51
|
Zhu J, Chiang C, Gack MU. Viral evasion of the interferon response at a glance. J Cell Sci 2023; 136:jcs260682. [PMID: 37341132 PMCID: PMC10411950 DOI: 10.1242/jcs.260682] [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] [Indexed: 06/22/2023] Open
Abstract
Re-emerging and new viral pathogens have caused significant morbidity and mortality around the world, as evidenced by the recent monkeypox, Ebola and Zika virus outbreaks and the ongoing COVID-19 pandemic. Successful viral infection relies on tactical viral strategies to derail or antagonize host innate immune defenses, in particular the production of type I interferons (IFNs) by infected cells. Viruses can thwart intracellular sensing systems that elicit IFN gene expression (that is, RIG-I-like receptors and the cGAS-STING axis) or obstruct signaling elicited by IFNs. In this Cell Science at a Glance article and the accompanying poster, we review the current knowledge about the major mechanisms employed by viruses to inhibit the activity of intracellular pattern-recognition receptors and their downstream signaling cascades leading to IFN-based antiviral host defenses. Advancing our understanding of viral immune evasion might spur unprecedented opportunities to develop new antiviral compounds or vaccines to prevent viral infectious diseases.
Collapse
Affiliation(s)
- Junji Zhu
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL 34987, USA
| | - Cindy Chiang
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL 34987, USA
| | - Michaela U. Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL 34987, USA
| |
Collapse
|
52
|
Rummel T, Sakellaridi L, Erhard F. grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis. Nat Commun 2023; 14:3559. [PMID: 37321987 PMCID: PMC10272207 DOI: 10.1038/s41467-023-39163-4] [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: 09/29/2022] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Metabolic labeling of RNA is a powerful technique for studying the temporal dynamics of gene expression. Nucleotide conversion approaches greatly facilitate the generation of data but introduce challenges for their analysis. Here we present grandR, a comprehensive package for quality control, differential gene expression analysis, kinetic modeling, and visualization of such data. We compare several existing methods for inference of RNA synthesis rates and half-lives using progressive labeling time courses. We demonstrate the need for recalibration of effective labeling times and introduce a Bayesian approach to study the temporal dynamics of RNA using snapshot experiments.
Collapse
Affiliation(s)
- Teresa Rummel
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Lygeri Sakellaridi
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany.
- Faculty for Informatics and Data Science, University of Regensburg, Bajuwarenstr. 4, 93053, Regensburg, Germany.
| |
Collapse
|
53
|
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.
Collapse
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
| |
Collapse
|
54
|
Mishra N, Kant R, Leung DW, Gross ML, Amarasinghe GK. Biochemical and HDX Mass Spectral Characterization of the SARS-CoV-2 Nsp1 Protein. Biochemistry 2023; 62:1744-1754. [PMID: 37205707 PMCID: PMC10228561 DOI: 10.1021/acs.biochem.3c00035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/29/2023] [Indexed: 05/21/2023]
Abstract
A major challenge in defining the pathophysiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is to better understand virally encoded multifunctional proteins and their interactions with host factors. Among the many proteins encoded by the positive-sense, single-stranded RNA genome, nonstructural protein 1 (Nsp1) stands out due to its impact on several stages of the viral replication cycle. Nsp1 is the major virulence factor that inhibits mRNA translation. Nsp1 also promotes host mRNA cleavage to modulate host and viral protein expression and to suppress host immune functions. To better define how this multifunctional protein can facilitate distinct functions, we characterize SARS-CoV-2 Nsp1 by using a combination of biophysical techniques, including light scattering, circular dichroism, hydrogen/deuterium exchange mass spectrometry (HDX-MS), and temperature-dependent HDX-MS. Our results reveal that the SARS-CoV-2 Nsp1 N- and C-terminus are unstructured in solution, and in the absence of other proteins, the C-terminus has an increased propensity to adopt a helical conformation. In addition, our data indicate that a short helix exists near the C-terminus and adjoins the region that binds the ribosome. Together, these findings provide insights into the dynamic nature of Nsp1 that impacts its functions during infection. Furthermore, our results will inform efforts to understand SARS-CoV-2 infection and antiviral development.
Collapse
Affiliation(s)
- Nawneet Mishra
- Department
of Pathology and Immunology, Washington
University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
| | - Ravi Kant
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Daisy W. Leung
- Department
of Pathology and Immunology, Washington
University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
- Department
of Medicine, Washington University School
of Medicine, St. Louis, Missouri 63110, United States
| | - Michael L. Gross
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Gaya K. Amarasinghe
- Department
of Pathology and Immunology, Washington
University School of Medicine in St. Louis, St. Louis, Missouri 63110, United States
| |
Collapse
|
55
|
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.
Collapse
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
| |
Collapse
|
56
|
Wöhnke E, Klupp BG, Blome S, Mettenleiter TC, Karger A. Mass-Spectrometric Evaluation of the African Swine Fever Virus-Induced Host Shutoff Using Dynamic Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC). Viruses 2023; 15:1283. [PMID: 37376583 DOI: 10.3390/v15061283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
African swine fever is a viral disease of swine caused by the African swine fever virus (ASFV). Currently, ASFV is spreading over the Eurasian continent and threatening global pig husbandry. One viral strategy to undermine an efficient host cell response is to establish a global shutoff of host protein synthesis. This shutoff has been observed in ASFV-infected cultured cells using two-dimensional electrophoresis combined with metabolic radioactive labeling. However, it remained unclear if this shutoff was selective for certain host proteins. Here, we characterized ASFV-induced shutoff in porcine macrophages by measurement of relative protein synthesis rates using a mass spectrometric approach based on stable isotope labeling with amino acids in cell culture (SILAC). The impact of ASFV infection on the synthesis of >2000 individual host proteins showed a high degree of variability, ranging from complete shutoff to a strong induction of proteins that are absent from naïve cells. GO-term enrichment analysis revealed that the most effective shutoff was observed for proteins related to RNA metabolism, while typical representatives of the innate immune system were strongly induced after infection. This experimental setup is suitable to quantify a virion-induced host shutoff (vhs) after infection with different viruses.
Collapse
Affiliation(s)
- Elisabeth Wöhnke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Barbara G Klupp
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Sandra Blome
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Thomas C Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Axel Karger
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| |
Collapse
|
57
|
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.
Collapse
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
| |
Collapse
|
58
|
Godbold GD, Hewitt FC, Kappell AD, Scholz MB, Agar SL, Treangen TJ, Ternus KL, Sandbrink JB, Koblentz GD. Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern. Front Bioeng Biotechnol 2023; 11:1124100. [PMID: 37180048 PMCID: PMC10167326 DOI: 10.3389/fbioe.2023.1124100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
Regulation of research on microbes that cause disease in humans has historically been focused on taxonomic lists of 'bad bugs'. However, given our increased knowledge of these pathogens through inexpensive genome sequencing, 5 decades of research in microbial pathogenesis, and the burgeoning capacity of synthetic biologists, the limitations of this approach are apparent. With heightened scientific and public attention focused on biosafety and biosecurity, and an ongoing review by US authorities of dual-use research oversight, this article proposes the incorporation of sequences of concern (SoCs) into the biorisk management regime governing genetic engineering of pathogens. SoCs enable pathogenesis in all microbes infecting hosts that are 'of concern' to human civilization. Here we review the functions of SoCs (FunSoCs) and discuss how they might bring clarity to potentially problematic research outcomes involving infectious agents. We believe that annotation of SoCs with FunSoCs has the potential to improve the likelihood that dual use research of concern is recognized by both scientists and regulators before it occurs.
Collapse
Affiliation(s)
| | | | | | | | - Stacy L. Agar
- Signature Science, LLC, Charlottesville, VA, United States
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, United States
| | | | - Jonas B. Sandbrink
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gregory D. Koblentz
- Schar School of Policy and Government, George Mason University, Arlington, VA, United States
| |
Collapse
|
59
|
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.
Collapse
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.
| |
Collapse
|
60
|
Abstract
SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has been associated with substantial global morbidity and mortality. Despite a tropism that is largely confined to the airways, COVID-19 is associated with multiorgan dysfunction and long-term cognitive pathologies. A major driver of this biology stems from the combined effects of virus-mediated interference with the host antiviral defences in infected cells and the sensing of pathogen-associated material by bystander cells. Such a dynamic results in delayed induction of type I and III interferons (IFN-I and IFN-III) at the site of infection, but systemic IFN-I and IFN-III priming in distal organs and barrier epithelial surfaces, respectively. In this Review, we examine the relationship between SARS-CoV-2 biology and the cellular response to infection, detailing how antagonism and dysregulation of host innate immune defences contribute to disease severity of COVID-19.
Collapse
Affiliation(s)
- Judith M Minkoff
- Department of Microbiology, New York University Langone Health, New York, NY, USA
| | - Benjamin tenOever
- Department of Microbiology, New York University Langone Health, New York, NY, USA.
| |
Collapse
|
61
|
Anreiter I, Tian YW, Soller M. The cap epitranscriptome: Early directions to a complex life as mRNA. Bioessays 2023; 45:e2200198. [PMID: 36529693 DOI: 10.1002/bies.202200198] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Animal, protist and viral messenger RNAs (mRNAs) are most prominently modified at the beginning by methylation of cap-adjacent nucleotides at the 2'-O-position of the ribose (cOMe) by dedicated cap methyltransferases (CMTrs). If the first nucleotide of an mRNA is an adenosine, PCIF1 can methylate at the N6 -position (m6 A), while internally the Mettl3/14 writer complex can methylate. These modifications are introduced co-transcriptionally to affect many aspects of gene expression including localisation to synapses and local translation. Of particular interest, transcription start sites of many genes are heterogeneous leading to sequence diversity at the beginning of mRNAs, which together with cOMe and m6 Am could constitute an extensive novel layer of gene expression control. Given the role of cOMe and m6 A in local gene expression at synapses and higher brain functions including learning and memory, such code could be implemented at the transcriptional level for lasting memories through local gene expression at synapses.
Collapse
Affiliation(s)
- Ina Anreiter
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada
| | - Yuan W Tian
- Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK.,School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Matthias Soller
- Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK.,School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| |
Collapse
|
62
|
Yang T, Wang SC, Ye L, Maimaitiyiming Y, Naranmandura H. Targeting viral proteins for restraining SARS-CoV-2: focusing lens on viral proteins beyond spike for discovering new drug targets. Expert Opin Drug Discov 2023; 18:247-268. [PMID: 36723288 DOI: 10.1080/17460441.2023.2175812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Emergence of highly infectious SARS-CoV-2 variants are reducing protection provided by current vaccines, requiring constant updates in antiviral approaches. The virus encodes four structural and sixteen nonstructural proteins which play important roles in viral genome replication and transcription, virion assembly, release , entry into cells, and compromising host cellular defenses. As alien proteins to host cells, many viral proteins represent potential targets for combating the SARS-CoV-2. AREAS COVERED Based on literature from PubMed and Web of Science databases, the authors summarize the typical characteristics of SARS-CoV-2 from the whole viral particle to the individual viral proteins and their corresponding functions in virus life cycle. The authors also discuss the potential and emerging targeted interventions to curb virus replication and spread in detail to provide unique insights into SARS-CoV-2 infection and countermeasures against it. EXPERT OPINION Our comprehensive analysis highlights the rationale to focus on non-spike viral proteins that are less mutated but have important functions. Examples of this include: structural proteins (e.g. nucleocapsid protein, envelope protein) and extensively-concerned nonstructural proteins (e.g. NSP3, NSP5, NSP12) along with the ones with relatively less attention (e.g. NSP1, NSP10, NSP14 and NSP16), for developing novel drugs to overcome resistance of SARS-CoV-2 variants to preexisting vaccines and antibody-based treatments.
Collapse
Affiliation(s)
- Tao Yang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Si Chun Wang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Linyan Ye
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yasen Maimaitiyiming
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, and MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hua Naranmandura
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| |
Collapse
|
63
|
Zhang L, Bisht P, Flamier A, Barrasa MI, Friesen M, Richards A, Hughes SH, Jaenisch R. LINE1-Mediated Reverse Transcription and Genomic Integration of SARS-CoV-2 mRNA Detected in Virus-Infected but Not in Viral mRNA-Transfected Cells. Viruses 2023; 15:629. [PMID: 36992338 PMCID: PMC10057545 DOI: 10.3390/v15030629] [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: 01/20/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
SARS-CoV-2 sequences can be reverse-transcribed and integrated into the genomes of virus-infected cells by a LINE1-mediated retrotransposition mechanism. Whole-genome sequencing (WGS) methods detected retrotransposed SARS-CoV-2 subgenomic sequences in virus-infected cells overexpressing LINE1, while an enrichment method (TagMap) identified retrotranspositions in cells that did not overexpress LINE1. LINE1 overexpression increased retrotranspositions about 1000-fold as compared to non-overexpressing cells. Nanopore WGS can directly recover retrotransposed viral and flanking host sequences, but its sensitivity depends on the depth of sequencing (a typical 20-fold sequencing depth would only examine 10 diploid cell equivalents). In contrast, TagMap enriches the host-virus junctions and can interrogate up to 20,000 cells and is able to detect rare viral retrotranspositions in LINE1 non-overexpressing cells. Although Nanopore WGS is 10-20-fold more sensitive per tested cell, TagMap can interrogate 1000-2000-fold more cells and, therefore, can identify infrequent retrotranspositions. When comparing SARS-CoV-2 infection and viral nucleocapsid mRNA transfection by TagMap, retrotransposed SARS-CoV-2 sequences were only detected in infected but not in transfected cells. Retrotransposition in virus-infected cells, in contrast to transfected cells, may be facilitated because virus infection, in contrast to viral RNA transfection, results in significantly higher viral RNA levels and stimulates LINE1 expression by causing cellular stress.
Collapse
Affiliation(s)
- Liguo Zhang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Punam Bisht
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Anthony Flamier
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Max Friesen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Alexsia Richards
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| |
Collapse
|
64
|
How the Competition for Cysteine May Promote Infection of SARS-CoV-2 by Triggering Oxidative Stress. Antioxidants (Basel) 2023; 12:antiox12020483. [PMID: 36830041 PMCID: PMC9952211 DOI: 10.3390/antiox12020483] [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: 12/06/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
SARS-CoV-2 induces a broad range of clinical manifestations. Besides the main receptor, ACE2, other putative receptors and co-receptors have been described and could become genuinely relevant to explain the different tropism manifested by new variants. In this study, we propose a biochemical model envisaging the competition for cysteine as a key mechanism promoting the infection and the selection of host receptors. The SARS-CoV-2 infection produces ROS and triggers a massive biosynthesis of proteins rich in cysteine; if this amino acid becomes limiting, glutathione levels are depleted and cannot control oxidative stress. Hence, infection succeeds. A receptor should be recognized as a marker of suitable intracellular conditions, namely the full availability of amino acids except for low cysteine. First, we carried out a comparative investigation of SARS-CoV-2 proteins and human ACE2. Then, using hierarchical cluster protein analysis, we searched for similarities between all human proteins and spike produced by the latest variant, Omicron BA.1. We found 32 human proteins very close to spike in terms of amino acid content. Most of these potential SARS-CoV-2 receptors have less cysteine than spike. We suggest that these proteins could signal an intracellular shortage of cysteine, predicting a burst of oxidative stress when used as viral entry mediators.
Collapse
|
65
|
Zhang L, Bisht P, Flamier A, Barrasa MI, Richards A, Hughes SH, Jaenisch R. LINE1-mediated reverse transcription and genomic integration of SARS-CoV-2 mRNA detected in virus-infected but not in viral mRNA-transfected cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.10.527906. [PMID: 37293025 PMCID: PMC10245962 DOI: 10.1101/2023.02.10.527906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
SARS-CoV-2 sequences can be reverse-transcribed and integrated into the genomes of virus-infected cells by a LINE1-mediated retrotransposition mechanism. Whole genome sequencing (WGS) methods detected retrotransposed SARS-CoV-2 subgenomic sequences in virus-infected cells overexpressing LINE1, while an enrichment method (TagMap) identified retrotranspositions in cells that did not overexpress LINE1. LINE1 overexpression increased retrotranspositions about 1,000-fold as compared to non-overexpressing cells. Nanopore WGS can directly recover retrotransposed viral and flanking host sequences but its sensitivity depends on the depth of sequencing (a typical 20-fold sequencing depth would only examine 10 diploid cell equivalents). In contrast, TagMap enriches for the host-virus junctions and can interrogate up to 20,000 cells and is able to detect rare viral retrotranspositions in LINE1 non-overexpressing cells. Although Nanopore WGS is 10 - 20-fold more sensitive per tested cell, TagMap can interrogate 1,000 - 2,000-fold more cells and therefore can identify infrequent retrotranspositions. When comparing SARS-CoV-2 infection and viral nucleocapsid mRNA transfection by TagMap, retrotransposed SARS-CoV-2 sequences were only detected in infected but not in transfected cells. Retrotransposition in virus-infected in contrast to transfected cells may be facilitated because virus infection in contrast to viral RNA transfection results in significantly higher viral RNA levels and stimulates LINE1-expression which causes cellular stress.
Collapse
|
66
|
Gottschalk CG, Peterson D, Armstrong J, Knox K, Roy A. Potential molecular mechanisms of chronic fatigue in long haul COVID and other viral diseases. Infect Agent Cancer 2023; 18:7. [PMID: 36750846 PMCID: PMC9902840 DOI: 10.1186/s13027-023-00485-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Historically, COVID-19 emerges as one of the most devastating diseases of humankind, which creates an unmanageable health crisis worldwide. Until now, this disease costs millions of lives and continues to paralyze human civilization's economy and social growth, leaving an enduring damage that will take an exceptionally long time to repair. While a majority of infected patients survive after mild to moderate reactions after two to six weeks, a growing population of patients suffers for months with severe and prolonged symptoms of fatigue, depression, and anxiety. These patients are no less than 10% of total COVID-19 infected individuals with distinctive chronic clinical symptomatology, collectively termed post-acute sequelae of COVID-19 (PASC) or more commonly long-haul COVID. Interestingly, Long-haul COVID and many debilitating viral diseases display a similar range of clinical symptoms of muscle fatigue, dizziness, depression, and chronic inflammation. In our current hypothesis-driven review article, we attempt to discuss the molecular mechanism of muscle fatigue in long-haul COVID, and other viral diseases as caused by HHV6, Powassan, Epstein-Barr virus (EBV), and HIV. We also discuss the pathological resemblance of virus-triggered muscle fatigue with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS).
Collapse
Affiliation(s)
- Carl Gunnar Gottschalk
- Simmaron Research INC, 948 Incline Way, Incline Village, NV 89451 USA ,grid.267468.90000 0001 0695 7223Research and Development Laboratory, Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI 53211 USA ,Coppe Laboratories, W229N1870 Westwood Dr, Waukesha, WI 53186 USA
| | - Daniel Peterson
- Simmaron Research INC, 948 Incline Way, Incline Village, NV 89451 USA ,Coppe Laboratories, W229N1870 Westwood Dr, Waukesha, WI 53186 USA
| | - Jan Armstrong
- Simmaron Research INC, 948 Incline Way, Incline Village, NV 89451 USA ,Coppe Laboratories, W229N1870 Westwood Dr, Waukesha, WI 53186 USA
| | - Konstance Knox
- grid.267468.90000 0001 0695 7223Research and Development Laboratory, Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI 53211 USA ,Coppe Laboratories, W229N1870 Westwood Dr, Waukesha, WI 53186 USA
| | - Avik Roy
- Simmaron Research INC, 948 Incline Way, Incline Village, NV, 89451, USA. .,Research and Development Laboratory, Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA. .,Coppe Laboratories, W229N1870 Westwood Dr, Waukesha, WI, 53186, USA.
| |
Collapse
|
67
|
Comparison of COVID-19 Vaccine-Associated Myocarditis and Viral Myocarditis Pathology. Vaccines (Basel) 2023; 11:vaccines11020362. [PMID: 36851240 PMCID: PMC9967770 DOI: 10.3390/vaccines11020362] [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: 12/12/2022] [Revised: 01/19/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
The COVID-19 pandemic has led to significant loss of life and severe disability, justifying the expedited testing and approval of messenger RNA (mRNA) vaccines. While found to be safe and effective, there have been increasing reports of myocarditis after COVID-19 mRNA vaccine administration. The acute events have been severe enough to require admission to the intensive care unit in some, but most patients fully recover with only rare deaths reported. The pathways involved in the development of vaccine-associated myocarditis are highly dependent on the specific vaccine. COVID-19 vaccine-associated myocarditis is believed to be primarily caused by uncontrolled cytokine-mediated inflammation with possible genetic components in the interleukin-6 signaling pathway. There is also a potential autoimmune component via molecular mimicry. Many of these pathways are similar to those seen in viral myocarditis, indicating a common pathophysiology. There is concern for residual cardiac fibrosis and increased risk for the development of cardiomyopathies later in life. This is of particular interest for patients with congenital heart defects who are already at increased risk for fibrotic cardiomyopathies. Though the risk for vaccine-associated myocarditis is important to consider, the risk of viral myocarditis and other injury is far greater with COVID-19 infection. Considering these relative risks, it is still recommended that the general public receive vaccination against COVID-19, and it is particularly important for congenital heart defect patients to receive vaccination for COVID-19.
Collapse
|
68
|
Rozman B, Fisher T, Stern-Ginossar N. Translation-A tug of war during viral infection. Mol Cell 2023; 83:481-495. [PMID: 36334591 DOI: 10.1016/j.molcel.2022.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/15/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Viral reproduction is contingent on viral protein synthesis that relies on the host ribosomes. As such, viruses have evolved remarkable strategies to hijack the host translational apparatus in order to favor viral protein production and to interfere with cellular innate defenses. Here, we describe the approaches viruses use to exploit the translation machinery, focusing on commonalities across diverse viral families, and discuss the functional relevance of this process. We illustrate the complementary strategies host cells utilize to block viral protein production and consider how cells ensure an efficient antiviral response that relies on translation during this tug of war over the ribosome. Finally, we highlight potential roles mRNA modifications and ribosome quality control play in translational regulation and innate immunity. We address these topics in the context of the COVID-19 pandemic and focus on the gaps in our current knowledge of these mechanisms, specifically in viruses with pandemic potential.
Collapse
Affiliation(s)
- Batsheva Rozman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tal Fisher
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
69
|
Kurhade C, Xie X, Shi PY. Reverse genetic systems of SARS-CoV-2 for antiviral research. Antiviral Res 2023; 210:105486. [PMID: 36657881 PMCID: PMC9776485 DOI: 10.1016/j.antiviral.2022.105486] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
Reverse genetic systems are widely used to engineer recombinant viruses with desired mutations. In response to the COVID-19 pandemic, four types of reverse genetic systems have been developed for SARS-CoV-2: (i) a full-length infectious clone that can be used to prepare recombinant SARS-CoV-2 at biosafety level 3 (BSL3), (ii) a trans-complementation system that can be used to produce single-round infectious SARS-CoV-2 at BSL2, (iii) an attenuated SARS-CoV-2 vaccine candidate (with deletions of viral accessory genes) that may be developed for veterinary use as well as for antiviral screening at BSL2, and (iv) replicon systems with deletions of viral structural genes that can be used at BSL2. Each of these genetic systems has its advantages and disadvantages that can be used to address different questions for basic and translational research. Due to the long genomic size and bacteria-toxic sequences of SARS-CoV-2, several experimental approaches have been established to rescue recombinant viruses and replicons, including (i) in vitro DNA ligation, (ii) bacterial artificial chromosome (BAC) system, (iii) yeast artificial chromosome (YAC) system, and (iv) circular polymerase extension reaction (CPER). This review summarizes the current status of SARS-CoV-2 genetic systems and their applications for studying viral replication, pathogenesis, vaccines, and therapeutics.
Collapse
Affiliation(s)
- Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
| |
Collapse
|
70
|
Modulation of NBAS-Related Functions in the Early Response to SARS-CoV-2 Infection. Int J Mol Sci 2023; 24:ijms24032634. [PMID: 36768954 PMCID: PMC9916797 DOI: 10.3390/ijms24032634] [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: 12/16/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Upon infection, severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is predicted to interact with diverse cellular functions, such as the nonsense-mediated decay (NMD) pathway, as suggested by the identification of the core NMD factor upframeshift-1 (UPF1) in the SARS-CoV-2 interactome, and the retrograde transport from the Golgi to the endoplasmic reticulum (ER) through the endoplasmic reticulum-Golgi intermediate compartment (ERGIC), where coronavirus assembly occurs. Here, we investigated the expression and localization of the neuroblastoma-amplified sequence (NBAS) protein, a UPF1 partner for the NMD at the ER, participating also in retrograde transport, and of its functional partners, at early time points after SARS-CoV-2 infection of the human lung epithelial cell line Calu3. We found a significant decrease of DExH-Box Helicase 34 (DHX34), suppressor with morphogenetic effect on genitalia 5 (SMG5), and SMG7 expression at 6 h post-infection, followed by a significant increase of these genes and also UPF1 and UPF2 at 9 h post-infection. Conversely, NBAS and other genes coding for NMD factors were not modulated. Known NMD substrates related to cell stress (Growth Arrest Specific 5, GAS5; transducin beta-like 2, TBL2; and DNA damage-inducible transcript 3, DDIT3) were increased in infected cells, possibly as a result of alterations in the NMD pathway and of a direct effect of the infection. We also found that the expression of unconventional SNARE in the ER 1, USE1 (p31) and Zeste White 10 homolog, ZW10, partners of NBAS in the retrograde transport function, significantly increased over time in infected cells. Co-localization of NBAS and UPF1 proteins did not change within 24 h of infection nor did it differ in infected versus non-infected cells at 1 and 24 h after infection; similarly, the co-localization of NBAS and p31 proteins was not altered by infection in this short time frame. Finally, both NBAS and UPF1 were found to co-localize with SARS-CoV-2 S and N proteins. Overall, these data are preliminary evidence of an interaction between NBAS and NBAS-related functions and SARS-CoV-2 in infected cells, deserving further investigation.
Collapse
|
71
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
72
|
Jiao L, Liu Y, Yu XY, Pan X, Zhang Y, Tu J, Song YH, Li Y. Ribosome biogenesis in disease: new players and therapeutic targets. Signal Transduct Target Ther 2023; 8:15. [PMID: 36617563 PMCID: PMC9826790 DOI: 10.1038/s41392-022-01285-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 01/10/2023] Open
Abstract
The ribosome is a multi-unit complex that translates mRNA into protein. Ribosome biogenesis is the process that generates ribosomes and plays an essential role in cell proliferation, differentiation, apoptosis, development, and transformation. The mTORC1, Myc, and noncoding RNA signaling pathways are the primary mediators that work jointly with RNA polymerases and ribosome proteins to control ribosome biogenesis and protein synthesis. Activation of mTORC1 is required for normal fetal growth and development and tissue regeneration after birth. Myc is implicated in cancer development by enhancing RNA Pol II activity, leading to uncontrolled cancer cell growth. The deregulation of noncoding RNAs such as microRNAs, long noncoding RNAs, and circular RNAs is involved in developing blood, neurodegenerative diseases, and atherosclerosis. We review the similarities and differences between eukaryotic and bacterial ribosomes and the molecular mechanism of ribosome-targeting antibiotics and bacterial resistance. We also review the most recent findings of ribosome dysfunction in COVID-19 and other conditions and discuss the consequences of ribosome frameshifting, ribosome-stalling, and ribosome-collision. We summarize the role of ribosome biogenesis in the development of various diseases. Furthermore, we review the current clinical trials, prospective vaccines for COVID-19, and therapies targeting ribosome biogenesis in cancer, cardiovascular disease, aging, and neurodegenerative disease.
Collapse
Affiliation(s)
- Lijuan Jiao
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Yuzhe Liu
- grid.452829.00000000417660726Department of Orthopedics, the Second Hospital of Jilin University, Changchun, Jilin 130000 P. R. China
| | - Xi-Yong Yu
- grid.410737.60000 0000 8653 1072Key Laboratory of Molecular Target & Clinical Pharmacology and the NMPA State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, Guangdong 511436 P. R. China
| | - Xiangbin Pan
- grid.506261.60000 0001 0706 7839Department of Structural Heart Disease, National Center for Cardiovascular Disease, China & Fuwai Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China ,Key Laboratory of Cardiovascular Appratus Innovation, Beijing, 100037 P. R. China
| | - Yu Zhang
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Junchu Tu
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Yao-Hua Song
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, P. R. China. .,State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, P. R. China.
| | - Yangxin Li
- Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu, 215123, P. R. China.
| |
Collapse
|
73
|
Pinto SM, Subbannayya Y, Kim H, Hagen L, Górna MW, Nieminen AI, Bjørås M, Espevik T, Kainov D, Kandasamy RK. Multi-OMICs landscape of SARS-CoV-2-induced host responses in human lung epithelial cells. iScience 2022; 26:105895. [PMID: 36590899 PMCID: PMC9794516 DOI: 10.1016/j.isci.2022.105895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/03/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
COVID-19 pandemic continues to remain a global health concern owing to the emergence of newer variants. Several multi-Omics studies have produced extensive evidence on host-pathogen interactions and potential therapeutic targets. Nonetheless, an increased understanding of host signaling networks regulated by post-translational modifications and their ensuing effect on the cellular dynamics is critical to expanding the current knowledge on SARS-CoV-2 infections. Through an unbiased transcriptomics, proteomics, acetylomics, phosphoproteomics, and exometabolome analysis of a lung-derived human cell line, we show that SARS-CoV-2 Norway/Trondheim-S15 strain induces time-dependent alterations in the induction of type I IFN response, activation of DNA damage response, dysregulated Hippo signaling, among others. We identified interplay of phosphorylation and acetylation dynamics on host proteins and its effect on the altered release of metabolites, especially organic acids and ketone bodies. Together, our findings serve as a resource of potential targets that can aid in designing novel host-directed therapeutic strategies.
Collapse
Affiliation(s)
- Sneha M. Pinto
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway,Corresponding author
| | - Yashwanth Subbannayya
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Hera Kim
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway,Proteomics and Modomics Experimental Core, PROMEC, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Maria W. Górna
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Anni I. Nieminen
- Institute for Molecular Medicine Finland, University of Helsinki, 00014Helsinki, Finland
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Terje Espevik
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Denis Kainov
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Richard K. Kandasamy
- Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, 7491 Trondheim, Norway,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway,Department of Laboratory Medicine and Pathology, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA,Corresponding author
| |
Collapse
|
74
|
Gisby JS, Buang NB, Papadaki A, Clarke CL, Malik TH, Medjeral-Thomas N, Pinheiro D, Mortimer PM, Lewis S, Sandhu E, McAdoo SP, Prendecki MF, Willicombe M, Pickering MC, Botto M, Thomas DC, Peters JE. Multi-omics identify falling LRRC15 as a COVID-19 severity marker and persistent pro-thrombotic signals in convalescence. Nat Commun 2022; 13:7775. [PMID: 36522333 PMCID: PMC9753891 DOI: 10.1038/s41467-022-35454-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Patients with end-stage kidney disease (ESKD) are at high risk of severe COVID-19. Here, we perform longitudinal blood sampling of ESKD haemodialysis patients with COVID-19, collecting samples pre-infection, serially during infection, and after clinical recovery. Using plasma proteomics, and RNA-sequencing and flow cytometry of immune cells, we identify transcriptomic and proteomic signatures of COVID-19 severity, and find distinct temporal molecular profiles in patients with severe disease. Supervised learning reveals that the plasma proteome is a superior indicator of clinical severity than the PBMC transcriptome. We show that a decreasing trajectory of plasma LRRC15, a proposed co-receptor for SARS-CoV-2, is associated with a more severe clinical course. We observe that two months after the acute infection, patients still display dysregulated gene expression related to vascular, platelet and coagulation pathways, including PF4 (platelet factor 4), which may explain the prolonged thrombotic risk following COVID-19.
Collapse
Affiliation(s)
- Jack S Gisby
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Norzawani B Buang
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Artemis Papadaki
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Candice L Clarke
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
- Renal and Transplant Centre, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Talat H Malik
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Nicholas Medjeral-Thomas
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
- Renal and Transplant Centre, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Damiola Pinheiro
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Paige M Mortimer
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Shanice Lewis
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Eleanor Sandhu
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
- Renal and Transplant Centre, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Stephen P McAdoo
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
- Renal and Transplant Centre, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Maria F Prendecki
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
- Renal and Transplant Centre, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Michelle Willicombe
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
- Renal and Transplant Centre, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Matthew C Pickering
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - Marina Botto
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK
| | - David C Thomas
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK.
- Renal and Transplant Centre, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK.
| | - James E Peters
- Centre for Inflammatory Disease, Dept of Immunology and Inflammation, Imperial College London, London, UK.
| |
Collapse
|
75
|
Vavougios GD, de Erausquin GA, Snyder HM. Type I interferon signaling in SARS-CoV-2 associated neurocognitive disorder (SAND): Mapping host-virus interactions to an etiopathogenesis. Front Neurol 2022; 13:1063298. [PMID: 36570454 PMCID: PMC9771386 DOI: 10.3389/fneur.2022.1063298] [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: 10/06/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Epidemiological, clinical, and radiological studies have provided insights into the phenomenology and biological basis of cognitive impairment in COVID-19 survivors. Furthermore, its association with biomarkers associated with neuroinflammation and neurodegeneration supports the notion that it is a distinct aspect of LongCOVID syndrome with specific underlying biology. Accounting for the latter, translational studies on SARS-CoV-2's interactions with its hosts have provided evidence on type I interferon dysregulation, which is seen in neuroinflammatory and neurodegenerative diseases. To date, studies attempting to describe this overlap have only described common mechanisms. In this manuscript, we attempt to propose a mechanistic model based on the host-virus interaction hypothesis. We discuss the molecular basis for a SARS-CoV-2-associated neurocognitive disorder (SAND) focusing on specific genes and pathways with potential mechanistic implications, several of which have been predicted by Vavougios and their research group. Furthermore, our hypothesis links translational evidence on interferon-responsive gene perturbations introduced by SARS-CoV-2 and known dysregulated pathways in dementia. Discussion emphasizes the crosstalk between central and peripheral immunity via danger-associated molecular patterns in inducing SAND's emergence in the absence of neuroinfection. Finally, we outline approaches to identifying targets that are both testable and druggable, and could serve in the design of future clinical and translational studies.
Collapse
Affiliation(s)
- George D. Vavougios
- Department of Neurology, University of Cyprus, Lefkosia, Cyprus,Department of Respiratory Medicine, University of Thessaly, Larisa, Greece,*Correspondence: George D. Vavougios ;
| | - Gabriel A. de Erausquin
- The Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UTHSA, San Antonio, TX, United States
| | - Heather M. Snyder
- Division of Medical and Scientific Relations, Alzheimer's Association, Chicago, IL, United States
| |
Collapse
|
76
|
Katz R, Attias E, Tuller T, Margaliot M. Translation in the cell under fierce competition for shared resources: a mathematical model. J R Soc Interface 2022; 19:20220535. [PMID: 36541059 PMCID: PMC9768467 DOI: 10.1098/rsif.2022.0535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
During translation, mRNAs 'compete' for shared resources. Under stress conditions, during viral infection and also in high-throughput heterologous gene expression, these resources may become scarce, e.g. the pool of free ribosomes is starved, and then the competition may have a dramatic effect on the global dynamics of translation in the cell. We model this scenario using a network that includes m ribosome flow models (RFMs) interconnected via a pool of free ribosomes. Each RFM models ribosome flow along an mRNA molecule, and the pool models the shared resource. We assume that the number of mRNAs is large, so many ribosomes are attached to the mRNAs, and the pool is starved. Our analysis shows that adding an mRNA has an intricate effect on the total protein production. The new mRNA produces new proteins, but the other mRNAs produce less proteins, as the pool that feeds these mRNAs now has a smaller abundance of ribosomes. As the number of mRNAs increases, the marginal utility of adding another mRNA diminishes, and the total protein production rate saturates to a limiting value. We demonstrate our approach using an example of insulin protein production in a cell-free system.
Collapse
Affiliation(s)
- Rami Katz
- School of Electrical Engineering, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Elad Attias
- School of Electrical Engineering, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Michael Margaliot
- School of Electrical Engineering, Tel Aviv University, Tel Aviv-Yafo, Israel
| |
Collapse
|
77
|
Kehrer T, Cupic A, Ye C, Yildiz S, Bouhhadou M, Crossland NA, Barrall E, Cohen P, Tseng A, Çağatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena N, Aslam S, Saqi A, Marin A, Rutkowska M, Ummadi MR, Pisanelli G, Richardson RB, Veit EC, Fabius JM, Soucheray M, Polacco BJ, Evans MJ, Swaney DL, Gonzalez-Reiche AS, Sordillo EM, van Bakel H, Simon V, Zuliani-Alvarez L, Fontoura BMA, Rosenberg BR, Krogan NJ, Martinez-Sobrido L, García-Sastre A, Miorin L. Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.18.512708. [PMID: 36299428 PMCID: PMC9603824 DOI: 10.1101/2022.10.18.512708] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We and others have previously shown that the SARS-CoV-2 accessory protein ORF6 is a powerful antagonist of the interferon (IFN) signaling pathway by directly interacting with Nup98-Rae1 at the nuclear pore complex (NPC) and disrupting bidirectional nucleo-cytoplasmic trafficking. In this study, we further assessed the role of ORF6 during infection using recombinant SARS-CoV-2 viruses carrying either a deletion or a well characterized M58R loss-of-function mutation in ORF6. We show that ORF6 plays a key role in the antagonism of IFN signaling and in viral pathogenesis by interfering with karyopherin(importin)-mediated nuclear import during SARS-CoV-2 infection both in vitro , and in the Syrian golden hamster model in vivo . In addition, we found that ORF6-Nup98 interaction also contributes to inhibition of cellular mRNA export during SARS-CoV-2 infection. As a result, ORF6 expression significantly remodels the host cell proteome upon infection. Importantly, we also unravel a previously unrecognized function of ORF6 in the modulation of viral protein expression, which is independent of its function at the nuclear pore. Lastly, we characterized the ORF6 D61L mutation that recently emerged in Omicron BA.2 and BA.4 and demonstrated that it is able to disrupt ORF6 protein functions at the NPC and to impair SARS-CoV-2 innate immune evasion strategies. Importantly, the now more abundant Omicron BA.5 lacks this loss-of-function polymorphism in ORF6. Altogether, our findings not only further highlight the key role of ORF6 in the antagonism of the antiviral innate immune response, but also emphasize the importance of studying the role of non-spike mutations to better understand the mechanisms governing differential pathogenicity and immune evasion strategies of SARS-CoV-2 and its evolving variants. ONE SENTENCE SUMMARY SARS-CoV-2 ORF6 subverts bidirectional nucleo-cytoplasmic trafficking to inhibit host gene expression and contribute to viral pathogenesis.
Collapse
|
78
|
Single-cell RNA-sequencing data analysis reveals a highly correlated triphasic transcriptional response to SARS-CoV-2 infection. Commun Biol 2022; 5:1302. [PMID: 36435849 PMCID: PMC9701238 DOI: 10.1038/s42003-022-04253-4] [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: 06/22/2022] [Accepted: 11/11/2022] [Indexed: 11/28/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is currently one of the most powerful techniques available to study the transcriptional response of thousands of cells to an external perturbation. Here, we perform a pseudotime analysis of SARS-CoV-2 infection using publicly available scRNA-seq data from human bronchial epithelial cells and colon and ileum organoids. Our results reveal that, for most genes, the transcriptional response to SARS-CoV-2 infection follows a non-linear pattern characterized by an initial and a final down-regulatory phase separated by an intermediate up-regulatory stage. A correlation analysis of transcriptional profiles suggests a common mechanism regulating the mRNA levels of most genes. Interestingly, genes encoded in the mitochondria or involved in translation exhibited distinct pseudotime profiles. To explain our results, we propose a simple model where nuclear export inhibition of nsp1-sensitive transcripts will be sufficient to explain the transcriptional shutdown of SARS-CoV-2 infected cells.
Collapse
|
79
|
Liu S, Stauft CB, Selvaraj P, Chandrasekaran P, D’Agnillo F, Chou CK, Wu WW, Lien CZ, Meseda CA, Pedro CL, Starost MF, Weir JP, Wang TT. Intranasal delivery of a rationally attenuated SARS-CoV-2 is immunogenic and protective in Syrian hamsters. Nat Commun 2022; 13:6792. [PMID: 36357440 PMCID: PMC9648440 DOI: 10.1038/s41467-022-34571-4] [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: 05/10/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
Few live attenuated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines are in pre-clinical or clinical development. We seek to attenuate SARS-CoV-2 (isolate WA1/2020) by removing the polybasic insert within the spike protein and the open reading frames (ORFs) 6-8, and by introducing mutations that abolish non-structural protein 1 (Nsp1)-mediated toxicity. The derived virus (WA1-ΔPRRA-ΔORF6-8-Nsp1K164A/H165A) replicates to 100- to 1000-fold-lower titers than the ancestral virus and induces little lung pathology in both K18-human ACE2 (hACE2) transgenic mice and Syrian hamsters. Immunofluorescence and transcriptomic analyses of infected hamsters confirm that three-pronged genetic modifications attenuate the proinflammatory pathways more than the removal of the polybasic cleavage site alone. Finally, intranasal administration of just 100 PFU of the WA1-ΔPRRA-ΔORF6-8-Nsp1K164A/H165A elicits robust antibody responses in Syrian hamsters and protects against SARS-CoV-2-induced weight loss and pneumonia. As a proof-of-concept study, we demonstrate that live but sufficiently attenuated SARS-CoV-2 vaccines may be attainable by rational design.
Collapse
Affiliation(s)
- Shufeng Liu
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Charles B. Stauft
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Prabhuanand Selvaraj
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Prabha Chandrasekaran
- grid.94365.3d0000 0001 2297 5165Laboratory of Clinical Investigation, National Institutes of Aging, National Institutes of Health, Baltimore, USA
| | - Felice D’Agnillo
- grid.417587.80000 0001 2243 3366Laboratory of Biochemistry and Vascular Biology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Chao-Kai Chou
- grid.417587.80000 0001 2243 3366Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Wells W. Wu
- grid.417587.80000 0001 2243 3366Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Christopher Z. Lien
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Clement A. Meseda
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Cyntia L. Pedro
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Matthew F. Starost
- grid.94365.3d0000 0001 2297 5165Division of Veterinary Resources, Diagnostic and Research Services Branch, National Institutes of Health, Rockville Pike, USA
| | - Jerry P. Weir
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Tony T. Wang
- grid.417587.80000 0001 2243 3366Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| |
Collapse
|
80
|
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.
Collapse
|
81
|
Girgis S, Xu Z, Oikonomopoulos S, Fedorova AD, Tchesnokov EP, Gordon CJ, Schmeing TM, Götte M, Sonenberg N, Baranov PV, Ragoussis J, Hobman TC, Pelletier J. Evolution of naturally arising SARS-CoV-2 defective interfering particles. Commun Biol 2022; 5:1140. [PMID: 36302891 PMCID: PMC9610340 DOI: 10.1038/s42003-022-04058-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/30/2022] [Indexed: 11/23/2022] Open
Abstract
Defective interfering (DI) particles arise during virus propagation, are conditional on parental virus for replication and packaging, and interfere with viral expansion. There is much interest in developing DIs as anti-viral agents. Here we characterize DI particles that arose following serial passaging of SARS-CoV-2 at high multiplicity of infection. The prominent DIs identified have lost ~84% of the SARS-CoV-2 genome and are capable of attenuating parental viral titers. Synthetic variants of the DI genomes also interfere with infection and can be used as conditional, gene delivery vehicles. In addition, the DI genomes encode an Nsp1-10 fusion protein capable of attenuating viral replication. These results identify naturally selected defective viral genomes that emerged and stably propagated in the presence of parental virus. Genomes from defective interfering (DI) particles following serial passaging of SARS-CoV-2 reveal a fusion protein that attenuates viral replication. Synthetic, recombinant DI genomes are designed to interfere with SARS-CoV-2 replication.
Collapse
Affiliation(s)
- Samer Girgis
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Zaikun Xu
- Department of Cell Biology, U Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Spyros Oikonomopoulos
- McGill Genome Centre, Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Alla D Fedorova
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.,SFI Centre for Research Training in Genomics Data Science, University College Cork, Cork, Ireland
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Calvin J Gordon
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada.,Rosalind and Morris Goodman Cancer Institute, Montreal, QC, H3A 1A3, Canada
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Jiannis Ragoussis
- McGill Genome Centre, Department of Human Genetics, McGill University, Montreal, QC, Canada.,Department of Bioengineering, McGill University, Montreal, QC, Canada
| | - Tom C Hobman
- Department of Cell Biology, U Alberta, Edmonton, AB, T6G 2H7, Canada. .,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada. .,Li Ka Shing Institute of Virology, U Alberta, Edmonton, AB, T6G 2E1, Canada. .,Women & Children's Health Research Institute, U Alberta, Edmonton, AB, T6G 1C9, Canada.
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada. .,Rosalind and Morris Goodman Cancer Institute, Montreal, QC, H3A 1A3, Canada. .,Department of Oncology, McGill University, Montreal, QC, H3A 1G5, Canada.
| |
Collapse
|
82
|
David M, Olender T, Mizrahi O, Weingarten-Gabbay S, Friedlander G, Meril S, Goldberg N, Savidor A, Levin Y, Salomon V, Stern-Ginossar N, Bialik S, Kimchi A. DAP5 drives translation of specific mRNA targets with upstream ORFs in human embryonic stem cells. RNA (NEW YORK, N.Y.) 2022; 28:1325-1336. [PMID: 35961752 PMCID: PMC9479741 DOI: 10.1261/rna.079194.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Death associated protein 5 (DAP5/eIF4G2/NAT1) is a member of the eIF4G translation initiation factors that has been shown to mediate noncanonical and/or cap-independent translation. It is essential for embryonic development and for differentiation of embryonic stem cells (ESCs), specifically its ability to drive translation of specific target mRNAs. In order to expand the repertoire of DAP5 target mRNAs, we compared ribosome profiles in control and DAP5 knockdown (KD) human ESCs (hESCs) to identify mRNAs with decreased ribosomal occupancy upon DAP5 silencing. A cohort of 68 genes showed decreased translation efficiency in DAP5 KD cells. Mass spectrometry confirmed decreased protein abundance of a significant portion of these targets. Among these was KMT2D, a histone methylase previously shown to be essential for ESC differentiation and embryonic development. We found that nearly half of the cohort of DAP5 target mRNAs displaying reduced translation efficiency of their main coding sequences upon DAP5 KD contained upstream open reading frames (uORFs) that are actively translated independently of DAP5. This is consistent with previously suggested mechanisms by which DAP5 mediates leaky scanning through uORFs and/or reinitiation at the main coding sequence. Crosslinking protein-RNA immunoprecipitation experiments indicated that a significant subset of DAP5 mRNA targets bound DAP5, indicating that direct binding between DAP5 protein and its target mRNAs is a frequent but not absolute requirement for DAP5-dependent translation of the main coding sequence. Thus, we have extended DAP5's function in translation of specific mRNAs in hESCs by a mechanism allowing translation of the main coding sequence following upstream translation of short ORFs.
Collapse
Affiliation(s)
- Maya David
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orel Mizrahi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Gilgi Friedlander
- The Mantoux Bioinformatics Institute, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sara Meril
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nadav Goldberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alon Savidor
- The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yishai Levin
- The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Vered Salomon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shani Bialik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adi Kimchi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| |
Collapse
|
83
|
Liu G, Gack MU. Insights into pandemic respiratory viruses: manipulation of the antiviral interferon response by SARS-CoV-2 and influenza A virus. Curr Opin Immunol 2022; 78:102252. [PMID: 36215931 PMCID: PMC9472579 DOI: 10.1016/j.coi.2022.102252] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 01/29/2023]
Abstract
The outbreak of the COVID-19 pandemic one year after the centennial of the 1918 influenza pandemic reaffirms the catastrophic impact respiratory viruses can have on global health and economy. A key feature of SARS-CoV-2 and influenza A viruses (IAV) is their remarkable ability to suppress or dysregulate human immune responses. Here, we summarize the growing knowledge about the interplay of SARS-CoV-2 and antiviral innate immunity, with an emphasis on the regulation of type-I or -III interferon responses that are critically implicated in COVID-19 pathogenesis. Furthermore, we draw parallels to IAV infection and discuss shared innate immune sensing mechanisms and the respective viral countermeasures.
Collapse
Affiliation(s)
- GuanQun Liu
- Cleveland Clinic Florida Research and Innovation Center, Port St. Lucie, FL, USA
| | - Michaela U Gack
- Cleveland Clinic Florida Research and Innovation Center, Port St. Lucie, FL, USA.
| |
Collapse
|
84
|
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.
Collapse
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;
| |
Collapse
|
85
|
Crozier TW, Greenwood EJ, Williamson JC, Guo W, Porter LM, Gabaev I, Teixeira-Silva A, Grice GL, Wickenhagen A, Stanton RJ, Wang ECY, Wilson SJ, Matheson NJ, Nathan JA, McCaughan F, Lehner PJ. Quantitative proteomic analysis of SARS-CoV-2 infection of primary human airway ciliated cells and lung epithelial cells demonstrates the effectiveness of SARS-CoV-2 innate immune evasion. Wellcome Open Res 2022; 7:224. [PMID: 36483314 PMCID: PMC9706147 DOI: 10.12688/wellcomeopenres.17946.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2022] [Indexed: 02/02/2023] Open
Abstract
Background: Quantitative proteomics is able to provide a comprehensive, unbiased description of changes to cells caused by viral infection, but interpretation may be complicated by differential changes in infected and uninfected 'bystander' cells, or the use of non-physiological cellular models. Methods: In this paper, we use fluorescence-activated cell sorting (FACS) and quantitative proteomics to analyse cell-autonomous changes caused by authentic SARS-CoV-2 infection of respiratory epithelial cells, the main target of viral infection in vivo. First, we determine the relative abundance of proteins in primary human airway epithelial cells differentiated at the air-liquid interface (basal, secretory and ciliated cells). Next, we specifically characterise changes caused by SARS-CoV-2 infection of ciliated cells. Finally, we compare temporal proteomic changes in infected and uninfected 'bystander' Calu-3 lung epithelial cells and compare infection with B.29 and B.1.1.7 (Alpha) variants. Results: Amongst 5,709 quantified proteins in primary human airway ciliated cells, the abundance of 226 changed significantly in the presence of SARS-CoV-2 infection (q <0.05 and >1.5-fold). Notably, viral replication proceeded without inducing a type-I interferon response. Amongst 6,996 quantified proteins in Calu-3 cells, the abundance of 645 proteins changed significantly in the presence of SARS-CoV-2 infection (q < 0.05 and > 1.5-fold). In contrast to the primary cell model, a clear type I interferon (IFN) response was observed. Nonetheless, induction of IFN-inducible proteins was markedly attenuated in infected cells, compared with uninfected 'bystander' cells. Infection with B.29 and B.1.1.7 (Alpha) variants gave similar results. Conclusions: Taken together, our data provide a detailed proteomic map of changes in SARS-CoV-2-infected respiratory epithelial cells in two widely used, physiologically relevant models of infection. As well as identifying dysregulated cellular proteins and processes, the effectiveness of strategies employed by SARS-CoV-2 to avoid the type I IFN response is illustrated in both models.
Collapse
Affiliation(s)
- Thomas W.M. Crozier
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Edward J.D. Greenwood
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - James C. Williamson
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Wenrui Guo
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Linsey M. Porter
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Ildar Gabaev
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Ana Teixeira-Silva
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Guinevere L. Grice
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Arthur Wickenhagen
- MRC - University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Richard J. Stanton
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Eddie C. Y. Wang
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Sam J. Wilson
- MRC - University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Nicholas J. Matheson
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
- NHS Blood and Transplant, Cambridge, CB2 0PT, UK
| | - James A. Nathan
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Frank McCaughan
- Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Paul J. Lehner
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| |
Collapse
|
86
|
Candido KL, Eich CR, de Fariña LO, Kadowaki MK, da Conceição Silva JL, Maller A, Simão RDCG. Spike protein of SARS-CoV-2 variants: a brief review and practical implications. Braz J Microbiol 2022; 53:1133-1157. [PMID: 35397075 PMCID: PMC8994061 DOI: 10.1007/s42770-022-00743-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/21/2022] [Indexed: 12/24/2022] Open
Abstract
The scientific community has been alarmed by the possible immunological evasion, higher infectivity, and severity of disease caused by the newest variants of SARS-CoV-2. The spike protein has an important role in the cellular invasion of viruses and is the target of several vaccines and therapeutic resources, such as monoclonal antibodies. In addition, some of the most relevant mutations in the different variants are on the spike (S) protein gene sequence that leads to structural alterations in the predicted protein, thus causing concern about the protection mediated by vaccines against these new strains. The present review highlights the most recent knowledge about COVID-19 and vaccines, emphasizing the different spike protein structures of SARS-CoV-2 and updating the reader about the emerging viral variants and their classifications, the more common viral mutations described and their distribution in Brazil. It also compiles a table with the most recent knowledge about all of the Omicron spike mutations.
Collapse
Affiliation(s)
- Kattlyn Laryssa Candido
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Caio Ricardo Eich
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Luciana Oliveira de Fariña
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Marina Kimiko Kadowaki
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - José Luis da Conceição Silva
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Alexandre Maller
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Rita de Cássia Garcia Simão
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| |
Collapse
|
87
|
Vaivode K, Verhovcova I, Skrastina D, Petrovska R, Kreismane M, Lapse D, Kalnina Z, Salmina K, Rubene D, Pjanova D. Bacteriophage-Derived Double-Stranded RNA Exerts Anti-SARS-CoV-2 Activity In Vitro and in Golden Syrian Hamsters In Vivo. Pharmaceuticals (Basel) 2022; 15:ph15091053. [PMID: 36145274 PMCID: PMC9504838 DOI: 10.3390/ph15091053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 01/08/2023] Open
Abstract
Bacteriophage-derived dsRNA, known as Larifan, is a nationally well-known broad-spectrum antiviral medication. This study aimed to ascertain the antiviral activity of Larifan against the novel SARS-CoV-2 virus. Larifan’s effect against SARS-CoV-2 in vitro was measured in human lung adenocarcinoma (Calu3) and primary human small airway epithelial cells (HSAEC), and in vivo in the SARS-CoV-2 infection model in golden Syrian hamsters. Larifan inhibited SARS-CoV-2 replication both in vitro and in vivo. Viral RNA copy numbers and titer of infectious virus in the supernatant of Calu3 cells dropped significantly: p = 0.0296 and p = 0.0286, respectively. A reduction in viral RNA copy number was also observed in HSAEC, especially when Larifan was added before infection (p = 0.0218). Larifan markedly reduced virus numbers in infected hamsters’ lungs post-infection, with a more pronounced effect after intranasal administration (p = 0.0032). The administration of Larifan also reduced the amount of infections virus titer in the lungs (p = 0.0039). Improvements in the infection-induced pathological lesion severity in the lungs of animals treated with Larifan were also demonstrated. The inhibition of SARS-CoV-2 replication in vitro and the reduction in the viral load in the lungs of infected hamsters treated with Larifan alongside the improved lung histopathology suggests a potential use of Larifan in also controlling the COVID-19 disease in humans.
Collapse
|
88
|
SARS-CoV-2 impairs interferon production via NSP2-induced repression of mRNA translation. Proc Natl Acad Sci U S A 2022; 119:e2204539119. [PMID: 35878012 PMCID: PMC9371684 DOI: 10.1073/pnas.2204539119] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A robust antiviral innate immune response is indispensable for combating infections. However, an exacerbated response can result in pathological inflammation and tissue damage. mRNA translational control mechanisms play a crucial role in maintaining the appropriate magnitude and duration of the immune response. We show that the GIGYF2/4EHP translational repressor complex represses translation of Ifnb1 mRNA, which encodes type I interferon β (IFN-β). We also demonstrate that the NSP2 protein encoded by SARS-CoV-2 virus further impedes translation of Ifnb1 mRNA through coopting the GIGYF2/4EHP complex, leading to evasion of a cellular innate immune response. The knowledge of the mechanism of action of NSP2-mediated IFN-β suppression provides valuable information for development of treatments for infections of SARS-CoV-2 and other coronaviruses. Viruses evade the innate immune response by suppressing the production or activity of cytokines such as type I interferons (IFNs). Here we report the discovery of a mechanism by which the SARS-CoV-2 virus coopts an intrinsic cellular machinery to suppress the production of the key immunostimulatory cytokine IFN-β. We reveal that the SARS-CoV-2 encoded nonstructural protein 2 (NSP2) directly interacts with the cellular GIGYF2 protein. This interaction enhances the binding of GIGYF2 to the mRNA cap-binding protein 4EHP, thereby repressing the translation of the Ifnb1 mRNA. Depletion of GIGYF2 or 4EHP significantly enhances IFN-β production, which inhibits SARS-CoV-2 replication. Our findings reveal a target for rescuing the antiviral innate immune response to SARS-CoV-2 and other RNA viruses.
Collapse
|
89
|
Hall R, Guedán A, Yap MW, Young GR, Harvey R, Stoye JP, Bishop KN. SARS-CoV-2 ORF6 disrupts innate immune signalling by inhibiting cellular mRNA export. PLoS Pathog 2022; 18:e1010349. [PMID: 36007063 PMCID: PMC9451085 DOI: 10.1371/journal.ppat.1010349] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 09/07/2022] [Accepted: 07/21/2022] [Indexed: 11/18/2022] Open
Abstract
SARS-CoV-2 is a betacoronavirus and the etiological agent of COVID-19, a devastating infectious disease. Due to its far-reaching effect on human health, there is an urgent and growing need to understand the viral molecular biology of SARS-CoV-2 and its interaction with the host cell. SARS-CoV-2 encodes 9 predicted accessory proteins, which are presumed to be dispensable for in vitro replication, most likely having a role in modulating the host cell environment to aid viral replication. Here we show that the ORF6 accessory protein interacts with cellular Rae1 to inhibit cellular protein production by blocking mRNA export. We utilised cell fractionation coupled with mRNAseq to explore which cellular mRNA species are affected by ORF6 expression and show that ORF6 can inhibit the export of many mRNA including those encoding antiviral factors such as IRF1 and RIG-I. We also show that export of these mRNA is blocked in the context of SARS-CoV-2 infection. Together, our studies identify a novel mechanism by which SARS-CoV-2 can manipulate the host cell environment to supress antiviral responses, providing further understanding to the replication strategies of a virus that has caused an unprecedented global health crisis.
Collapse
Affiliation(s)
- Ross Hall
- Retroviral Replication Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Anabel Guedán
- Retroviral Replication Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Melvyn W. Yap
- Retroviral Replication Laboratory, The Francis Crick Institute, London, United Kingdom
| | - George R. Young
- Bioinformatics and Biostatistics STP, The Francis Crick Institute, London, United Kingdom
| | - Ruth Harvey
- World Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Jonathan P. Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, Imperial College London, United Kingdom
| | - Kate N. Bishop
- Retroviral Replication Laboratory, The Francis Crick Institute, London, United Kingdom
| |
Collapse
|
90
|
Chen M, Ma Y, Chang W. SARS-CoV-2 and the Nucleus. Int J Biol Sci 2022; 18:4731-4743. [PMID: 35874947 PMCID: PMC9305274 DOI: 10.7150/ijbs.72482] [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: 02/28/2022] [Accepted: 06/20/2022] [Indexed: 11/22/2022] Open
Abstract
The ongoing COVID-19 pandemic is caused by an RNA virus, SARS-CoV-2. The genome of SARS-CoV-2 lacks a nuclear phase in its life cycle and is replicated in the cytoplasm. However, interfering with nuclear trafficking using pharmacological inhibitors greatly reduces virus infection and virus replication of other coronaviruses is blocked in enucleated cells, suggesting a critical role of the nucleus in virus infection. Here, we summarize the alternations of nuclear pathways caused by SARS-CoV-2, including nuclear translocation pathways, innate immune responses, mRNA metabolism, epigenetic mechanisms, DNA damage response, cytoskeleton regulation, and nuclear rupture. We consider how these alternations contribute to virus replication and discuss therapeutic treatments that target these pathways, focusing on small molecule drugs that are being used in clinical studies.
Collapse
Affiliation(s)
- Mengqi Chen
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Yue Ma
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Wakam Chang
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| |
Collapse
|
91
|
Zitzmann C, Dächert C, Schmid B, van der Schaar H, van Hemert M, Perelson AS, van Kuppeveld FJ, Bartenschlager R, Binder M, Kaderali L. Mathematical modeling of plus-strand RNA virus replication to identify broad-spectrum antiviral treatment strategies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.07.25.501353. [PMID: 35923314 PMCID: PMC9347285 DOI: 10.1101/2022.07.25.501353] [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: 11/25/2022]
Abstract
Plus-strand RNA viruses are the largest group of viruses. Many are human pathogens that inflict a socio-economic burden. Interestingly, plus-strand RNA viruses share remarkable similarities in their replication. A hallmark of plus-strand RNA viruses is the remodeling of intracellular membranes to establish replication organelles (so-called "replication factories"), which provide a protected environment for the replicase complex, consisting of the viral genome and proteins necessary for viral RNA synthesis. In the current study, we investigate pan-viral similarities and virus-specific differences in the life cycle of this highly relevant group of viruses. We first measured the kinetics of viral RNA, viral protein, and infectious virus particle production of hepatitis C virus (HCV), dengue virus (DENV), and coxsackievirus B3 (CVB3) in the immuno-compromised Huh7 cell line and thus without perturbations by an intrinsic immune response. Based on these measurements, we developed a detailed mathematical model of the replication of HCV, DENV, and CVB3 and show that only small virus-specific changes in the model were necessary to describe the in vitro dynamics of the different viruses. Our model correctly predicted virus-specific mechanisms such as host cell translation shut off and different kinetics of replication organelles. Further, our model suggests that the ability to suppress or shut down host cell mRNA translation may be a key factor for in vitro replication efficiency which may determine acute self-limited or chronic infection. We further analyzed potential broad-spectrum antiviral treatment options in silico and found that targeting viral RNA translation, especially polyprotein cleavage, and viral RNA synthesis may be the most promising drug targets for all plus-strand RNA viruses. Moreover, we found that targeting only the formation of replicase complexes did not stop the viral replication in vitro early in infection, while inhibiting intracellular trafficking processes may even lead to amplified viral growth. Author summary Plus-strand RNA viruses comprise a large group of related and medically relevant viruses. The current global pandemic of COVID-19 caused by the SARS-coronavirus-2 as well as the constant spread of diseases such as dengue and chikungunya fever show the necessity of a comprehensive and precise analysis of plus-strand RNA virus infections. Plus-strand RNA viruses share similarities in their life cycle. To understand their within-host replication strategies, we developed a mathematical model that studies pan-viral similarities and virus-specific differences of three plus-strand RNA viruses, namely hepatitis C, dengue, and coxsackievirus. By fitting our model to in vitro data, we found that only small virus-specific variations in the model were required to describe the dynamics of all three viruses. Furthermore, our model predicted that ribosomes involved in viral RNA translation seem to be a key player in plus-strand RNA replication efficiency, which may determine acute or chronic infection outcome. Furthermore, our in-silico drug treatment analysis suggests that targeting viral proteases involved in polyprotein cleavage, in combination with viral RNA replication, may represent promising drug targets with broad-spectrum antiviral activity.
Collapse
Affiliation(s)
- Carolin Zitzmann
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Christopher Dächert
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”, Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bianca Schmid
- Dept of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Hilde van der Schaar
- Division of infectious Diseases and Immunology, Virology Section, Dept of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Martijn van Hemert
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Frank J.M. van Kuppeveld
- Division of infectious Diseases and Immunology, Virology Section, Dept of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Ralf Bartenschlager
- Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Dept of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg partner site, Heidelberg, Germany
| | - Marco Binder
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”, Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
92
|
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.
Collapse
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
| |
Collapse
|
93
|
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: 15] [Impact Index Per Article: 7.5] [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.
Collapse
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
| |
Collapse
|
94
|
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.
Collapse
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
| |
Collapse
|
95
|
Zou L, Moch C, Graille M, Chapat C. The SARS-CoV-2 protein NSP2 impairs the silencing capacity of the human 4EHP-GIGYF2 complex. iScience 2022; 25:104646. [PMID: 35756894 PMCID: PMC9213009 DOI: 10.1016/j.isci.2022.104646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/12/2022] [Accepted: 06/15/2022] [Indexed: 01/20/2023] Open
Abstract
There is an urgent need for a molecular understanding of how SARS-CoV-2 influences the machineries of the host cell. Herein, we focused our attention on the capacity of the SARS-CoV-2 protein NSP2 to bind the human 4EHP-GIGYF2 complex, a key factor involved in microRNA-mediated silencing of gene expression. Using in vitro interaction assays, our data demonstrate that NSP2 physically associates with both 4EHP and a central segment in GIGYF2 in the cytoplasm. We also provide functional evidence showing that NSP2 impairs the function of GIGYF2 in mediating translation repression using reporter-based assays. Collectively, these data reveal the potential impact of NSP2 on the post-transcriptional silencing of gene expression in human cells, pointing out 4EHP-GIGYF2 targeting as a possible strategy of SARS-CoV-2 to take over the silencing machinery and to suppress host defenses.
Collapse
Affiliation(s)
- Limei Zou
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris. F-91128 Palaiseau, France
| | - Clara Moch
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris. F-91128 Palaiseau, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris. F-91128 Palaiseau, France
| | - Clément Chapat
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris. F-91128 Palaiseau, France
| |
Collapse
|
96
|
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: 33] [Impact Index Per Article: 16.5] [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.
Collapse
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.
| |
Collapse
|
97
|
Designing and characterization of a SARS-CoV-2 immunogen with receptor binding motif grafted on a protein scaffold: An epitope-focused vaccine approach. Int J Biol Macromol 2022; 209:1359-1367. [PMID: 35469951 PMCID: PMC9033297 DOI: 10.1016/j.ijbiomac.2022.04.148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 12/24/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has a significant burden on the economy and healthcare around the world. Vaccines are the most effective tools to fight infectious diseases by containing the spread of the disease. The current vaccines against SARS-CoV-2 are mostly based on the spike protein of SARS-CoV-2, which is large and has many immune-dominant non-neutralizing epitopes that may effectively skew the antibody response towards non-neutralizing antibodies. Here, we have explored the possibility of immune-focusing the receptor binding motif (RBM) of the spike protein of SARS-CoV-2 that induces mostly neutralizing antibodies in natural infection or in vacinees. The result shows that the scaffolded RBM can bind to Angiotensin Converting Enzyme 2 (ACE2) although with low affinity and induces a strong antibody response in mice. The immunized sera can bind both, the receptor binding domain (RBD) and the spike protein, which holds the RBM in its natural context. Sera from the immunized mice showed robust interferon γ response but poor neutralization of SARS-CoV-2 suggesting presence of a predominant T cell epitope on scaffolded RBM. Together, we provide a strategy for inducing strong antigenic T cell response which could be exploited further for future vaccine designing and development against SARS-CoV-2 infection.
Collapse
|
98
|
Debnath SK, Debnath M, Srivastava R, Omri A. Drugs repurposing for SARS-CoV-2: new insight of COVID-19 druggability. Expert Rev Anti Infect Ther 2022; 20:1187-1204. [PMID: 35615888 DOI: 10.1080/14787210.2022.2082944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION The ongoing epidemic of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) creates a massive panic worldwide due to the absence of effective medicines. Developing a new drug or vaccine is time-consuming to pass safety and efficacy testing. Therefore, repurposing drugs have been introduced to treat COVID-19 until effective drugs are developed. AREA COVERED A detailed search of repurposing drugs against SARS-CoV-2 was carried out using the PubMed database, focusing on articles published 2020 years onward. A different class of drugs has been described in this article to target hosts and viruses. Based on the previous pandemic experience of SARS-CoV and MERS, several antiviral and antimalarial drugs are discussed here. This review covers the failure of some repurposed drugs that showed promising activity in the earlier CoV-pandemic but were found ineffective against SARS-CoV-2. All these discussions demand a successful drug development strategy for screening and identifying an effective drug for better management of COVID-19. The drug development strategies described here will serve a new scope of research for academicians and researchers. EXPERT OPINION Repurposed drugs have been used since COVID-19 to eradicate disease propagation. Drugs found effective for MERS and SARS may not be effective against SARS-CoV-2. Drug libraries and artificial intelligence are helpful tools to screen and identify different molecules targeting viruses or hosts.
Collapse
Affiliation(s)
- Sujit Kumar Debnath
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Monalisha Debnath
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Rohit Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Abdelwahab Omri
- Department of Chemistry and Biochemistry, The Novel Drug & Vaccine Delivery Systems Facility, Laurentian University, Sudbury, Canada
| |
Collapse
|
99
|
The Translational Landscape of SARS-CoV-2-infected Cells Reveals Suppression of Innate Immune Genes. mBio 2022; 13:e0081522. [PMID: 35604092 PMCID: PMC9239271 DOI: 10.1128/mbio.00815-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes a number of strategies to modulate viral and host mRNA translation. Here, we used ribosome profiling in SARS-CoV-2-infected model cell lines and primary airway cells grown at an air-liquid interface to gain a deeper understanding of the translationally regulated events in response to virus replication. We found that SARS-CoV-2 mRNAs dominate the cellular mRNA pool but are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy despite notable accumulation of ribosomes within the slippery sequence on the frameshifting element. In a highly permissive cell line model, although SARS-CoV-2 infection induced the transcriptional upregulation of numerous chemokine, cytokine, and interferon-stimulated genes, many of these mRNAs were not translated efficiently. The impact of SARS-CoV-2 on host mRNA translation was more subtle in primary cells, with marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function. Together, these data reveal the key role of mRNA translation in SARS-CoV-2 replication and highlight unique mechanisms for therapeutic development.
Collapse
|
100
|
Aloul KM, Nielsen JE, Defensor EB, Lin JS, Fortkort JA, Shamloo M, Cirillo JD, Gombart AF, Barron AE. Upregulating Human Cathelicidin Antimicrobial Peptide LL-37 Expression May Prevent Severe COVID-19 Inflammatory Responses and Reduce Microthrombosis. Front Immunol 2022; 13:880961. [PMID: 35634307 PMCID: PMC9134243 DOI: 10.3389/fimmu.2022.880961] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/11/2022] [Indexed: 01/08/2023] Open
Abstract
COVID-19 is characterized by hyperactivation by inflammatory cytokines and recruitment of macrophages, neutrophils, and other immune cells, all hallmarks of a strong inflammatory response that can lead to severe complications and multi-organ damage. Mortality in COVID-19 patients is associated with a high prevalence of neutrophil extracellular trap (NET) formation and microthrombosis that are exacerbated by hyperglycemia, diabetes, and old age. SARS-CoV-2 infection in humans and non-human primates have revealed long-term neurological consequences of COVID-19, possibly concomitant with the formation of Lewy bodies in the brain and invasion of the nervous system via the olfactory bulb. In this paper, we review the relevance of the human cathelicidin LL-37 in SARS-CoV-2 infections. LL-37 is an immunomodulatory, host defense peptide with direct anti-SARS-CoV-2 activity, and pleiotropic effects on the inflammatory response, neovascularization, Lewy body formation, and pancreatic islet cell function. The bioactive form of vitamin D and a number of other compounds induce LL-37 expression and one might predict its upregulation, could reduce the prevalence of severe COVID-19. We hypothesize upregulation of LL-37 will act therapeutically, facilitating efficient NET clearance by macrophages, speeding endothelial repair after inflammatory tissue damage, preventing α-synuclein aggregation, and supporting blood-glucose level stabilization by facilitating insulin release and islet β-cell neogenesis. In addition, it has been postulated that LL-37 can directly bind the S1 domain of SARS-CoV-2, mask angiotensin converting enzyme 2 (ACE2) receptors, and limit SARS-CoV-2 infection. Purposeful upregulation of LL-37 could also serve as a preventative and therapeutic strategy for SARS-CoV-2 infections.
Collapse
Affiliation(s)
- Karim M. Aloul
- Department of Bioengineering, Schools of Medicine and of Engineering, Stanford University, Stanford, CA, United States
| | - Josefine Eilsø Nielsen
- Department of Bioengineering, Schools of Medicine and of Engineering, Stanford University, Stanford, CA, United States
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Erwin B. Defensor
- Department of Neurosurgery, School of Medicine, Stanford University, Stanford, CA, United States
| | - Jennifer S. Lin
- Department of Bioengineering, Schools of Medicine and of Engineering, Stanford University, Stanford, CA, United States
| | - John A. Fortkort
- Department of Bioengineering, Schools of Medicine and of Engineering, Stanford University, Stanford, CA, United States
| | - Mehrdad Shamloo
- Department of Neurosurgery, School of Medicine, Stanford University, Stanford, CA, United States
| | - Jeffrey D. Cirillo
- Department of Microbial Pathogenesis and Immunology, Texas A&M College of Medicine, Bryan, TX, United States
| | - Adrian F. Gombart
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
- The Linus Pauling Institute, Oregon State University, Corvallis, OR, United States
| | - Annelise E. Barron
- Department of Bioengineering, Schools of Medicine and of Engineering, Stanford University, Stanford, CA, United States
| |
Collapse
|