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Ivanov KI, Yang H, Sun R, Li C, Guo D. The emerging role of SARS-CoV-2 nonstructural protein 1 (nsp1) in epigenetic regulation of host gene expression. FEMS Microbiol Rev 2024; 48:fuae023. [PMID: 39231808 PMCID: PMC11418652 DOI: 10.1093/femsre/fuae023] [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: 06/19/2024] [Revised: 08/30/2024] [Accepted: 09/03/2024] [Indexed: 09/06/2024] Open
Abstract
Infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes widespread changes in epigenetic modifications and chromatin architecture in the host cell. Recent evidence suggests that SARS-CoV-2 nonstructural protein 1 (nsp1) plays an important role in driving these changes. Previously thought to be primarily involved in host translation shutoff and cellular mRNA degradation, nsp1 has now been shown to be a truly multifunctional protein that affects host gene expression at multiple levels. The functions of nsp1 are surprisingly diverse and include not only the downregulation of cellular mRNA translation and stability, but also the inhibition of mRNA export from the nucleus, the suppression of host immune signaling, and, most recently, the epigenetic regulation of host gene expression. In this review, we first summarize the current knowledge on SARS-CoV-2-induced changes in epigenetic modifications and chromatin structure. We then focus on the role of nsp1 in epigenetic reprogramming, with a particular emphasis on the silencing of immune-related genes. Finally, we discuss potential molecular mechanisms underlying the epigenetic functions of nsp1 based on evidence from SARS-CoV-2 interactome studies.
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Affiliation(s)
- Konstantin I Ivanov
- Guangzhou National Laboratory, Guangzhou, 510320, China
- Department of Microbiology, University of Helsinki, Helsinki, 00014, Finland
| | - Haibin Yang
- MOE Key Laboratory of Tropical Disease Control, Center for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Ruixue Sun
- Guangzhou National Laboratory, Guangzhou, 510320, China
| | - Chunmei Li
- MOE Key Laboratory of Tropical Disease Control, Center for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Deyin Guo
- Guangzhou National Laboratory, Guangzhou, 510320, China
- MOE Key Laboratory of Tropical Disease Control, Center for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518107, China
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China
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2
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Liu D, Leung KY, Zhang R, Lam HY, Fan Y, Xie X, Chan KH, Hung IFN. Efficacy of molnupiravir and interferon for the treatment of SARS-CoV-2 in golden Syrian hamster. J Med Virol 2024; 96:e29901. [PMID: 39210614 DOI: 10.1002/jmv.29901] [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: 06/17/2024] [Revised: 07/31/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
The mortality and hospitalization rate by COVID-19 dropped significantly currently, but its seasonal outbreaks make antiviral treatment still vital. The mortality and hospitazation rate by COVID-19 dropped significantly currently, but its seasonal ourbreaks make antiviral treatment still vital. In our study, syrian golden hamsters were treated with molnupiravir and interferons (IFNs) after SARS-CoV-2 infection. Their weight changes, pathological changes, virus replication and inflammation levels were evaluated. In the IFNs single treatment, only IFN-α group reduced viral load (p < 0.05) and virus titer in hamster lungs. The TNF-α expression decreased significantly in both IFNs treatment at 2dpi. Histological and immunofluorescence results showed lung damage in the IFNs groups were milder at 4dpi. In the molnupiravir/IFN-α combination treatment, weight loss and virus replication in lung were significantly decreased in the mono-molnupiravir group and combination group (p < 0.05), the expression of IL-6, TNF-α, IL-1β and MIP-1α also decreased significantly (p < 0.05), but the combination treatment was not more effective than the mono-molnupiravir treatment. Histological and immunofluorescence results showed the lung damage and inflammation in mono-molnupiravir and combination groups were milder. In summary, IFNs treatment had anti-inflammatory effect against SARS-CoV-2, only IFN-α showed a weak antiviral effect. Molnupiravir/IFN-α combination treatment was effective against SARS-CoV-2 but was not superior to mono-molnupiravir treatment. IFN-α could be considered for immunocompromised patients to stimulate and activate early immune responses.
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Affiliation(s)
- Danlei Liu
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Ka-Yi Leung
- Department of Microbiology, Li Ka Shing faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Ruiqi Zhang
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Hoi-Yan Lam
- Department of Microbiology, Li Ka Shing faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Yujing Fan
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Xiaochun Xie
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Kwok-Hung Chan
- Department of Microbiology, Li Ka Shing faculty of Medicine, University of Hong Kong, Hong Kong, China
- State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Ivan Fan-Ngai Hung
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
- State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, Li Ka Shing faculty of Medicine, University of Hong Kong, Hong Kong, China
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3
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Nguyen H, Nguyen HL, Li MS. Binding of SARS-CoV-2 Nonstructural Protein 1 to 40S Ribosome Inhibits mRNA Translation. J Phys Chem B 2024; 128:7033-7042. [PMID: 39007765 DOI: 10.1021/acs.jpcb.4c01391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Experimental evidence has established that SARS-CoV-2 NSP1 acts as a factor that restricts cellular gene expression and impedes mRNA translation within the ribosome's 40S subunit. However, the precise molecular mechanisms underlying this phenomenon have remained elusive. To elucidate this issue, we employed a combination of all-atom steered molecular dynamics and coarse-grained alchemical simulations to explore the binding affinity of mRNA to the 40S ribosome, both in the presence and absence of SARS-CoV-2 NSP1. Our investigations revealed that the binding of SARS-CoV-2 NSP1 to the 40S ribosome leads to a significant enhancement in the binding affinity of mRNA. This observation, which aligns with experimental findings, strongly suggests that SARS-CoV-2 NSP1 has the capability to inhibit mRNA translation. Furthermore, we identified electrostatic interactions between mRNA and the 40S ribosome as the primary driving force behind mRNA translation. Notably, water molecules were found to play a pivotal role in stabilizing the mRNA-40S ribosome complex, underscoring their significance in this process. We successfully pinpointed the specific SARS-CoV-2 NSP1 residues that play a critical role in triggering the translation arrest.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang City 550000, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Quang Trung Software City, Life Science Lab, Institute for Computational Science and Technology, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 729110, Vietnam
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4
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Zhao J, Huang Y, Liukang C, Yang R, Tang L, Sun L, Zhao Y, Zhang G. Dissecting infectious bronchitis virus-induced host shutoff at the translation level. J Virol 2024; 98:e0083024. [PMID: 38940559 PMCID: PMC11265393 DOI: 10.1128/jvi.00830-24] [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: 05/14/2024] [Accepted: 06/01/2024] [Indexed: 06/29/2024] Open
Abstract
Viruses have evolved a range of strategies to utilize or manipulate the host's cellular translational machinery for efficient infection, although the mechanisms by which infectious bronchitis virus (IBV) manipulates the host translation machinery remain unclear. In this study, we firstly demonstrate that IBV infection causes host shutoff, although viral protein synthesis is not affected. We then screened 23 viral proteins, and identified that more than one viral protein is responsible for IBV-induced host shutoff, the inhibitory effects of proteins Nsp15 were particularly pronounced. Ribosome profiling was used to draw the landscape of viral mRNA and cellular genes expression model, and the results showed that IBV mRNAs gradually dominated the cellular mRNA pool, the translation efficiency of the viral mRNAs was lower than the median efficiency (about 1) of cellular mRNAs. In the analysis of viral transcription and translation, higher densities of RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq) reads were observed for structural proteins and 5' untranslated regions, which conformed to the typical transcriptional characteristics of nested viruses. Translational halt events and the number of host genes increased significantly after viral infection. The translationally paused genes were enriched in translation, unfolded-protein-related response, and activation of immune response pathways. Immune- and inflammation-related mRNAs were inefficiently translated in infected cells, and IBV infection delayed the production of IFN-β and IFN-λ. Our results describe the translational landscape of IBV-infected cells and demonstrate new strategies by which IBV induces host gene shutoff to promote its replication. IMPORTANCE Infectious bronchitis virus (IBV) is a γ-coronavirus that causes huge economic losses to the poultry industry. Understanding how the virus manipulates cellular biological processes to facilitate its replication is critical for controlling viral infections. Here, we used Ribo-seq to determine how IBV infection remodels the host's biological processes and identified multiple viral proteins involved in host gene shutoff. Immune- and inflammation-related mRNAs were inefficiently translated, the translation halt of unfolded proteins and immune activation-related genes increased significantly, benefitting IBV replication. These data provide new insights into how IBV modulates its host's antiviral responses.
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Affiliation(s)
- Jing Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yahui Huang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chengyin Liukang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ruihua Yang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lihua Tang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lu Sun
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ye Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Guozhong Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Guillen JV, Glaunsinger BA. SARS-CoV-2 Nsp1 traps RNA in the nucleus to escape immune detection. Proc Natl Acad Sci U S A 2024; 121:e2408794121. [PMID: 38843251 PMCID: PMC11194585 DOI: 10.1073/pnas.2408794121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2024] Open
Affiliation(s)
- Jaresley V. Guillen
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA94720
| | - Britt A. Glaunsinger
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA94720
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA94720
- HHMI, Berkeley, CA94720
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6
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Mei M, Cupic A, Miorin L, Ye C, Cagatay T, Zhang K, Patel K, Wilson N, McDonald WH, Crossland NA, Lo M, Rutkowska M, Aslam S, Mena I, Martinez-Sobrido L, Ren Y, García-Sastre A, Fontoura BMA. Inhibition of mRNA nuclear export promotes SARS-CoV-2 pathogenesis. Proc Natl Acad Sci U S A 2024; 121:e2314166121. [PMID: 38768348 PMCID: PMC11145185 DOI: 10.1073/pnas.2314166121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/09/2024] [Indexed: 05/22/2024] Open
Abstract
The nonstructural protein 1 (Nsp1) of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is a virulence factor that targets multiple cellular pathways to inhibit host gene expression and antiviral response. However, the underlying mechanisms of the various Nsp1-mediated functions and their contributions to SARS-CoV-2 virulence remain unclear. Among the targets of Nsp1 is the mRNA (messenger ribonucleic acid) export receptor NXF1-NXT1, which mediates nuclear export of mRNAs from the nucleus to the cytoplasm. Based on Nsp1 crystal structure, we generated mutants on Nsp1 surfaces and identified an acidic N-terminal patch that is critical for interaction with NXF1-NXT1. Photoactivatable Nsp1 probe reveals the RNA Recognition Motif (RRM) domain of NXF1 as an Nsp1 N-terminal binding site. By mutating the Nsp1 N-terminal acidic patch, we identified a separation-of-function mutant of Nsp1 that retains its translation inhibitory function but substantially loses its interaction with NXF1 and reverts Nsp1-mediated mRNA export inhibition. We then generated a recombinant (r)SARS-CoV-2 mutant on the Nsp1 N-terminal acidic patch and found that this surface is key to promote NXF1 binding and inhibition of host mRNA nuclear export, viral replication, and pathogenicity in vivo. Thus, these findings provide a mechanistic understanding of Nsp1-mediated mRNA export inhibition and establish the importance of this pathway in the virulence of SARS-CoV-2.
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Affiliation(s)
- Menghan Mei
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN37232
| | - Anastasija Cupic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX78227
| | - Tolga Cagatay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Ke Zhang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX75390
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai200031, China
| | - Komal Patel
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN37232
- Arpirnaut Program, Vanderbilt University School of Medicine, Nashville, TN37232
| | - Natalie Wilson
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN37232
| | - W. Hayes McDonald
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN37232
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN37232
| | - Nicholas A. Crossland
- Comparative Pathology Laboratory, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02215
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA02118
| | - Ming Lo
- Comparative Pathology Laboratory, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02215
| | - Magdalena Rutkowska
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Sadaf Aslam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | | | - Yi Ren
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN37232
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY10029
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Beatriz M. A. Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX75390
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7
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Morales M, Yang MY, Goddard WA, Gray HB, Winkler JR. Copper(II) coordination to the intrinsically disordered region of SARS-CoV-2 Nsp1. Proc Natl Acad Sci U S A 2024; 121:e2402653121. [PMID: 38722808 PMCID: PMC11098128 DOI: 10.1073/pnas.2402653121] [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: 02/06/2024] [Accepted: 04/04/2024] [Indexed: 05/18/2024] Open
Abstract
The intrinsically disordered C-terminal peptide region of severe acute respiratory syndrome coronavirus 2 nonstructural protein-1 (Nsp1-CT) inhibits host protein synthesis by blocking messenger RNA (mRNA) access to the 40S ribosome entrance tunnel. Aqueous copper(II) ions bind to the disordered peptide with micromolar affinity, creating a possible strategy to restore protein synthesis during host infection. Electron paramagnetic resonance (EPR) and tryptophan fluorescence measurements on a 10-residue model of the disordered protein region (Nsp1-CT10), combined with advanced quantum mechanics calculations, suggest that the peptide binds to copper(II) as a multidentate ligand. Two optimized computational models of the copper(II)-peptide complexes were derived: One corresponding to pH 6.5 and the other describing the complex at pH 7.5 to 8.5. Simulated EPR spectra based on the calculated model structures are in good agreement with experimental spectra.
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Affiliation(s)
- Maryann Morales
- Beckman Institute, California Institute of Technology, Pasadena, CA91125
| | - Moon Young Yang
- Beckman Institute, California Institute of Technology, Pasadena, CA91125
| | - William A. Goddard
- Beckman Institute, California Institute of Technology, Pasadena, CA91125
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena, CA91125
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena, CA91125
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8
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Gori Savellini G, Anichini G, Manetti F, Trivisani CI, Cusi MG. Deletion of 82-85 N-Terminal Residues in SARS-CoV-2 Nsp1 Restricts Virus Replication. Viruses 2024; 16:689. [PMID: 38793572 PMCID: PMC11125901 DOI: 10.3390/v16050689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Non-structural protein 1 (Nsp1) represents one of the most crucial SARS-CoV-2 virulence factors by inhibiting the translation of host mRNAs and promoting their degradation. We selected naturally occurring virus lineages with specific Nsp1 deletions located at both the N- and C-terminus of the protein. Our data provide new insights into how Nsp1 coordinates these functions on host and viral mRNA recognition. Residues 82-85 in the N-terminal part of Nsp1 likely play a role in docking the 40S mRNA entry channel, preserving the inhibition of host gene expression without affecting cellular mRNA decay. Furthermore, this domain prevents viral mRNAs containing the 5'-leader sequence to escape translational repression. These findings support the presence of distinct domains within the Nsp1 protein that differentially modulate mRNA recognition, translation and turnover. These insights have implications for the development of drugs targeting viral proteins and provides new evidences of how specific mutations in SARS-CoV-2 Nsp1 could attenuate the virus.
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Affiliation(s)
| | - Gabriele Anichini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
| | - Fabrizio Manetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy (C.I.T.)
| | | | - Maria Grazia Cusi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
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9
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Karousis ED. The art of hijacking: how Nsp1 impacts host gene expression during coronaviral infections. Biochem Soc Trans 2024; 52:481-490. [PMID: 38385526 PMCID: PMC10903449 DOI: 10.1042/bst20231119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Non-structural protein 1 (Nsp1) is one of the first proteins produced during coronaviral infections. It plays a pivotal role in hijacking and rendering the host gene expression under the service of the virus. With a focus on SARS-CoV-2, this review presents how Nsp1 selectively inhibits host protein synthesis and induces mRNA degradation of host but not viral mRNAs and blocks nuclear mRNA export. The clinical implications of this protein are highlighted by showcasing the pathogenic role of Nsp1 through the repression of interferon expression pathways and the features of viral variants with mutations in the Nsp1 coding sequence. The ability of SARS-CoV-2 Nsp1 to hinder host immune responses at an early step, the absence of homology to any human proteins, and the availability of structural information render this viral protein an ideal drug target with therapeutic potential.
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Affiliation(s)
- Evangelos D Karousis
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
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10
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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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11
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Saksena NK, Reddy SB, Miranda-Saksena M, Cardoso THS, Silva EMA, Ferreira JC, Rabeh WM. SARS-CoV-2 variants, its recombinants and epigenomic exploitation of host defenses. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166836. [PMID: 37549720 DOI: 10.1016/j.bbadis.2023.166836] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 07/17/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
Since 2003, we have seen the emergence of novel viruses, such as SARS-CoV-1, MERS, ZIKA, swine flu virus H1N1, Marburg, Monkeypox, Ebola, and SARS-CoV-2, but none of them gained pandemic proportions similar to SARS-CoV-2. This could be attributed to unique viral traits, allowing its rapid global dissemination following its emergence in October 2019 in Wuhan, China, which appears to be primarily driven by the emergence of highly transmissible and virulent variants that also associate, in some cases, with severe disease and considerable mortality caused by fatal pneumonia, acute respiratory distress syndrome (ARDS) in infected individuals. Mechanistically, several factors are involved in viral pathogenesis, and epigenetic alterations take the front seat in host-virus interactions. The molecular basis of all viral infections, including SARS-CoV-2, tightly hinges on the transitory silencing of the host gene machinery via epigenetic modulation. SARS-CoV-2 also hijacks and subdues the host gene machinery, leading to epigenetic modulation of the critical host elements responsible for antiviral immunity. Epigenomics is a powerful, unexplored avenue that can provide a profound understanding of virus-host interactions and lead to the development of epigenome-based therapies and vaccines to counter viruses. This review discusses current developments in SARS-CoV-2 variation and its role in epigenetic modulation in infected hosts. This review provides an overview, especially in the context of emerging viral strains, their recombinants, and their possible roles in the epigenetic exploitation of host defense and viral pathogenesis. It provides insights into host-virus interactions at the molecular, genomic, and immunological levels and sheds light on the future of epigenomics-based therapies for SARS-CoV-2 infection.
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Affiliation(s)
- Nitin K Saksena
- Victoria University, Footscray Campus, Melbourne, VIC. Australia.
| | - Srinivasa Bonam Reddy
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | - Thyago H S Cardoso
- OMICS Centre of Excellence, G42 Healthcare, Mazdar City, Abu Dhabi, United Arab Emirates.
| | - Edson M A Silva
- Science Division, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Juliana C Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.
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12
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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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13
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Adam L, Stanifer M, Springer F, Mathony J, Brune M, Di Ponzio C, Eils R, Boulant S, Niopek D, Kallenberger SM. Transcriptomics-inferred dynamics of SARS-CoV-2 interactions with host epithelial cells. Sci Signal 2023; 16:eabl8266. [PMID: 37751479 DOI: 10.1126/scisignal.abl8266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/06/2023] [Indexed: 09/28/2023]
Abstract
Virus-host interactions can reveal potentially effective and selective therapeutic targets for treating infection. Here, we performed an integrated analysis of the dynamics of virus replication and the host cell transcriptional response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection using human Caco-2 colon cancer cells as a model. Time-resolved RNA sequencing revealed that, upon infection, cells immediately transcriptionally activated genes associated with inflammatory pathways that mediate the antiviral response, which was followed by an increase in the expression of genes involved in ribosome and mitochondria function, thus suggesting rapid alterations in protein production and cellular energy supply. At later stages, between 24 and 48 hours after infection, the expression of genes involved in metabolic processes-in particular, those related to xenobiotic metabolism-was decreased. Mathematical modeling incorporating SARS-CoV-2 replication suggested that SARS-CoV-2 proteins inhibited the host antiviral response and that virus transcripts exceeded the translation capacity of the host cells. Targeting kinase-dependent pathways that exhibited increases in transcription in host cells was as effective as a virus-targeted inhibitor at repressing viral replication. Our findings in this model system delineate a sequence of SARS-CoV-2 virus-host interactions that may facilitate the identification of druggable host pathways to suppress infection.
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Affiliation(s)
- Lukas Adam
- Health Data Science Unit, University Hospital Heidelberg and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany
| | - Megan Stanifer
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg 69120, Germany
- Department of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Fabian Springer
- Health Data Science Unit, University Hospital Heidelberg and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany
| | - Jan Mathony
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
- Center for Synthetic Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
- BZH Graduate School, Heidelberg University, Heidelberg 69120, Germany
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Faculty of Engineering Sciences, Heidelberg University, Heidelberg 69120, Germany
| | - Maik Brune
- Clinic of Endocrinology, Diabetology, Metabolism, and Clinical Chemistry, Central Laboratory, Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Chiara Di Ponzio
- Health Data Science Unit, University Hospital Heidelberg and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin 10178, Germany
| | - Roland Eils
- Health Data Science Unit, University Hospital Heidelberg and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin 10178, Germany
| | - Steeve Boulant
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg 69120, Germany
- Department of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL 32603, USA
- Research Group "Cellular polarity and viral infection" (F140), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Dominik Niopek
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
- Center for Synthetic Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Faculty of Engineering Sciences, Heidelberg University, Heidelberg 69120, Germany
| | - Stefan M Kallenberger
- Health Data Science Unit, University Hospital Heidelberg and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany
- Division of Applied Bioinformatics (G200), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- National Center for Tumor Diseases, Department of Medical Oncology, Heidelberg University Hospital, Heidelberg 69120, Germany
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14
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Sarantidi E, Ainatzoglou A, Papadimitriou C, Stamoula E, Maghiorou K, Miflidi A, Trichopoulou A, Mountzouris KC, Anagnostopoulos AK. Egg White and Yolk Protein Atlas: New Protein Insights of a Global Landmark Food. Foods 2023; 12:3470. [PMID: 37761179 PMCID: PMC10528800 DOI: 10.3390/foods12183470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/30/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
(1) Background: The chicken egg is an animal product of great agronomic interest. The egg white and yolk constitute high-quality protein sources for humans with high digestibility and well-balanced amino acid profiles. Despite the egg white and yolk protein's undisputed value, research to unravel their full proteome content and its properties is still ongoing. We aimed to exhaustively analyze the proteome of egg white and yolk by applying intrinsic proteomics and bioinformatics approaches in order to unravel the full protein potential of this landmark food. (2) Methods: A total of 45 freshly laid, unfertilized, chicken eggs were subjected to nanoLC-MS/MS Orbitrap analysis following a peptide pre-fractionation step. A comprehensive bioinformatics processing step was undertaken towards elucidating potential activities and roles of identified molecules. In parallel, the literature was mined concerning all reported egg white and yolk protein identifications. (3) Results: Our analysis revealed 371 and 428 new proteins, reported for the first time to be present in the egg white and yolk, respectively. From the bioactivity standpoint, egg white and yolk proteins showed high enrichment for antioxidant and anti-inflammatory processes, while exerting high relevance for the apoptosis and focal adhesion pathways. (4) Conclusions: Egg white and yolk proteins exert diverse and multifaceted properties. A total of 799 proteins were reported for the first time as being part of the egg and yolk. Our novel protein data enriched those already published in the literature and the first ever chicken egg white and yolk Protein Atlas, comprising 1392 protein entries, was generated. This dataset will provide a cornerstone reference for future studies involving egg proteins.
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Affiliation(s)
- Eleana Sarantidi
- Department of Biotechnology, Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Alexandra Ainatzoglou
- Department of Biotechnology, Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Christine Papadimitriou
- Department of Biotechnology, Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Eleni Stamoula
- Department of Biotechnology, Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Katerina Maghiorou
- Department of Biotechnology, Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Argyro Miflidi
- Department of Biotechnology, Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Antonia Trichopoulou
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | | | - Athanasios K. Anagnostopoulos
- Department of Biotechnology, Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
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15
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Tardivat Y, Sosnowski P, Tidu A, Westhof E, Eriani G, Martin F. SARS-CoV-2 NSP1 induces mRNA cleavages on the ribosome. Nucleic Acids Res 2023; 51:8677-8690. [PMID: 37503833 PMCID: PMC10484668 DOI: 10.1093/nar/gkad627] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023] Open
Abstract
In severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the non-structural protein NSP1 inhibits translation of host mRNAs by binding to the mRNA entry channel of the ribosome and, together with the 5'-untranslated region (UTR) of the viral mRNAs, allows the evasion of that inhibition. Here, we show that NSP1 mediates endonucleolytic cleavages of both host and viral mRNAs in the 5'UTR, but with different cleavage patterns. The first pattern is observed in host mRNAs with cleavages interspersed regularly and close to the 5' cap (6-11 nt downstream of the cap). Those cleavage positions depend more on the position relative to the 5' cap than on the sequence itself. The second cleavage pattern occurs at high NSP1 concentrations and only in SARS-CoV-2 RNAs, with the cleavages clustered at positions 45, 46 and 49. Both patterns of cleavage occur with the mRNA and NSP1 bound to the ribosome, with the SL1 hairpin at the 5' end sufficient to protect from NSP1-mediated degradation at low NSP1 concentrations. We show further that the N-terminal domain of NSP1 is necessary and sufficient for efficient cleavage. We suggest that in the ribosome-bound NSP1 protein the catalytic residues of the N-terminal domain are unmasked by the remodelling of the α1- and α2-helices of the C-terminal domain.
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Affiliation(s)
- Yann Tardivat
- 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
| | - Piotr Sosnowski
- 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
| | - Antonin Tidu
- 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
| | - Eric Westhof
- 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
| | - 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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16
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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: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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17
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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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18
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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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19
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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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20
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Oh S, Lee S. Recent advances in ZBP1-derived PANoptosis against viral infections. Front Immunol 2023; 14:1148727. [PMID: 37261341 PMCID: PMC10228733 DOI: 10.3389/fimmu.2023.1148727] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/03/2023] [Indexed: 06/02/2023] Open
Abstract
Innate immunity is an important first line of defense against pathogens, including viruses. These pathogen- and damage-associated molecular patterns (PAMPs and DAMPs, respectively), resulting in the induction of inflammatory cell death, are detected by specific innate immune sensors. Recently, Z-DNA binding protein 1 (ZBP1), also called the DNA-dependent activator of IFN regulatory factor (DAI) or DLM1, is reported to regulate inflammatory cell death as a central mediator during viral infection. ZBP1 is an interferon (IFN)-inducible gene that contains two Z-form nucleic acid-binding domains (Zα1 and Zα2) in the N-terminus and two receptor-interacting protein homotypic interaction motifs (RHIM1 and RHIM2) in the middle, which interact with other proteins with the RHIM domain. By sensing the entry of viral RNA, ZBP1 induces PANoptosis, which protects host cells against viral infections, such as influenza A virus (IAV) and herpes simplex virus (HSV1). However, some viruses, particularly coronaviruses (CoVs), induce PANoptosis to hyperactivate the immune system, leading to cytokine storm, organ failure, tissue damage, and even death. In this review, we discuss the molecular mechanism of ZBP1-derived PANoptosis and pro-inflammatory cytokines that influence the double-edged sword of results in the host cell. Understanding the ZBP1-derived PANoptosis mechanism may be critical for improving therapeutic strategies.
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21
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Davies ER, Ryan KA, Bewley KR, Coombes NS, Salguero FJ, Carnell OT, Biddlecombe S, Charlton M, Challis A, Cross ES, Handley A, Ngabo D, Weldon TM, Hall Y, Funnell SGP. The Omicron Sub-Variant BA.4 Displays a Remarkable Lack of Clinical Signs in a Golden Syrian Hamster Model of SARS-CoV-2 Infection. Viruses 2023; 15:1133. [PMID: 37243219 PMCID: PMC10224153 DOI: 10.3390/v15051133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The ongoing emergence of SARS-CoV-2 virus variants remains a source of concern because it is accompanied by the potential for increased virulence as well as evasion of immunity. Here we show that, although having an almost identical spike gene sequence as another Omicron variant (BA.5.2.1), a BA.4 isolate lacked all the typical disease characteristics of other isolates seen in the Golden Syrian hamster model despite replicating almost as effectively. Animals infected with BA.4 had similar viral shedding profiles to those seen with BA.5.2.1 (up to day 6 post-infection), but they all failed to lose weight or present with any other significant clinical signs. We hypothesize that this lack of detectable signs of disease during infection with BA.4 was due to a small (nine nucleotide) deletion (∆686-694) in the viral genome (ORF1ab) responsible for the production of non-structural protein 1, which resulted in the loss of three amino acids (aa 141-143).
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Affiliation(s)
- Elizabeth R. Davies
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Kathryn A. Ryan
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Kevin R. Bewley
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Naomi S. Coombes
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Francisco J. Salguero
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Oliver T. Carnell
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Sarah Biddlecombe
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Michael Charlton
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Amy Challis
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Eleanor S. Cross
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Alastair Handley
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Didier Ngabo
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Thomas M. Weldon
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Yper Hall
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Simon G. P. Funnell
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- World Health Organization, Appia 20, 1211 Geneva, Switzerland
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22
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Chen SC, Xu CT, Chang CF, Chao TY, Lin CC, Fu PW, Yu CH. Optimization of 5'UTR to evade SARS-CoV-2 Nonstructural protein 1-directed inhibition of protein synthesis in cells. Appl Microbiol Biotechnol 2023; 107:2451-2468. [PMID: 36843199 PMCID: PMC9968647 DOI: 10.1007/s00253-023-12442-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/28/2023]
Abstract
Maximizing the expression level of therapeutic proteins in cells is the general goal for DNA/mRNA therapies. It is particularly challenging to achieve efficient protein expression in the cellular contexts with inhibited translation machineries, such as in the presence of cellular Nonstructural protein 1 (Nsp1) of coronaviruses (CoVs) that has been reported to inhibit overall protein synthesis of host genes and exogenously delivered mRNAs/DNAs. In this study, we thoroughly examined the sequence and structure contexts of viral and non-viral 5'UTRs that determine the protein expression levels of exogenously delivered DNAs and mRNAs in cells expressing SARS-CoV-2 Nsp1. It was found that high 5'-proximal A/U content promotes an escape from Nsp1-directed inhibition of protein synthesis and results in selective protein expression. Furthermore, 5'-proximal Cs were found to significantly enhance the protein expression in an Nsp1-dependent manner, while Gs located at a specific window close to the 5'-end counteract such enhancement. The distinct protein expression levels resulted from different 5'UTRs were found correlated to Nsp1-induced mRNA degradations. These findings ultimately enabled rational designs for optimized 5'UTRs that lead to strong expression of exogenous proteins regardless of the translationally repressive Nsp1. On the other hand, we have also identified several 5'-proximal sequences derived from host genes that are capable of mediating the escapes. These results provided novel perspectives to the optimizations of 5'UTRs for DNA/mRNA therapies and/or vaccinations, as well as shedding light on the potential host escapees from Nsp1-directed translational shutoffs. KEY POINTS: • The 5'-proximal SL1 and 5a/b derived from SARS-CoV-2 genomic RNA promote exogenous protein synthesis in cells expressing Nsp1 comparing with non-specific 5'UTRs. • Specific 5'-proximal sequence contexts are the key determinants of the escapes from Nsp1-directed translational repression and thereby enhance protein expressions. • Systematic mutagenesis identified optimized 5'UTRs that strongly enhance protein expression and promote resistance to Nsp1-induced translational repression and RNA degradation.
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Affiliation(s)
- Shih-Cheng Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, New Taipei, Taiwan
| | - Cui-Ting Xu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chuan-Fu Chang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ting-Yu Chao
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Chi Lin
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Wen Fu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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23
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Korneeva N, Khalil MI, Ghosh I, Fan R, Arnold T, De Benedetti A. SARS-CoV-2 viral protein Nsp2 stimulates translation under normal and hypoxic conditions. Virol J 2023; 20:55. [PMID: 36998012 PMCID: PMC10060939 DOI: 10.1186/s12985-023-02021-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
AbstractWhen viruses like SARS-CoV-2 infect cells, they reprogram the repertoire of cellular and viral transcripts that are being translated to optimize their strategy of replication, often targeting host translation initiation factors, particularly eIF4F complex consisting of eIF4E, eIF4G and eIF4A. A proteomic analysis of SARS-CoV-2/human proteins interaction revealed viral Nsp2 and initiation factor eIF4E2, but a role of Nsp2 in regulating translation is still controversial. HEK293T cells stably expressing Nsp2 were tested for protein synthesis rates of synthetic and endogenous mRNAs known to be translated via cap- or IRES-dependent mechanism under normal and hypoxic conditions. Both cap- and IRES-dependent translation were increased in Nsp2-expressing cells under normal and hypoxic conditions, especially mRNAs that require high levels of eIF4F. This could be exploited by the virus to maintain high translation rates of both viral and cellular proteins, particularly in hypoxic conditions as may arise in SARS-CoV-2 patients with poor lung functioning.
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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: 7] [Impact Index Per Article: 7.0] [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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25
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Waisner H, Grieshaber B, Saud R, Henke W, Stephens EB, Kalamvoki M. SARS-CoV-2 Harnesses Host Translational Shutoff and Autophagy To Optimize Virus Yields: the Role of the Envelope (E) Protein. Microbiol Spectr 2023; 11:e0370722. [PMID: 36622177 PMCID: PMC9927098 DOI: 10.1128/spectrum.03707-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/07/2022] [Indexed: 01/10/2023] Open
Abstract
The SARS-CoV-2 virion is composed of four structural proteins: spike (S), nucleocapsid (N), membrane (M), and envelope (E). E spans the membrane a single time and is the smallest, yet most enigmatic of the structural proteins. E is conserved among coronaviruses and has an essential role in virus-mediated pathogenesis. We found that ectopic expression of E had deleterious effects on the host cell as it activated stress responses, leading to LC3 lipidation and phosphorylation of the translation initiation factor eIF2α that resulted in host translational shutoff. During infection E is highly expressed, although only a small fraction is incorporated into virions, suggesting that E activity is regulated and harnessed by the virus to its benefit. Consistently, we found that proteins from heterologous viruses, such as the γ1 34.5 protein of herpes simplex virus 1, prevented deleterious effects of E on the host cell and allowed for E protein accumulation. This observation prompted us to investigate whether other SARS-CoV-2 structural proteins regulate E. We found that the N and M proteins enabled E protein accumulation, whereas S did not. While γ1 34.5 protein prevented deleterious effects of E on the host cells, it had a negative effect on SARS-CoV-2 replication. The negative effect of γ1 34.5 was most likely associated with failure of SARS-CoV-2 to divert the translational machinery and with deregulation of autophagy. Overall, our data suggest that SARS-CoV-2 causes stress responses and subjugates these pathways, including host protein synthesis (phosphorylated eIF2α) and autophagy, to support optimal virus replication. IMPORTANCE In late 2019, a new β-coronavirus, SARS-CoV-2, entered the human population causing a pandemic that has resulted in over 6 million deaths worldwide. Although closely related to SARS-CoV, the mechanisms of SARS-CoV-2 pathogenesis are not fully understood. We found that ectopic expression of the SARS-CoV-2 E protein had detrimental effects on the host cell, causing metabolic alterations, including shutoff of protein synthesis and mobilization of cellular resources through autophagy activation. Coexpression of E with viral proteins known to subvert host antiviral responses such as autophagy and translational inhibition, either from SARS-CoV-2 or from heterologous viruses, increased cell survival and E protein accumulation. However, such factors were found to negatively impact SARS-CoV-2 infection, as autophagy contributes to formation of viral membrane factories and translational control offers an advantage for viral gene expression. Overall, SARS-CoV-2 has evolved mechanisms to harness host functions that are essential for virus replication.
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Affiliation(s)
- Hope Waisner
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Brandon Grieshaber
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Rabina Saud
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Wyatt Henke
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Edward B. Stephens
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
| | - Maria Kalamvoki
- University of Kansas Medical Center, Department of Microbiology, Molecular Genetics, and Immunology, Kansas City, Kansas, USA
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26
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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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27
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Bermudez Y, Miles J, Muller M. Nonstructural protein 1 widespread RNA decay phenotype varies among coronaviruses. iScience 2023; 26:105887. [PMID: 36590901 PMCID: PMC9794394 DOI: 10.1016/j.isci.2022.105887] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/15/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Extensive remodeling of host gene expression by nonstructural protein 1 (nsp1) of coronaviruses is a well-documented and conserved aspect of coronavirus-host takeover. Using comparative transcriptomics we investigated the diversity of transcriptional targets between various nsp1 proteins. Additionally, affinity purification followed by mass spectrometry was implemented to identify common interactors between the different nsp1 proteins. Although we detected widespread RNA destabilization, closely related nsp1 showed little similarities in clustering of targeted genes. We observed a partial overlap in transcriptional targeting between α-CoV 229E and MERS nsp1, which may suggest a common targeting mechanism, as MERS nsp1 preferentially targets nuclear transcripts. Our interactome data show great variability between nsp1 interactions, with 229E nsp1, the smallest nsp1 tested here, interacting with the most number of host proteins. Although nsp1 is a rather well-conserved protein with conserved functions across different coronaviruses, our data indicate that its precise effects on the host cell are virus specific.
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Affiliation(s)
- Yahaira Bermudez
- Department of Microbiology, University of Massachusetts, Amherst, 639 North Pleasant street, Morrill IV North, MA 01003 USA
| | - Jacob Miles
- Department of Microbiology, University of Massachusetts, Amherst, 639 North Pleasant street, Morrill IV North, MA 01003 USA
| | - Mandy Muller
- Department of Microbiology, University of Massachusetts, Amherst, 639 North Pleasant street, Morrill IV North, MA 01003 USA,Corresponding author
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28
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Ghaleh SS, Rahimian K, Mahmanzar M, Mahdavi B, Tokhanbigli S, Sisakht MM, Farhadi A, Bakhtiari MM, Kuehu DL, Deng Y. SARS-CoV-2 Non-structural protein 1(NSP1) mutation virulence and natural selection: Evolutionary trends in the six continents. Virus Res 2023; 323:199016. [PMID: 36473671 PMCID: PMC9721189 DOI: 10.1016/j.virusres.2022.199016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Rapid transmission and reproduction of RNA viruses prepare conducive conditions to have a high rate of mutations in their genetic sequence. The viral mutations make adapt the severe acute respiratory syndrome coronavirus 2 in the host environment and help the evolution of the virus then also caused a high mortality rate by the virus that threatens worldwide health. Mutations and adaptation help the virus to escape confrontations that are done against it. METHODS In the present study, we analyzed 6,510,947 sequences of non-structural protein 1 as one of the conserved regions of the virus to find out frequent mutations and substitute amino acids in comparison with the wild type. NSP1 mutations rate divided into continents were different. RESULTS Based on this continental categorization, E87D in global vision and also in Europe notably increased. The E87D mutation has signed up to January 2022 as the first frequent mutation observed. The remarkable mutations, H110Y and R24C have the second and third frequencies, respectively. CONCLUSION According to the important role of non-structural protein 1 on the host mRNA translation, developing drug design against the protein could be so hopeful to find more effective ways the control and then treatment of the global pandemic coronavirus disease 2019.
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Affiliation(s)
| | - Karim Rahimian
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics. Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammadamin Mahmanzar
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Bahar Mahdavi
- Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Samaneh Tokhanbigli
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran (IAUPS)
| | - Mahsa Mollapour Sisakht
- Department of Biochemistry, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Amin Farhadi
- Department of Biology, Payame Noor University, Tehran, Iran
| | - Mahsa Mousakhan Bakhtiari
- Pediatric Cell Therapy Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Donna Lee Kuehu
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA.
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29
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Dolliver SM, Kleer M, Bui-Marinos MP, Ying S, Corcoran JA, Khaperskyy DA. Nsp1 proteins of human coronaviruses HCoV-OC43 and SARS-CoV2 inhibit stress granule formation. PLoS Pathog 2022; 18:e1011041. [PMID: 36534661 PMCID: PMC9810206 DOI: 10.1371/journal.ppat.1011041] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/03/2023] [Accepted: 12/03/2022] [Indexed: 12/23/2022] Open
Abstract
Stress granules (SGs) are cytoplasmic condensates that often form as part of the cellular antiviral response. Despite the growing interest in understanding the interplay between SGs and other biological condensates and viral replication, the role of SG formation during coronavirus infection remains poorly understood. Several proteins from different coronaviruses have been shown to suppress SG formation upon overexpression, but there are only a handful of studies analyzing SG formation in coronavirus-infected cells. To better understand SG inhibition by coronaviruses, we analyzed SG formation during infection with the human common cold coronavirus OC43 (HCoV-OC43) and the pandemic SARS-CoV2. We did not observe SG induction in infected cells and both viruses inhibited eukaryotic translation initiation factor 2α (eIF2α) phosphorylation and SG formation induced by exogenous stress. Furthermore, in SARS-CoV2 infected cells we observed a sharp decrease in the levels of SG-nucleating protein G3BP1. Ectopic overexpression of nucleocapsid (N) and non-structural protein 1 (Nsp1) from both HCoV-OC43 and SARS-CoV2 inhibited SG formation. The Nsp1 proteins of both viruses inhibited arsenite-induced eIF2α phosphorylation, and the Nsp1 of SARS-CoV2 alone was sufficient to cause a decrease in G3BP1 levels. This phenotype was dependent on the depletion of cytoplasmic mRNA mediated by Nsp1 and associated with nuclear accumulation of the SG-nucleating protein TIAR. To test the role of G3BP1 in coronavirus replication, we infected cells overexpressing EGFP-tagged G3BP1 with HCoV-OC43 and observed a significant decrease in virus replication compared to control cells expressing EGFP. The antiviral role of G3BP1 and the existence of multiple SG suppression mechanisms that are conserved between HCoV-OC43 and SARS-CoV2 suggest that SG formation may represent an important antiviral host defense that coronaviruses target to ensure efficient replication.
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Affiliation(s)
- Stacia M. Dolliver
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Canada
| | - Mariel Kleer
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
- Snyder Institute for Chronic Diseases and Charbonneau Institute for Cancer Research, University of Calgary, Calgary, Canada
| | - Maxwell P. Bui-Marinos
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
- Snyder Institute for Chronic Diseases and Charbonneau Institute for Cancer Research, University of Calgary, Calgary, Canada
| | - Shan Ying
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Canada
| | - Jennifer A. Corcoran
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
- Snyder Institute for Chronic Diseases and Charbonneau Institute for Cancer Research, University of Calgary, Calgary, Canada
| | - Denys A. Khaperskyy
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Canada
- * E-mail:
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30
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Wang X, Zhu J, Zhang D, Liu G. Ribosomal control in RNA virus-infected cells. Front Microbiol 2022; 13:1026887. [PMID: 36419416 PMCID: PMC9677555 DOI: 10.3389/fmicb.2022.1026887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
Viruses are strictly intracellular parasites requiring host cellular functions to complete their reproduction cycle involving virus infection of host cell, viral genome replication, viral protein translation, and virion release. Ribosomes are protein synthesis factories in cells, and viruses need to manipulate ribosomes to complete their protein synthesis. Viruses use translation initiation factors through their own RNA structures or cap structures, thereby inducing ribosomes to synthesize viral proteins. Viruses also affect ribosome production and the assembly of mature ribosomes, and regulate the recognition of mRNA by ribosomes, thereby promoting viral protein synthesis and inhibiting the synthesis of host antiviral immune proteins. Here, we review the remarkable mechanisms used by RNA viruses to regulate ribosomes, in particular, the mechanisms by which RNA viruses induce the formation of specific heterogeneous ribosomes required for viral protein translation. This review provides valuable insights into the control of viral infection and diseases from the perspective of viral protein synthesis.
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31
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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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32
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Patra SK, Szyf M. Epigenetic perspectives of COVID-19: Virus infection to disease progression and therapeutic control. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166527. [PMID: 36002132 PMCID: PMC9393109 DOI: 10.1016/j.bbadis.2022.166527] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/05/2022] [Accepted: 08/18/2022] [Indexed: 11/20/2022]
Abstract
COVID-19 has caused numerous deaths as well as imposed social isolation and upheaval world-wide. Although, the genome and the composition of the virus, the entry process and replication mechanisms are well investigated from by several laboratories across the world, there are many unknown remaining questions. For example, what are the functions of membrane lipids during entry, packaging and exit of virus particles? Also, the metabolic aspects of the infected tissue cells are poorly understood. In the course of virus replication and formation of virus particles within the host cell, the enhanced metabolic activities of the host is directly proportional to viral loads. The epigenetic landscape of the host cells is also altered, particularly the expression/repression of genes associated with cellular metabolism as well as cellular processes that are antagonistic to the virus. Metabolic pathways are enzyme driven processes and the expression profile and mechanism of regulations of the respective genes encoding those enzymes during the course of pathogen invasion might be highly informative on the course of the disease. Recently, the metabolic profile of the patients' sera have been analysed from few patients. In view of this, and to gain further insights into the roles that epigenetic mechanisms might play in this scenario in regulation of metabolic pathways during the progression of COVID-19 are discussed and summarised in this contribution for ensuring best therapy.
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Affiliation(s)
- Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McIntyre Medical Sciences Building, McGill University, Montreal, QC H3G 1Y6, Canada
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Rashid F, Xie Z, Suleman M, Shah A, Khan S, Luo S. Roles and functions of SARS-CoV-2 proteins in host immune evasion. Front Immunol 2022; 13:940756. [PMID: 36003396 PMCID: PMC9394213 DOI: 10.3389/fimmu.2022.940756] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/07/2022] [Indexed: 12/27/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evades the host immune system through a variety of regulatory mechanisms. The genome of SARS-CoV-2 encodes 16 non-structural proteins (NSPs), four structural proteins, and nine accessory proteins that play indispensable roles to suppress the production and signaling of type I and III interferons (IFNs). In this review, we discussed the functions and the underlying mechanisms of different proteins of SARS-CoV-2 that evade the host immune system by suppressing the IFN-β production and TANK-binding kinase 1 (TBK1)/interferon regulatory factor 3 (IRF3)/signal transducer and activator of transcription (STAT)1 and STAT2 phosphorylation. We also described different viral proteins inhibiting the nuclear translocation of IRF3, nuclear factor-κB (NF-κB), and STATs. To date, the following proteins of SARS-CoV-2 including NSP1, NSP6, NSP8, NSP12, NSP13, NSP14, NSP15, open reading frame (ORF)3a, ORF6, ORF8, ORF9b, ORF10, and Membrane (M) protein have been well studied. However, the detailed mechanisms of immune evasion by NSP5, ORF3b, ORF9c, and Nucleocapsid (N) proteins are not well elucidated. Additionally, we also elaborated the perspectives of SARS-CoV-2 proteins.
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Affiliation(s)
- Farooq Rashid
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Zhixun Xie
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- *Correspondence: Zhixun Xie,
| | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Abdullah Shah
- Department of Biotechnology, Shaheed Benazir Bhutto University, Sheringal, Pakistan
| | - Suliman Khan
- Department of Medical Lab Technology, The University of Haripur, Haripur, Pakistan
| | - Sisi Luo
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
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Salami Ghaleh S, Rahimian K, Mahmanzar M, Mahdavi B, Tokhanbigli S, Mollapour Sisakht M, Farhadi A, Mousakhan Bakhtiari M, Lee Kuehu D, Deng Y. SARS-CoV-2 Non-Structural Protein 1(NSP1) Mutation Virulence and Natural Selection: Evolutionary Trends in the Six Continents. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.07.22.501212. [PMID: 35923310 PMCID: PMC9347281 DOI: 10.1101/2022.07.22.501212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an unsegmented positivesense single-stranded RNA virus that belongs to the β-coronavirus . This virus was the cause of a novel severe acute respiratory syndrome in 2019 (COVID-19) that emerged in Wuhan, China at the early stage of the pandemic and rapidly spread around the world. Rapid transmission and reproduction of SARS-CoV-2 threaten worldwide health with a high mortality rate from the virus. According to the significant role of non-structural protein 1 (NSP1) in inhibiting host mRNA translation, this study focuses on the link between amino acid sequences of NSP1 and alterations of them spreading around the world. The SARS-CoV-2 NSP1 protein sequences were analyzed and FASTA files were processed by Python language programming libraries. Reference sequences compared with each NSP1 sample to identify every mutation and categorize them were based on continents and frequencies. NSP1 mutations rate divided into continents were different. Based on continental studies, E87D in global vision and also in Europe notably increased. The E87D mutation has significantly risen especially in the last months of the study as the first frequent mutation observed. The remarkable mutations, H110Y and R24C, have the second and third frequencies, respectively. Based on this mutational information, despite NSP1 being a conserved sequence occurrence, these mutations change the rate of flexibility and stability of the NSP1 protein, which can eventually affect inhibiting the host translation. IMPORTANCE In this study, we analyzed 6,510,947 sequences of non-structural protein 1 as a conserved region of SARS-CoV-2. According to the obtained results, 93.4819% of samples had no mutant regions on their amino acid sequences. Heat map data of mutational samples demonstrated high percentages of mutations that occurred in the region of 72 to 126 amino acids indicating a hot spot region of the protein. Increased rates of E87D, H110Y, and R24C mutations in the timeline of our study were reported as significant compared to available mutant samples. Analyzing the details of replacing amino acids in the most frequent E87D mutation reveals the role of this alteration in increasing molecule flexibility and destabilizing the structure of the protein.
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35
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Loh D, Reiter RJ. Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19. Int J Mol Sci 2022; 23:8122. [PMID: 35897696 PMCID: PMC9368024 DOI: 10.3390/ijms23158122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/09/2022] [Accepted: 07/20/2022] [Indexed: 01/27/2023] Open
Abstract
The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA;
| | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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36
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Slobodin B, Sehrawat U, Lev A, Hayat D, Zuckerman B, Fraticelli D, Ogran A, Ben-Shmuel A, Bar-David E, Levy H, Ulitsky I, Dikstein R. Cap-independent translation and a precisely located RNA sequence enable SARS-CoV-2 to control host translation and escape anti-viral response. Nucleic Acids Res 2022; 50:8080-8092. [PMID: 35849342 PMCID: PMC9371909 DOI: 10.1093/nar/gkac615] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 06/09/2022] [Accepted: 07/04/2022] [Indexed: 12/29/2022] Open
Abstract
Translation of SARS-CoV-2-encoded mRNAs by the host ribosomes is essential for its propagation. Following infection, the early expressed viral protein NSP1 binds the ribosome, represses translation, and induces mRNA degradation, while the host elicits an anti-viral response. The mechanisms enabling viral mRNAs to escape this multifaceted repression remain obscure. Here we show that expression of NSP1 leads to destabilization of multi-exon cellular mRNAs, while intron-less transcripts, such as viral mRNAs and anti-viral interferon genes, remain relatively stable. We identified a conserved and precisely located cap-proximal RNA element devoid of guanosines that confers resistance to NSP1-mediated translation inhibition. Importantly, the primary sequence rather than the secondary structure is critical for protection. We further show that the genomic 5'UTR of SARS-CoV-2 drives cap-independent translation and promotes expression of NSP1 in an eIF4E-independent and Torin1-resistant manner. Upon expression, NSP1 further enhances cap-independent translation. However, the sub-genomic 5'UTRs are highly sensitive to eIF4E availability, rendering viral propagation partially sensitive to Torin1. We conclude that the combined NSP1-mediated degradation of spliced mRNAs and translation inhibition of single-exon genes, along with the unique features present in the viral 5'UTRs, ensure robust expression of viral mRNAs. These features can be exploited as potential therapeutic targets.
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Affiliation(s)
- Boris Slobodin
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Urmila Sehrawat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.,Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anastasia Lev
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Daniel Hayat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Binyamin Zuckerman
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel.,Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Davide Fraticelli
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ariel Ogran
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Amir Ben-Shmuel
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 7410001 Israel
| | - Elad Bar-David
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 7410001 Israel
| | - Haim Levy
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 7410001 Israel
| | - Igor Ulitsky
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rivka Dikstein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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37
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Jin Y, Ouyang M, Yu T, Zhuang J, Wang W, Liu X, Duan F, Guo D, Peng X, Pan JA. Genome-Wide Analysis of the Indispensable Role of Non-structural Proteins in the Replication of SARS-CoV-2. Front Microbiol 2022; 13:907422. [PMID: 35722274 PMCID: PMC9198553 DOI: 10.3389/fmicb.2022.907422] [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: 03/29/2022] [Accepted: 04/21/2022] [Indexed: 11/27/2022] Open
Abstract
Understanding the process of replication and transcription of SARS-CoV-2 is essential for antiviral strategy development. The replicase polyprotein is indispensable for viral replication. However, whether all nsps derived from the replicase polyprotein of SARS-CoV-2 are indispensable is not fully understood. In this study, we utilized the SARS-CoV-2 replicon as the system to investigate the role of each nsp in viral replication. We found that except for nsp16, all the nsp deletions drastically impair the replication of the replicon, and nsp14 could recover the replication deficiency caused by its deletion in the viral replicon. Due to the unsuccessful expressions of nsp1, nsp3, and nsp16, we could not draw a conclusion about their in trans-rescue functions. Our study provided a new angle to understand the role of each nsp in viral replication and transcription, helping the evaluation of nsps as the target for antiviral drug development.
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Affiliation(s)
- Yunyun Jin
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Muzi Ouyang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Ting Yu
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Jiaxin Zhuang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Wenhao Wang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Xue Liu
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Fangfang Duan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Deyin Guo
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Xiaoxue Peng
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Ji-An Pan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
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38
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Morales M, Ravanfar R, Oyala PH, Gray HB, Winkler JR. Copper(II) Binding to the Intrinsically Disordered C-Terminal Peptide of SARS-CoV-2 Virulence Factor Nsp1. Inorg Chem 2022; 61:8992-8996. [PMID: 35658408 PMCID: PMC9195567 DOI: 10.1021/acs.inorgchem.2c01329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Indexed: 11/28/2022]
Abstract
The first encoded SARS-CoV-2 protein (Nsp1) binds to the human 40S ribosome and blocks synthesis of host proteins, thereby inhibiting critical elements of the innate immune response. The final 33 residues of the natively unstructured Nsp1 C-terminus adopt a helix-turn-helix geometry upon binding to the ribosome. We have characterized the fluctuating conformations of this peptide using circular dichroism spectroscopy along with measurements of tryptophan fluorescence and energy transfer. Tryptophan fluorescence decay kinetics reveal that copper(II) binds to the peptide at micromolar concentrations, and electron paramagnetic resonance spectroscopy indicates that the metal ion coordinates to the lone histidine residue.
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Affiliation(s)
- Maryann Morales
- Beckman Institute, California Institute of Technology, Pasadena, California 91125 United States
| | - Raheleh Ravanfar
- Beckman Institute, California Institute of Technology, Pasadena, California 91125 United States
| | - Paul H. Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125 United States
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena, California 91125 United States
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39
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Fisher T, Gluck A, Narayanan K, Kuroda M, Nachshon A, Hsu JC, Halfmann PJ, Yahalom-Ronen Y, Tamir H, Finkel Y, Schwartz M, Weiss S, Tseng CTK, Israely T, Paran N, Kawaoka Y, Makino S, Stern-Ginossar N. Parsing the role of NSP1 in SARS-CoV-2 infection. Cell Rep 2022; 39:110954. [PMID: 35671758 PMCID: PMC9133101 DOI: 10.1016/j.celrep.2022.110954] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/06/2022] [Accepted: 05/23/2022] [Indexed: 11/18/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) leads to shutoff of protein synthesis, and nsp1, a central shutoff factor in coronaviruses, inhibits cellular mRNA translation. However, the diverse molecular mechanisms employed by nsp1 as well as its functional importance are unresolved. By overexpressing various nsp1 mutants and generating a SARS-CoV-2 mutant, we show that nsp1, through inhibition of translation and induction of mRNA degradation, targets translated cellular mRNA and is the main driver of host shutoff during infection. The propagation of nsp1 mutant virus is inhibited exclusively in cells with intact interferon (IFN) pathway as well as in vivo, in hamsters, and this attenuation is associated with stronger induction of type I IFN response. Therefore, although nsp1's shutoff activity is broad, it plays an essential role, specifically in counteracting the IFN response. Overall, our results reveal the multifaceted approach nsp1 uses to shut off cellular protein synthesis and uncover nsp1's explicit role in blocking the IFN response.
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Affiliation(s)
- Tal Fisher
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Avi Gluck
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Krishna Narayanan
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
| | - Makoto Kuroda
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711, USA
| | - Aharon Nachshon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jason C Hsu
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711, USA
| | - Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Hadas Tamir
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Yaara Finkel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shay Weiss
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Chien-Te K Tseng
- Department of Microbiology and Immunology, 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
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel.
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711, USA; Department of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan.
| | - Shinji Makino
- Department of Microbiology and Immunology, 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.
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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40
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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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41
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Bujanic L, Shevchuk O, von Kügelgen N, Kalinina A, Ludwik K, Koppstein D, Zerna N, Sickmann A, Chekulaeva M. The key features of SARS-CoV-2 leader and NSP1 required for viral escape of NSP1-mediated repression. RNA (NEW YORK, N.Y.) 2022; 28:766-779. [PMID: 35232816 PMCID: PMC9014875 DOI: 10.1261/rna.079086.121] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
SARS-CoV-2, responsible for the ongoing global pandemic, must overcome a conundrum faced by all viruses. To achieve its own replication and spread, it simultaneously depends on and subverts cellular mechanisms. At the early stage of infection, SARS-CoV-2 expresses the viral nonstructural protein 1 (NSP1), which inhibits host translation by blocking the mRNA entry tunnel on the ribosome; this interferes with the binding of cellular mRNAs to the ribosome. Viral mRNAs, on the other hand, overcome this blockade. We show that NSP1 enhances expression of mRNAs containing the SARS-CoV-2 leader. The first stem-loop (SL1) in the viral leader is both necessary and sufficient for this enhancement mechanism. Our analysis pinpoints specific residues within SL1 (three cytosine residues at the positions 15, 19, and 20) and another within NSP1 (R124), which are required for viral evasion, and thus might present promising drug targets. We target SL1 with the antisense oligo (ASO) to efficiently and specifically down-regulate SARS-CoV-2 mRNA. Additionally, we carried out analysis of a functional interactome of NSP1 using BioID and identified components of antiviral defense pathways. Our analysis therefore suggests a mechanism by which NSP1 inhibits the expression of host genes while enhancing that of viral RNA. This analysis helps reconcile conflicting reports in the literature regarding the mechanisms by which the virus avoids NSP1 silencing.
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Affiliation(s)
- Lucija Bujanic
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Olga Shevchuk
- Leibniz-Institut für Analytische Wissenschaften-ISAS, 44139 Dortmund, Germany
| | - Nicolai von Kügelgen
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Anna Kalinina
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Katarzyna Ludwik
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - David Koppstein
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Nadja Zerna
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS, 44139 Dortmund, Germany
| | - Marina Chekulaeva
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
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42
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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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43
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Anjum F, Mohammad T, Asrani P, Shafie A, Singh S, Yadav DK, Uversky VN, Hassan MI. Identification of intrinsically disorder regions in non-structural proteins of SARS-CoV-2: New insights into drug and vaccine resistance. Mol Cell Biochem 2022; 477:1607-1619. [PMID: 35211823 PMCID: PMC8869350 DOI: 10.1007/s11010-022-04393-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/10/2022] [Indexed: 02/06/2023]
Abstract
The outbreak of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged in December 2019 and caused coronavirus disease 2019 (COVID-19), which causes pneumonia and severe acute respiratory distress syndrome. It is a highly infectious pathogen that promptly spread. Like other beta coronaviruses, SARS-CoV-2 encodes some non-structural proteins (NSPs), playing crucial roles in viral transcription and replication. NSPs likely have essential roles in viral pathogenesis by manipulating many cellular processes. We performed a sequence-based analysis of NSPs to get insights into their intrinsic disorders, and their functions in viral replication were annotated and discussed in detail. Here, we provide newer insights into the structurally disordered regions of SARS-CoV-2 NSPs. Our analysis reveals that the SARS-CoV-2 proteome has a chunk of the disordered region that might be responsible for increasing its virulence. In addition, mutations in these regions are presumably responsible for drug and vaccine resistance. These findings suggested that the structurally disordered regions of SARS-CoV-2 NSPs might be invulnerable in COVID-19.
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Affiliation(s)
- Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Purva Asrani
- Department of Microbiology, University of Delhi, New Delhi, 110021, India
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP, Pune University Campus, Pune, 411007, India
| | - Dharmendra Kumar Yadav
- College of Pharmacy, Gachon University of Medicine and Science, Hambakmoeiro, Yeonsu-gu, Incheon City, 21924, South Korea.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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44
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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: 5] [Impact Index Per Article: 2.5] [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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45
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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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46
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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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47
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Fisher T, Gluck A, Narayanan K, Kuroda M, Nachshon A, Hsu JC, Halfmann PJ, Yahalom-Ronen Y, Finkel Y, Schwartz M, Weiss S, Tseng CTK, Israely T, Paran N, Kawaoka Y, Makino S, Stern-Ginossar N. Parsing the role of NSP1 in SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.03.14.484208. [PMID: 35313595 PMCID: PMC8936099 DOI: 10.1101/2022.03.14.484208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 19 (COVID-19) pandemic. Despite its urgency, we still do not fully understand the molecular basis of SARS-CoV-2 pathogenesis and its ability to antagonize innate immune responses. SARS-CoV-2 leads to shutoff of cellular protein synthesis and over-expression of nsp1, a central shutoff factor in coronaviruses, inhibits cellular gene translation. However, the diverse molecular mechanisms nsp1 employs as well as its functional importance in infection are still unresolved. By overexpressing various nsp1 mutants and generating a SARS-CoV-2 mutant in which nsp1 does not bind ribosomes, we untangle the effects of nsp1. We uncover that nsp1, through inhibition of translation and induction of mRNA degradation, is the main driver of host shutoff during SARS-CoV-2 infection. Furthermore, we find the propagation of nsp1 mutant virus is inhibited specifically in cells with intact interferon (IFN) response as well as in-vivo , in infected hamsters, and this attenuation is associated with stronger induction of type I IFN response. This illustrates that nsp1 shutoff activity has an essential role mainly in counteracting the IFN response. Overall, our results reveal the multifaceted approach nsp1 uses to shut off cellular protein synthesis and uncover the central role it plays in SARS-CoV-2 pathogenesis, explicitly through blockage of the IFN response.
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Affiliation(s)
- Tal Fisher
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
- T. Fisher, A. Gluck, K. Narayanan, and K. Makoto contributed equally to the studies
| | - Avi Gluck
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
- T. Fisher, A. Gluck, K. Narayanan, and K. Makoto contributed equally to the studies
| | - Krishna Narayanan
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
- T. Fisher, A. Gluck, K. Narayanan, and K. Makoto contributed equally to the studies
| | - Makoto Kuroda
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711, USA
- T. Fisher, A. Gluck, K. Narayanan, and K. Makoto contributed equally to the studies
| | - Aharon Nachshon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jason C. Hsu
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
| | - Peter J. Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711, USA
| | - Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Yaara Finkel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shay Weiss
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Chien-Te K. Tseng
- Department of Microbiology and Immunology, 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
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 74100, Israel
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711, USA
- Department of Virology, Institute of Medical Science, University of Tokyo, 108-8639 Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, 162-8655 Tokyo, Japan
| | - Shinji Makino
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
- Department of Virology, Institute of Medical Science, University of Tokyo, 108-8639 Tokyo, Japan
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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48
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Agback P, Agback T, Dominguez F, Frolova EI, Seisenbaeva GA, Kessler VG. Site-specific recognition of SARS-CoV-2 nsp1 protein with a tailored titanium dioxide nanoparticle - elucidation of the complex structure using NMR data and theoretical calculation. NANOSCALE ADVANCES 2022; 4:1527-1532. [PMID: 36134379 PMCID: PMC9419012 DOI: 10.1039/d1na00855b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/16/2022] [Indexed: 06/16/2023]
Abstract
The ongoing world-wide Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) pandemic shows the need for new potential sensing and therapeutic means against the CoV viruses. The SARS-CoV-2 nsp1 protein is important, both for replication and pathogenesis, making it an attractive target for intervention. In this study we investigated the interaction of this protein with two types of titania nanoparticles by NMR and discovered that while lactate capped particles essentially did not interact with the protein chain, the aminoalcohol-capped ones showed strong complexation with a distinct part of an ordered α-helix fragment. The structure of the forming complex was elucidated based on NMR data and theoretical calculation. To the best of our knowledge, this is the first time that a tailored titanium oxide nanoparticle was shown to interact specifically with a unique site of the full-length SARS-CoV-2 nsp1 protein, possibly interfering with its functionality.
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Affiliation(s)
- Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences Box 7015 SE-75007 Uppsala Sweden
| | - Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences Box 7015 SE-75007 Uppsala Sweden
| | - Francisco Dominguez
- Department of Microbiology, University of Alabama at Birmingham 1720 2nd Ave South Birmingham AL 35294 USA
| | - Elena I Frolova
- Department of Microbiology, University of Alabama at Birmingham 1720 2nd Ave South Birmingham AL 35294 USA
| | - Gulaim A Seisenbaeva
- Department of Molecular Sciences, Swedish University of Agricultural Sciences Box 7015 SE-75007 Uppsala Sweden
| | - Vadim G Kessler
- Department of Molecular Sciences, Swedish University of Agricultural Sciences Box 7015 SE-75007 Uppsala Sweden
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49
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Xue W, Ding C, Qian K, Liao Y. The Interplay Between Coronavirus and Type I IFN Response. Front Microbiol 2022; 12:805472. [PMID: 35317429 PMCID: PMC8934427 DOI: 10.3389/fmicb.2021.805472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/24/2021] [Indexed: 12/14/2022] Open
Abstract
In the past few decades, newly evolved coronaviruses have posed a global threat to public health and animal breeding. To control and prevent the coronavirus-related diseases, understanding the interaction of the coronavirus and the host immune system is the top priority. Coronaviruses have evolved multiple mechanisms to evade or antagonize the host immune response to ensure their replication. As the first line and main component of innate immune response, type I IFN response is able to restrict virus in the initial infection stage; it is thus not surprising that the primary aim of the virus is to evade or antagonize the IFN response. Gaining a profound understanding of the interaction between coronaviruses and type I IFN response will shed light on vaccine development and therapeutics. In this review, we provide an update on the current knowledge on strategies employed by coronaviruses to evade type I IFN response.
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Affiliation(s)
- Wenxiang Xue
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Kun Qian
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Ying Liao,
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50
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Gupta S, Singh V, Varadwaj PK, Chakravartty N, Katta AVSKM, Lekkala SP, Thomas G, Narasimhan S, Reddy AR, Reddy Lachagari VB. Secondary metabolites from spice and herbs as potential multitarget inhibitors of SARS-CoV-2 proteins. J Biomol Struct Dyn 2022; 40:2264-2283. [PMID: 33107812 PMCID: PMC7605658 DOI: 10.1080/07391102.2020.1837679] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/11/2020] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for the current global pandemic that has caused a death toll of >1.12 million worldwide and number continues to climb in several countries. Currently, there are neither specific antiviral drugs nor vaccines for the treatment and prevention of COVID-19. We screened in silico, a group of natural spice and herbal secondary metabolites (SMs) for their inhibition efficacy against multiple target proteins of SARS-CoV-2 as well as the human angiotensin-converting enzyme 2 protein. Docking and simulation results indicated that epicatechin, embelin, hesperidin, cafestol, murrayanine and murrayaquinone-A have higher inhibition efficacy over at least one of the known antiviral drugs such as Hydroxychloroquine, Remdesivir and Ribavirin. Combination of these potentially effective SMs from their respective plant sources was analysed, and its absorption and acute oral toxicity were examined in Wistar rats and classified as category 5 as per the Globally Harmonized System. The identified SMs may be useful in the development of preventive nutraceuticals, food supplements and antiviral drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Vishal Singh
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, India
| | - Pritish Kumar Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology, Allahabad, India
| | | | | | | | | | | | - Arjula R. Reddy
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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