-end of SARS-CoV-2’s RNA (called SL1), the molecular mechanism underlying the recognition has been poorly understood. We investigated the mechanism of selective translation using the all-atom molecular dynamics simulation of nsp1-SL1 complex. Our simulation results suggest that the binding between nsp1 and SL1 is multi-modal. The results also imply that both the N-terminal globular part and the C-terminal flexible tail of nsp1 are involved in the binding. The residues involved in nsp1-SL1 binding coincides with the known mutant analyses of SARS-CoV-1 and SARS-CoV-2, as well as experimental evidence about nsp1-ribosome interactions.
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33
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Agback T, Dominguez F, Frolov I, Frolova EI, Agback P. 1H, 13C and 15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution. PLoS One 2021; 16:e0251834. [PMID: 34874953 PMCID: PMC8651119 DOI: 10.1371/journal.pone.0251834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/27/2021] [Indexed: 11/30/2022] Open
Abstract
Structural characterization of the SARS-CoV-2 full length nsp1 protein will be an essential tool for developing new target-directed antiviral drugs against SARS-CoV-2 and for further understanding of intra- and intermolecular interactions of this protein. As a first step in the NMR studies of the protein, we report the 1H, 13C and 15N resonance backbone assignment as well as the Cβ of the apo form of the full-lengthSARS-CoV-2 nsp1 including the folded domain together with the flaking N- and C- terminal intrinsically disordered fragments. The 19.8 kD protein was characterized by high-resolution NMR. Validation of assignment have been done by using two different mutants, H81P and K129E/D48E as well as by amino acid specific experiments. According to the obtained assignment, the secondary structure of the folded domain in solution was almost identical to its previously published X-ray structure as well as another published secondary structure obtained by NMR, but some discrepancies have been detected. In the solution SARS-CoV-2 nsp1 exhibited disordered, flexible N- and C-termini with different dynamic characteristics. The short peptide in the beginning of the disordered C-terminal domain adopted two different conformations distinguishable on the NMR time scale. We propose that the disordered and folded nsp1 domains are not fully independent units but are rather involved in intramolecular interactions. Studies of the structure and dynamics of the SARS-CoV-2 mutant in solution are on-going and will provide important insights into the molecular mechanisms underlying these interactions.
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Affiliation(s)
- Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Francisco Dominguez
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Ilya Frolov
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Elena I. Frolova
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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34
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Gerassimovich YA, Miladinovski-Bangall SJ, Bridges KM, Boateng L, Ball LE, Valafar H, Nag A. Proximity-dependent biotinylation detects associations between SARS coronavirus nonstructural protein 1 and stress granule-associated proteins. J Biol Chem 2021; 297:101399. [PMID: 34774526 PMCID: PMC8580555 DOI: 10.1016/j.jbc.2021.101399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 10/28/2021] [Accepted: 11/08/2021] [Indexed: 11/17/2022] Open
Abstract
The nonstructural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus and severe acute respiratory syndrome coronavirus 2 is a critical viral protein that suppresses host gene expression by blocking the assembly of the ribosome on host mRNAs. To understand the mechanism of inhibition of host gene expression, we sought to identify cellular proteins that interact with nsp1. Using proximity-dependent biotinylation followed by proteomic analyses of biotinylated proteins, here we captured multiple dynamic interactions of nsp1 with host cell proteins. In addition to ribosomal proteins, we identified several pre-mRNA processing proteins that interact with nsp1, including splicing factors and transcription termination proteins, as well as exosome, and stress granule (SG)-associated proteins. We found that the interactions with transcription termination factors are primarily governed by the C-terminal region of nsp1 and are disrupted by the mutation of amino acids K164 and H165 that are essential for its host shutoff function. We further show that nsp1 interacts with Ras GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) and colocalizes with G3BP1 in SGs under sodium arsenite-induced stress. Finally, we observe that the presence of nsp1 disrupts the maturation of SGs over a long period. Isolation of SG core at different times shows a gradual loss of G3BP1 in the presence of nsp1.
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Affiliation(s)
- Yevgeniy A Gerassimovich
- Natural Sciences and Engineering, University of South Carolina Upstate, Spartanburg, South Carolina, USA
| | | | - Kaitlin M Bridges
- Natural Sciences and Engineering, University of South Carolina Upstate, Spartanburg, South Carolina, USA
| | - Linkel Boateng
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina, USA
| | - Lauren E Ball
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Homayoun Valafar
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina, USA
| | - Anita Nag
- Natural Sciences and Engineering, University of South Carolina Upstate, Spartanburg, South Carolina, USA.
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35
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Zanchi FB, Mariúba LA, Nascimento V, Souza V, Corado A, Nascimento F, Costa ÁK, Duarte D, Silva G, Mejía M, Pessoa K, Gonçalves L, Brandão MJ, Jesus M, Glória J, Silva M, Mattos T, da Costa C, Naveca FG. Structural analysis of SARS-Cov-2 nonstructural protein 1 polymorphisms found in the Brazilian Amazon. Exp Biol Med (Maywood) 2021; 246:2332-2337. [PMID: 34749522 DOI: 10.1177/15353702211021348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The coronavirus disease COVID-19 has been the cause of millions of deaths worldwide. Among the SARS-CoV-2 proteins, the non-structural protein 1 (NSP1) has great importance during the virus infection process and is present in both alpha and beta-CoVs. Therefore, monitoring of NSP1 polymorphisms is crucial in order to understand their role during infection and virus-induced pathogenicity. Herein, we analyzed how mutations detected in the circulating SARS-CoV-2 in the population of the city of Manaus, Amazonas state, Brazil could modify the tertiary structure of the NSP1 protein. Three mutations were detected in the SARS-CoV-2 NSP1 gene: deletion of the amino acids KSF from positions 141 to 143 (delKSF), SARS-CoV-2, lineage B.1.195; and two substitutions, R29H and R43C, SARS-CoV-2 lineage B.1.1.28 and B.1.1.33, respectively. The delKSF was found in 47 samples, whereas R29H and R43C were found in two samples, one for each mutation. The NSP1 structures carrying the mutations R43C and R29H on the N-terminal portion (e.g. residues 10 to 127) showed minor backbone divergence compared to the Wuhan model. However, the NSP1 C-terminal region (residues 145 to 180) was severely affected in the delKSF and R29H mutants. The intermediate variable region (residues 144 to 148) leads to changes in the C-terminal region, particularly in the delKSF structure. New investigations must be carried out to analyze how these changes affect NSP1 activity during the infection. Our results reinforce the need for continuous genomic surveillance of SARS-CoV-2 to better understand virus evolution and assess the potential impact of the viral mutations on the approved vaccines and future therapies.
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Affiliation(s)
- Fernando Berton Zanchi
- Laboratório de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz, FIOCRUZ, Unidade Rondônia, Porto Velho, RO 76812-245, Brazil.,Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, RO 76801-059, Brazil.,Instituto Nacional de Epidemiologia na Amazônia Ocidental - EPIAMO, Porto Velho, RO 76812-245, Brazil
| | - Luis André Mariúba
- Programa Multi-institucional de Pós-graduação em Biotecnologia, Universidade Federal do Amazonas (PPGBIOTEC-UFAM), Manaus, AM 69067-005, Brazil.,Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (PPGIBA-UFAM), Manaus, AM 69067-005, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Programa de Pós-Graduação em Biologia Celular e Molecular, Rio de Janeiro, RJ 21040-360, Brazil
| | - Valdinete Nascimento
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Programa de Pós-Graduação em Biologia Celular e Molecular, Rio de Janeiro, RJ 21040-360, Brazil.,Rede Genômica de Vigilância em Saúde do Estado do Amazonas, Manaus, AM 69057-070, Brazil
| | - Victor Souza
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Programa de Pós-Graduação em Biologia Celular e Molecular, Rio de Janeiro, RJ 21040-360, Brazil.,Rede Genômica de Vigilância em Saúde do Estado do Amazonas, Manaus, AM 69057-070, Brazil
| | - André Corado
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Programa de Pós-Graduação em Biologia Celular e Molecular, Rio de Janeiro, RJ 21040-360, Brazil
| | - Fernanda Nascimento
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane, Programa de Pós-Graduação em Biologia da Interação Patógeno-Hospedeiro, Manaus, AM 69057-070, Brazil
| | - Ágatha Kelly Costa
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil
| | - Débora Duarte
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil
| | - George Silva
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil
| | - Matilde Mejía
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil
| | - Karina Pessoa
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane, Programa de Pós-Graduação em Biologia da Interação Patógeno-Hospedeiro, Manaus, AM 69057-070, Brazil
| | - Luciana Gonçalves
- Fundação de Vigilância em Saúde do Amazonas, Manaus, AM 69093-018, Brazil
| | - Maria Júlia Brandão
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil
| | - Michele Jesus
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil
| | - Juliane Glória
- Programa Multi-institucional de Pós-graduação em Biotecnologia, Universidade Federal do Amazonas (PPGBIOTEC-UFAM), Manaus, AM 69067-005, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil
| | - Marineide Silva
- Fundação de Vigilância em Saúde do Amazonas, Manaus, AM 69093-018, Brazil
| | - Tirza Mattos
- Fundação de Vigilância em Saúde do Amazonas, Manaus, AM 69093-018, Brazil
| | - Cristiano da Costa
- Fundação de Vigilância em Saúde do Amazonas, Manaus, AM 69093-018, Brazil
| | - Felipe Gomes Naveca
- Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (PPGIBA-UFAM), Manaus, AM 69067-005, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Programa de Pós-Graduação em Biologia Celular e Molecular, Rio de Janeiro, RJ 21040-360, Brazil.,Rede Genômica de Vigilância em Saúde do Estado do Amazonas, Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane, Programa de Pós-Graduação em Biologia da Interação Patógeno-Hospedeiro, Manaus, AM 69057-070, Brazil
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36
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Wang Y, Kirkpatrick J, Zur Lage S, Korn SM, Neißner K, Schwalbe H, Schlundt A, Carlomagno T. 1H, 13C, and 15N backbone chemical-shift assignments of SARS-CoV-2 non-structural protein 1 (leader protein). BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:287-295. [PMID: 33770349 PMCID: PMC7996116 DOI: 10.1007/s12104-021-10019-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/13/2021] [Indexed: 05/30/2023]
Abstract
The current COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has become a worldwide health crisis, necessitating coordinated scientific research and urgent identification of new drug targets for treatment of COVID-19 lung disease. The covid19-nmr consortium seeks to support drug development by providing publicly accessible NMR data on the viral RNA elements and proteins. The SARS-CoV-2 genome comprises a single RNA of about 30 kb in length, in which 14 open reading frames (ORFs) have been annotated, and encodes approximately 30 proteins. The first two-thirds of the SARS-CoV-2 genome is made up of two large overlapping open-reading-frames (ORF1a and ORF1b) encoding a replicase polyprotein, which is subsequently cleaved to yield 16 so-called non-structural proteins. The non-structural protein 1 (Nsp1), which is considered to be a major virulence factor, suppresses host immune functions by associating with host ribosomal complexes at the very end of its C-terminus. Furthermore, Nsp1 facilitates initiation of viral RNA translation via an interaction of its N-terminal domain with the 5' untranslated region (UTR) of the viral RNA. Here, we report the near-complete backbone chemical-shift assignments of full-length SARS-CoV-2 Nsp1 (19.8 kDa), which reveal the domain organization, secondary structure and backbone dynamics of Nsp1, and which will be of value to further NMR-based investigations of both the biochemical and physiological functions of Nsp1.
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Affiliation(s)
- Ying Wang
- Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - John Kirkpatrick
- Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Susanne Zur Lage
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Sophie M Korn
- Institute for Molecular Biosciences, St Lucia, QLD, 4072, Australia
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Konstantin Neißner
- Institute for Molecular Biosciences, St Lucia, QLD, 4072, Australia
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences, St Lucia, QLD, 4072, Australia
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Teresa Carlomagno
- Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany.
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
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37
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Yuan S, Balaji S, Lomakin IB, Xiong Y. Coronavirus Nsp1: Immune Response Suppression and Protein Expression Inhibition. Front Microbiol 2021; 12:752214. [PMID: 34659188 PMCID: PMC8512706 DOI: 10.3389/fmicb.2021.752214] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/24/2021] [Indexed: 12/30/2022] Open
Abstract
Coronaviruses have brought severe challenges to public health all over the world in the past 20years. SARS-CoV-2, the causative agent of the COVID-19 pandemic that has led to millions of deaths, belongs to the genus beta-coronavirus. Alpha- and beta-coronaviruses encode a unique protein, nonstructural protein 1 (Nsp1) that both suppresses host immune responses and reduces global gene expression levels in the host cells. As a key pathogenicity factor of coronaviruses, Nsp1 redirects the host translation machinery to increase synthesis of viral proteins. Through multiple mechanisms, coronaviruses impede host protein expression through Nsp1, while escaping inhibition to allow the translation of viral RNA. In this review, we discuss current data about suppression of the immune responses and inhibition of protein synthesis induced by coronavirus Nsp1, as well as the prospect of live-attenuated vaccine development with virulence-attenuated viruses with mutations in Nsp1.
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Affiliation(s)
- Shuai Yuan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Shravani Balaji
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Ivan B Lomakin
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, United States
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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38
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O’Donoghue SI, Schafferhans A, Sikta N, Stolte C, Kaur S, Ho BK, Anderson S, Procter JB, Dallago C, Bordin N, Adcock M, Rost B. SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms. Mol Syst Biol 2021; 17:e10079. [PMID: 34519429 PMCID: PMC8438690 DOI: 10.15252/msb.202010079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/18/2023] Open
Abstract
We modeled 3D structures of all SARS-CoV-2 proteins, generating 2,060 models that span 69% of the viral proteome and provide details not available elsewhere. We found that ˜6% of the proteome mimicked human proteins, while ˜7% was implicated in hijacking mechanisms that reverse post-translational modifications, block host translation, and disable host defenses; a further ˜29% self-assembled into heteromeric states that provided insight into how the viral replication and translation complex forms. To make these 3D models more accessible, we devised a structural coverage map, a novel visualization method to show what is-and is not-known about the 3D structure of the viral proteome. We integrated the coverage map into an accompanying online resource (https://aquaria.ws/covid) that can be used to find and explore models corresponding to the 79 structural states identified in this work. The resulting Aquaria-COVID resource helps scientists use emerging structural data to understand the mechanisms underlying coronavirus infection and draws attention to the 31% of the viral proteome that remains structurally unknown or dark.
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MESH Headings
- Amino Acid Transport Systems, Neutral/chemistry
- Amino Acid Transport Systems, Neutral/genetics
- Amino Acid Transport Systems, Neutral/metabolism
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/metabolism
- Binding Sites
- COVID-19/genetics
- COVID-19/metabolism
- COVID-19/virology
- Computational Biology/methods
- Coronavirus Envelope Proteins/chemistry
- Coronavirus Envelope Proteins/genetics
- Coronavirus Envelope Proteins/metabolism
- Coronavirus Nucleocapsid Proteins/chemistry
- Coronavirus Nucleocapsid Proteins/genetics
- Coronavirus Nucleocapsid Proteins/metabolism
- Host-Pathogen Interactions/genetics
- Humans
- Mitochondrial Membrane Transport Proteins/chemistry
- Mitochondrial Membrane Transport Proteins/genetics
- Mitochondrial Membrane Transport Proteins/metabolism
- Mitochondrial Precursor Protein Import Complex Proteins
- Models, Molecular
- Molecular Mimicry
- Neuropilin-1/chemistry
- Neuropilin-1/genetics
- Neuropilin-1/metabolism
- Phosphoproteins/chemistry
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Interaction Mapping/methods
- Protein Multimerization
- Protein Processing, Post-Translational
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Viral Matrix Proteins/chemistry
- Viral Matrix Proteins/genetics
- Viral Matrix Proteins/metabolism
- Viroporin Proteins/chemistry
- Viroporin Proteins/genetics
- Viroporin Proteins/metabolism
- Virus Replication
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Affiliation(s)
- Seán I O’Donoghue
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
- CSIRO Data61CanberraACTAustralia
- School of Biotechnology and Biomolecular Sciences (UNSW)KensingtonNSWAustralia
| | - Andrea Schafferhans
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
- Department of Bioengineering SciencesWeihenstephan‐Tr. University of Applied SciencesFreisingGermany
- Department of InformaticsBioinformatics & Computational BiologyTechnical University of MunichMunichGermany
| | - Neblina Sikta
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
| | | | - Sandeep Kaur
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
- School of Biotechnology and Biomolecular Sciences (UNSW)KensingtonNSWAustralia
| | - Bosco K Ho
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
| | | | | | - Christian Dallago
- Department of InformaticsBioinformatics & Computational BiologyTechnical University of MunichMunichGermany
| | - Nicola Bordin
- Institute of Structural and Molecular BiologyUniversity College LondonLondonUK
| | | | - Burkhard Rost
- Department of InformaticsBioinformatics & Computational BiologyTechnical University of MunichMunichGermany
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39
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Salleh MZ, Derrick JP, Deris ZZ. Structural Evaluation of the Spike Glycoprotein Variants on SARS-CoV-2 Transmission and Immune Evasion. Int J Mol Sci 2021; 22:7425. [PMID: 34299045 PMCID: PMC8306177 DOI: 10.3390/ijms22147425] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/07/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents significant social, economic and political challenges worldwide. SARS-CoV-2 has caused over 3.5 million deaths since late 2019. Mutations in the spike (S) glycoprotein are of particular concern because it harbours the domain which recognises the angiotensin-converting enzyme 2 (ACE2) receptor and is the target for neutralising antibodies. Mutations in the S protein may induce alterations in the surface spike structures, changing the conformational B-cell epitopes and leading to a potential reduction in vaccine efficacy. Here, we summarise how the more important variants of SARS-CoV-2, which include cluster 5, lineages B.1.1.7 (Alpha variant), B.1.351 (Beta), P.1 (B.1.1.28/Gamma), B.1.427/B.1.429 (Epsilon), B.1.526 (Iota) and B.1.617.2 (Delta) confer mutations in their respective spike proteins which enhance viral fitness by improving binding affinity to the ACE2 receptor and lead to an increase in infectivity and transmission. We further discuss how these spike protein mutations provide resistance against immune responses, either acquired naturally or induced by vaccination. This information will be valuable in guiding the development of vaccines and other therapeutics for protection against the ongoing coronavirus disease 2019 (COVID-19) pandemic.
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Affiliation(s)
- Mohd Zulkifli Salleh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Malaysia;
| | - Jeremy P. Derrick
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester M13 9PL, UK;
| | - Zakuan Zainy Deris
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Malaysia;
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40
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Chaudhuri A. Comparative analysis of non structural protein 1 of SARS-CoV2 with SARS-CoV1 and MERS-CoV: An in silico study. J Mol Struct 2021; 1243:130854. [PMID: 34121768 PMCID: PMC8188392 DOI: 10.1016/j.molstruc.2021.130854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 12/21/2022]
Abstract
The recently emerged SARS-CoV2 caused a major pandemic of coronavirus disease (COVID-19). Non structural protein 1 (nsp1) is found in all beta coronavirus that cause severe respiratory disease. This protein is considered as a virulence factor and has an important role in pathogenesis. This study aims to elucidate the structural conformations of nsp1 to aid in the prediction of epitope sites and identification of important residues for targeted therapy against COVID-19. In this study, molecular modelling coupled with molecular dynamics simulations were performed to analyse the conformational landscape of nsp1 homologs of SARS-CoV1, SARS-CoV2 and MERS-CoV. Principal component analysis escorted by free energy landscape revealed that SARS-CoV2 nsp1 protein shows greater flexibility compared to SARS-CoV1 and MERS-CoV nsp1. Sequence comparison reveals that 28 mutations are present in SARS-CoV2 nsp1 protein compared to SARS-CoV1 nsp1. Several B-cell and T-cell epitopes were identified by an immunoinformatics approach. SARS-CoV2 nsp1 protein binds with the interface region of the palm and finger domain of POLA1 via hydrogen bonding and salt bridge interactions. Taken together, these in silico findings may help in the development of therapeutics specific against COVID-19.
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Affiliation(s)
- Ankur Chaudhuri
- Department of Microbiology, West Bengal State University, Barasat, Kolkata 700126, India
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41
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Altincekic N, Korn SM, Qureshi NS, Dujardin M, Ninot-Pedrosa M, Abele R, Abi Saad MJ, Alfano C, Almeida FCL, Alshamleh I, de Amorim GC, Anderson TK, Anobom CD, Anorma C, Bains JK, Bax A, Blackledge M, Blechar J, Böckmann A, Brigandat L, Bula A, Bütikofer M, Camacho-Zarco AR, Carlomagno T, Caruso IP, Ceylan B, Chaikuad A, Chu F, Cole L, Crosby MG, de Jesus V, Dhamotharan K, Felli IC, Ferner J, Fleischmann Y, Fogeron ML, Fourkiotis NK, Fuks C, Fürtig B, Gallo A, Gande SL, Gerez JA, Ghosh D, Gomes-Neto F, Gorbatyuk O, Guseva S, Hacker C, Häfner S, Hao B, Hargittay B, Henzler-Wildman K, Hoch JC, Hohmann KF, Hutchison MT, Jaudzems K, Jović K, Kaderli J, Kalniņš G, Kaņepe I, Kirchdoerfer RN, Kirkpatrick J, Knapp S, Krishnathas R, Kutz F, zur Lage S, Lambertz R, Lang A, Laurents D, Lecoq L, Linhard V, Löhr F, Malki A, Bessa LM, Martin RW, Matzel T, Maurin D, McNutt SW, Mebus-Antunes NC, Meier BH, Meiser N, Mompeán M, Monaca E, Montserret R, Mariño Perez L, Moser C, Muhle-Goll C, Neves-Martins TC, Ni X, Norton-Baker B, Pierattelli R, Pontoriero L, Pustovalova Y, Ohlenschläger O, Orts J, Da Poian AT, Pyper DJ, Richter C, Riek R, Rienstra CM, Robertson A, Pinheiro AS, Sabbatella R, Salvi N, Saxena K, Schulte L, Schiavina M, Schwalbe H, Silber M, Almeida MDS, Sprague-Piercy MA, Spyroulias GA, Sreeramulu S, Tants JN, Tārs K, Torres F, Töws S, Treviño MÁ, Trucks S, Tsika AC, Varga K, Wang Y, Weber ME, Weigand JE, Wiedemann C, Wirmer-Bartoschek J, Wirtz Martin MA, Zehnder J, Hengesbach M, Schlundt A. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications. Front Mol Biosci 2021; 8:653148. [PMID: 34041264 PMCID: PMC8141814 DOI: 10.3389/fmolb.2021.653148] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/04/2021] [Indexed: 01/18/2023] Open
Abstract
The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium's collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.
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Affiliation(s)
- Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sophie Marianne Korn
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Dujardin
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Martí Ninot-Pedrosa
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Rupert Abele
- Institute for Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Jose Abi Saad
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Caterina Alfano
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Fabio C. L. Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Islam Alshamleh
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gisele Cardoso de Amorim
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multidisciplinary Center for Research in Biology (NUMPEX), Campus Duque de Caxias Federal University of Rio de Janeiro, Duque de Caxias, Brazil
| | - Thomas K. Anderson
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Cristiane D. Anobom
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chelsea Anorma
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Adriaan Bax
- LCP, NIDDK, NIH, Bethesda, MD, United States
| | | | - Julius Blechar
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Louis Brigandat
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Anna Bula
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Matthias Bütikofer
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | | | - Teresa Carlomagno
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Icaro Putinhon Caruso
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Marquise G. Crosby
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Karthikeyan Dhamotharan
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Isabella C. Felli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Yanick Fleischmann
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Christin Fuks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Angelo Gallo
- Department of Pharmacy, University of Patras, Patras, Greece
| | - Santosh L. Gande
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Juan Atilio Gerez
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Dhiman Ghosh
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Francisco Gomes-Neto
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Oksana Gorbatyuk
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | | | - Sabine Häfner
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Bing Hao
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Bruno Hargittay
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - K. Henzler-Wildman
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Jeffrey C. Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie T. Hutchison
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Katarina Jović
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Janina Kaderli
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Iveta Kaņepe
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Robert N. Kirchdoerfer
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - John Kirkpatrick
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Robin Krishnathas
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Felicitas Kutz
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Susanne zur Lage
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Roderick Lambertz
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andras Lang
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Douglas Laurents
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Verena Linhard
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Frank Löhr
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anas Malki
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Tobias Matzel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Damien Maurin
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Seth W. McNutt
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Nathane Cunha Mebus-Antunes
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Beat H. Meier
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Nathalie Meiser
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Mompeán
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Elisa Monaca
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Roland Montserret
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Celine Moser
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | | - Thais Cristtina Neves-Martins
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Xiamonin Ni
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Brenna Norton-Baker
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Roberta Pierattelli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Letizia Pontoriero
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Yulia Pustovalova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | - Julien Orts
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Andrea T. Da Poian
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dennis J. Pyper
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Roland Riek
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Chad M. Rienstra
- Department of Biochemistry and National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Anderson S. Pinheiro
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Nicola Salvi
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Linda Schulte
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marco Schiavina
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mara Silber
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marcius da Silva Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marc A. Sprague-Piercy
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | | | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jan-Niklas Tants
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Felix Torres
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Sabrina Töws
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Á. Treviño
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Krisztina Varga
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Ying Wang
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Marco E. Weber
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Julia E. Weigand
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Christoph Wiedemann
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria Alexandra Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johannes Zehnder
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andreas Schlundt
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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Kumar A, Kumar A, Kumar P, Garg N, Giri R. SARS-CoV-2 NSP1 C-terminal (residues 131-180) is an intrinsically disordered region in isolation. CURRENT RESEARCH IN VIROLOGICAL SCIENCE 2021; 2:100007. [PMID: 34189489 PMCID: PMC8020630 DOI: 10.1016/j.crviro.2021.100007] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/12/2021] [Accepted: 03/31/2021] [Indexed: 02/07/2023]
Abstract
The NSP1- C terminal structure in complex with ribosome using cryo-EM is available now, and the N-terminal region structure in isolation is also deciphered in literature. However, as a reductionist approach, the conformation of NSP1- C terminal region (NSP1-CTR; amino acids 131-180) has not been studied in isolation. We found that NSP1-CTR conformation is disordered in an aqueous solution. Further, we examined the conformational propensity towards alpha-helical structure using trifluoroethanol, we observed induction of helical structure conformation using CD spectroscopy. Additionally, in SDS, NSP1-CTR shows a conformational change from disordered to ordered, possibly gaining alpha-helix in part. But in the presence of neutral lipid DOPC, a slight change in conformation is observed, which implies the possible role of hydrophobic interaction and electrostatic interaction on the conformational changes of NSP1. Fluorescence-based studies have shown a blue shift and fluorescence quenching in the presence of SDS, TFE, and lipid vesicles. In agreement with these results, fluorescence lifetime and fluorescence anisotropy decay suggest a change in conformational dynamics. The zeta potential studies further validated that the conformational dynamics are primarily because of hydrophobic interaction. These experimental studies were complemented through Molecular Dynamics (MD) simulations, which have shown a good correlation and testifies our experiments. We believe that the intrinsically disordered nature of the NSP1-CTR will have implications for enhanced molecular recognition feature properties of this IDR, which may add disorder to order transition and disorder-based binding promiscuity with its interacting proteins.
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Affiliation(s)
- Amit Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
| | - Ankur Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
| | - Neha Garg
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
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43
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Lin JW, Tang C, Wei HC, Du B, Chen C, Wang M, Zhou Y, Yu MX, Cheng L, Kuivanen S, Ogando NS, Levanov L, Zhao Y, Li CL, Zhou R, Li Z, Zhang Y, Sun K, Wang C, Chen L, Xiao X, Zheng X, Chen SS, Zhou Z, Yang R, Zhang D, Xu M, Song J, Wang D, Li Y, Lei S, Zeng W, Yang Q, He P, Zhang Y, Zhou L, Cao L, Luo F, Liu H, Wang L, Ye F, Zhang M, Li M, Fan W, Li X, Li K, Ke B, Xu J, Yang H, He S, Pan M, Yan Y, Zha Y, Jiang L, Yu C, Liu Y, Xu Z, Li Q, Jiang Y, Sun J, Hong W, Wei H, Lu G, Vapalahti O, Luo Y, Wei Y, Connor T, Tan W, Snijder EJ, Smura T, Li W, Geng J, Ying B, Chen L. Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response. Cell Host Microbe 2021; 29:489-502.e8. [PMID: 33548198 PMCID: PMC7846228 DOI: 10.1016/j.chom.2021.01.015] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 02/05/2023]
Abstract
The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent variants, some of which are associated with clinical phenotypes related to severity. One variant, containing a deletion in the Nsp1-coding region (Δ500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-β levels of infected patients. Deletion variants in this locus were found in 37 countries worldwide, and viruses isolated from clinical samples or engineered by reverse genetics with related deletions in Nsp1 also induce lower IFN-β responses in infected Calu-3 cells. Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics and drug design.
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Affiliation(s)
- Jing-Wen Lin
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
| | - Chao Tang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Han-Cheng Wei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Baowen Du
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Chuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Minjin Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Yongzhao Zhou
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ming-Xia Yu
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Lu Cheng
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Department of Computer Science, School of Science, Aalto University, Aalto FI-00076, Finland
| | - Suvi Kuivanen
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland
| | - Natacha S Ogando
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lev Levanov
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland
| | - Yuancun Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Chang-Ling Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ran Zhou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Zhidan Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yiming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ke Sun
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Chengdi Wang
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Li Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Xia Xiao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Xiuran Zheng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Sha-Sha Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Zhen Zhou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ruirui Yang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Dan Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Mengying Xu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Junwei Song
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Danrui Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yupeng Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - ShiKun Lei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Wanqin Zeng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Qingxin Yang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ping He
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yaoyao Zhang
- Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Lifang Zhou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ling Cao
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Feng Luo
- Wuhan Chain Medical Labs, Wuhan, Hubei 430011, China
| | - Huayi Liu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Liping Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Fei Ye
- NHC Key Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Mengjiao Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Wei Fan
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xinqiong Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Bowen Ke
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Jiannan Xu
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Huiping Yang
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Shusen He
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Ming Pan
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Yichen Yan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Yi Zha
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Lingyu Jiang
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Changxiu Yu
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Yingfen Liu
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Zhiyong Xu
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Qingfeng Li
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Yongmei Jiang
- Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Jiufeng Sun
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong 511430, China
| | - Wei Hong
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangwen Lu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Olli Vapalahti
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland; University of Helsinki and Helsinki University Hospital, Department of Virology, Helsinki, Finland; Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Yunzi Luo
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yuquan Wei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Thomas Connor
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Wenjie Tan
- NHC Key Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Teemu Smura
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland; University of Helsinki and Helsinki University Hospital, Department of Virology, Helsinki, Finland.
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China.
| | - Binwu Ying
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China.
| | - Lu Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
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Lapointe CP, Grosely R, Johnson AG, Wang J, Fernández IS, Puglisi JD. Dynamic competition between SARS-CoV-2 NSP1 and mRNA on the human ribosome inhibits translation initiation. Proc Natl Acad Sci U S A 2021; 118:e2017715118. [PMID: 33479166 PMCID: PMC8017934 DOI: 10.1073/pnas.2017715118] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a beta-CoV that recently emerged as a human pathogen and is the causative agent of the COVID-19 pandemic. A molecular framework of how the virus manipulates host cellular machinery to facilitate infection remains unclear. Here, we focus on SARS-CoV-2 NSP1, which is proposed to be a virulence factor that inhibits protein synthesis by directly binding the human ribosome. We demonstrate biochemically that NSP1 inhibits translation of model human and SARS-CoV-2 messenger RNAs (mRNAs). NSP1 specifically binds to the small (40S) ribosomal subunit, which is required for translation inhibition. Using single-molecule fluorescence assays to monitor NSP1-40S subunit binding in real time, we determine that eukaryotic translation initiation factors (eIFs) allosterically modulate the interaction of NSP1 with ribosomal preinitiation complexes in the absence of mRNA. We further elucidate that NSP1 competes with RNA segments downstream of the start codon to bind the 40S subunit and that the protein is unable to associate rapidly with 80S ribosomes assembled on an mRNA. Collectively, our findings support a model where NSP1 proteins from viruses in at least two subgenera of beta-CoVs associate with the open head conformation of the 40S subunit to inhibit an early step of translation, by preventing accommodation of mRNA within the entry channel.
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Affiliation(s)
- Christopher P Lapointe
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Alex G Johnson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Israel S Fernández
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, NY 10032
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305;
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45
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Shamsi A, Mohammad T, Anwar S, Amani S, Khan MS, Husain FM, Rehman MT, Islam A, Hassan MI. Potential drug targets of SARS-CoV-2: From genomics to therapeutics. Int J Biol Macromol 2021; 177:1-9. [PMID: 33577820 PMCID: PMC7871800 DOI: 10.1016/j.ijbiomac.2021.02.071] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 01/18/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from China has become a global threat due to the continuous rise in cases of Coronavirus disease 2019 (COVID-19). The problem with COVID-19 therapeutics is due to complexity of the mechanism of the pathogenesis of this virus. In this review, an extensive analysis of genome architecture and mode of pathogenesis of SARS-CoV-2 with an emphasis on therapeutic approaches is performed. SARS-CoV-2 genome consists of a single, ~29.9 kb long RNA having significant sequence similarity to BAT-CoV, SARS-CoV and MERS-CoV genome. Two-third part of SARS-Cov-2 genome comprises of ORF (ORF1ab) resulting in the formation of 2 polyproteins, pp1a and pp1ab, later processed into 16 smaller non-structural proteins (NSPs). The four major structural proteins of SARS-CoV-2 are the spike surface glycoprotein (S), a small envelope (E), membrane (M), and nucleocapsid (N) proteins. S protein helps in receptor binding and membrane fusion and hence plays the most important role in the transmission of CoVs. Priming of S protein is done by serine 2 transmembrane protease and thus plays a key role in virus and host cell fusion. This review highlights the possible mechanism of action of SARS-CoV-2 to search for possible therapeutic options.
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Affiliation(s)
- Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Samreen Amani
- Department of Biochemistry, F/O Life Science, Aligarh Muslim University, Aligarh, India
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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46
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Lapointe CP, Grosely R, Johnson AG, Wang J, Fernández IS, Puglisi JD. Dynamic competition between SARS-CoV-2 NSP1 and mRNA on the human ribosome inhibits translation initiation. Proc Natl Acad Sci U S A 2021. [PMID: 33479166 DOI: 10.1101/2020.08.20.259770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a beta-CoV that recently emerged as a human pathogen and is the causative agent of the COVID-19 pandemic. A molecular framework of how the virus manipulates host cellular machinery to facilitate infection remains unclear. Here, we focus on SARS-CoV-2 NSP1, which is proposed to be a virulence factor that inhibits protein synthesis by directly binding the human ribosome. We demonstrate biochemically that NSP1 inhibits translation of model human and SARS-CoV-2 messenger RNAs (mRNAs). NSP1 specifically binds to the small (40S) ribosomal subunit, which is required for translation inhibition. Using single-molecule fluorescence assays to monitor NSP1-40S subunit binding in real time, we determine that eukaryotic translation initiation factors (eIFs) allosterically modulate the interaction of NSP1 with ribosomal preinitiation complexes in the absence of mRNA. We further elucidate that NSP1 competes with RNA segments downstream of the start codon to bind the 40S subunit and that the protein is unable to associate rapidly with 80S ribosomes assembled on an mRNA. Collectively, our findings support a model where NSP1 proteins from viruses in at least two subgenera of beta-CoVs associate with the open head conformation of the 40S subunit to inhibit an early step of translation, by preventing accommodation of mRNA within the entry channel.
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Affiliation(s)
- Christopher P Lapointe
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Alex G Johnson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Israel S Fernández
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, NY 10032
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305;
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47
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Nakagawa K, Makino S. Mechanisms of Coronavirus Nsp1-Mediated Control of Host and Viral Gene Expression. Cells 2021; 10:cells10020300. [PMID: 33540583 PMCID: PMC7912902 DOI: 10.3390/cells10020300] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/20/2022] Open
Abstract
Many viruses disrupt host gene expression by degrading host mRNAs and/or manipulating translation activities to create a cellular environment favorable for viral replication. Often, virus-induced suppression of host gene expression, including those involved in antiviral responses, contributes to viral pathogenicity. Accordingly, clarifying the mechanisms of virus-induced disruption of host gene expression is important for understanding virus–host cell interactions and virus pathogenesis. Three highly pathogenic human coronaviruses (CoVs), including severe acute respiratory syndrome (SARS)-CoV, Middle East respiratory syndrome (MERS)-CoV, and SARS-CoV-2, have emerged in the past two decades. All of them encode nonstructural protein 1 (nsp1) in their genomes. Nsp1 of SARS-CoV and MERS-CoV exhibit common biological functions for inducing endonucleolytic cleavage of host mRNAs and inhibition of host translation, while viral mRNAs evade the nsp1-induced mRNA cleavage. SARS-CoV nsp1 is a major pathogenic determinant for this virus, supporting the notion that a viral protein that suppresses host gene expression can be a virulence factor, and further suggesting the possibility that SARS-CoV-2 nsp1, which has high amino acid identity with SARS-CoV nsp1, may serve as a major virulence factor. This review summarizes the gene expression suppression functions of nsp1 of CoVs, with a primary focus on SARS-CoV nsp1 and MERS-CoV nsp1.
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Affiliation(s)
- Keisuke Nakagawa
- Laboratory of Veterinary Microbiology, Joint Department of Veterinary Medicine, Gifu University, Gifu 501-1193, Japan;
| | - Shinji Makino
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
- Center for Biodefense and Emerging Infectious Diseases, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
- UTMB Center for Tropical Diseases, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
- Sealy Center for Vaccine Development, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
- Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
- Correspondence: ; Tel.: +1-409-772-2323
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48
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Zhang K, Miorin L, Makio T, Dehghan I, Gao S, Xie Y, Zhong H, Esparza M, Kehrer T, Kumar A, Hobman TC, Ptak C, Gao B, Minna JD, Chen Z, García-Sastre A, Ren Y, Wozniak RW, Fontoura BMA. Nsp1 protein of SARS-CoV-2 disrupts the mRNA export machinery to inhibit host gene expression. SCIENCE ADVANCES 2021; 7:7/6/eabe7386. [PMID: 33547084 PMCID: PMC7864571 DOI: 10.1126/sciadv.abe7386] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/16/2020] [Indexed: 05/04/2023]
Abstract
The ongoing unprecedented severe acute respiratory syndrome caused by the SARS-CoV-2 outbreak worldwide has highlighted the need for understanding viral-host interactions involved in mechanisms of virulence. Here, we show that the virulence factor Nsp1 protein of SARS-CoV-2 interacts with the host messenger RNA (mRNA) export receptor heterodimer NXF1-NXT1, which is responsible for nuclear export of cellular mRNAs. Nsp1 prevents proper binding of NXF1 to mRNA export adaptors and NXF1 docking at the nuclear pore complex. As a result, a significant number of cellular mRNAs are retained in the nucleus during infection. Increased levels of NXF1 rescues the Nsp1-mediated mRNA export block and inhibits SARS-CoV-2 infection. Thus, antagonizing the Nsp1 inhibitory function on mRNA export may represent a strategy to restoring proper antiviral host gene expression in infected cells.
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Affiliation(s)
- Ke Zhang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tadashi Makio
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Ishmael Dehghan
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shengyan Gao
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yihu Xie
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Hualin Zhong
- Department of Biological Sciences, Hunter College, New York, NY 10065, USA
| | - Matthew Esparza
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anil Kumar
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Tom C Hobman
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Christopher Ptak
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Boning Gao
- Nancy B. and Jake L. Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John D Minna
- Nancy B. and Jake L. Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Departments of Internal Medicine and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhijian Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Richard W Wozniak
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Beatriz M A Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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49
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Giri R, Bhardwaj T, Shegane M, Gehi BR, Kumar P, Gadhave K, Oldfield CJ, Uversky VN. Understanding COVID-19 via comparative analysis of dark proteomes of SARS-CoV-2, human SARS and bat SARS-like coronaviruses. Cell Mol Life Sci 2021; 78:1655-1688. [PMID: 32712910 DOI: 10.1101/2020.03.13.990598] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/03/2020] [Accepted: 07/17/2020] [Indexed: 05/18/2023]
Abstract
The recently emerged coronavirus designated as SARS-CoV-2 (also known as 2019 novel coronavirus (2019-nCoV) or Wuhan coronavirus) is a causative agent of coronavirus disease 2019 (COVID-19), which is rapidly spreading throughout the world now. More than 1.21 million cases of SARS-CoV-2 infection and more than 67,000 COVID-19-associated mortalities have been reported worldwide till the writing of this article, and these numbers are increasing every passing hour. The World Health Organization (WHO) has declared the SARS-CoV-2 spread as a global public health emergency and admitted COVID-19 as a pandemic now. Multiple sequence alignment data correlated with the already published reports on SARS-CoV-2 evolution indicated that this virus is closely related to the bat severe acute respiratory syndrome-like coronavirus (bat SARS-like CoV) and the well-studied human SARS coronavirus (SARS-CoV). The disordered regions in viral proteins are associated with the viral infectivity and pathogenicity. Therefore, in this study, we have exploited a set of complementary computational approaches to examine the dark proteomes of SARS-CoV-2, bat SARS-like, and human SARS CoVs by analysing the prevalence of intrinsic disorder in their proteins. According to our findings, SARS-CoV-2 proteome contains very significant levels of structural order. In fact, except for nucleocapsid, Nsp8, and ORF6, the vast majority of SARS-CoV-2 proteins are mostly ordered proteins containing less intrinsically disordered protein regions (IDPRs). However, IDPRs found in SARS-CoV-2 proteins are functionally important. For example, cleavage sites in its replicase 1ab polyprotein are found to be highly disordered, and almost all SARS-CoV-2 proteins contains molecular recognition features (MoRFs), which are intrinsic disorder-based protein-protein interaction sites that are commonly utilized by proteins for interaction with specific partners. The results of our extensive investigation of the dark side of SARS-CoV-2 proteome will have important implications in understanding the structural and non-structural biology of SARS or SARS-like coronaviruses.
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Affiliation(s)
- Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India.
| | - Taniya Bhardwaj
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | - Meenakshi Shegane
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | - Bhuvaneshwari R Gehi
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | - Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Moscow region, Pushchino, 142290, Russia
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50
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Structure of Nonstructural Protein 1 from SARS-CoV-2. J Virol 2021; 95:JVI.02019-20. [PMID: 33234675 PMCID: PMC7851544 DOI: 10.1128/jvi.02019-20] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/19/2020] [Indexed: 12/16/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. One protein known to play a critical role in the coronavirus life cycle is nonstructural protein 1 (nsp1). The periodic emergence of novel coronaviruses (CoVs) represents an ongoing public health concern with significant health and financial burdens worldwide. The most recent occurrence originated in the city of Wuhan, China, where a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) emerged causing severe respiratory illness and pneumonia. The continual emergence of novel coronaviruses underscores the importance of developing effective vaccines as well as novel therapeutic options that target either viral functions or host factors recruited to support coronavirus replication. The CoV nonstructural protein 1 (nsp1) has been shown to promote cellular mRNA degradation, block host cell translation, and inhibit the innate immune response to virus infection. Interestingly, deletion of the nsp1-coding region in infectious clones prevented the virus from productively infecting cultured cells. Because of nsp1’s importance in the CoV life cycle, it has been highlighted as a viable target for both antiviral therapy and vaccine development. However, the fundamental molecular and structural mechanisms that underlie nsp1 function remain poorly understood, despite its critical role in the viral life cycle. Here, we report the high-resolution crystal structure of the amino globular portion of SARS-CoV-2 nsp1 (residues 10 to 127) at 1.77-Å resolution. A comparison of our structure with the SARS-CoV-1 nsp1 structure reveals how mutations alter the conformation of flexible loops, inducing the formation of novel secondary structural elements and new surface features. Paired with the recently published structure of the carboxyl end of nsp1 (residues 148 to 180), our results provide the groundwork for future studies focusing on SARS-CoV-2 nsp1 structure and function during the viral life cycle. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. One protein known to play a critical role in the coronavirus life cycle is nonstructural protein 1 (nsp1). As such, it has been highlighted in numerous studies as a target for both the development of antivirals and the design of live-attenuated vaccines. Here, we report the high-resolution crystal structure of nsp1 derived from SARS-CoV-2 at 1.77-Å resolution. This structure will facilitate future studies focusing on understanding the relationship between structure and function for nsp1. In turn, understanding these structure-function relationships will allow nsp1 to be fully exploited as a target for both antiviral development and vaccine design.
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