SARS-CoV-2 viral proteins NSP1 and NSP13 inhibit interferon activation through distinct mechanisms

Vazquez, Christine; Swanson, Sydnie; Negatu, Seble G; Dittmar, Mark; Miller, JoAnn; Ramage, Holly; Cherry, Sara; Jurado, Kellie Ann

doi:10.1371/journal.pone.0253089

Cited by 87 publications

(89 citation statements)

References 43 publications

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“…Many viruses that have co-evolved with their hosts have developed complex and multiple strategies to subvert or antagonize the host innate immune response as a mechanism to evade immune detection and elimination. Indeed, it has become increasingly clear that multiple SARS-CoV-2 encoded genes products target innate immune signaling pathways at various levels ( Xia et al., 2020 ; Fung et al., 2021 ; Han et al., 2021 ; Kumar et al., 2021 ; Sui et al., 2021a ; Vazquez et al., 2021 ; Zhao et al., 2021 ). Here we identify the Spike protein of SARS-CoV-2 as a key negative regulator of IFN-I activation in the RIG-I pathway that targets the IRF3 transcription factor and mediates its proteasomal degradation.…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 Spike Antagonizes Innate Antiviral Immunity by Targeting Interferon Regulatory Factor 3

Freitas

Crum

Parvatiyar

2022

Front. Cell. Infect. Microbiol.

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Corona virus disease 2019 (COVID-19) pathogenesis is intimately linked to the severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) and disease severity has been associated with compromised induction of type I interferon (IFN-I) cytokines which coordinate the innate immune response to virus infections. Here we identified the SARS-CoV-2 encoded protein, Spike, as an inhibitor of IFN-I that antagonizes viral RNA pattern recognition receptor RIG-I signaling. Ectopic expression of SARS-CoV-2 Spike blocked RIG-I mediated activation of IFNβ and downstream induction of interferon stimulated genes. Consequently, SARS-CoV-2 Spike expressing cells harbored increased RNA viral burden compared to control cells. Co-immunoprecipitation experiments revealed SARS-CoV-2 Spike associated with interferon regulatory factor 3 (IRF3), a key transcription factor that governs IFN-I activation. Co-expression analysis via immunoassays further indicated Spike specifically suppressed IRF3 expression as NF-κB and STAT1 transcription factor levels remained intact. Further biochemical experiments uncovered SARS-CoV-2 Spike potentiated proteasomal degradation of IRF3, implicating a novel mechanism by which SARS-CoV-2 evades the host innate antiviral immune response to facilitate COVID-19 pathogenesis.

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Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 Spike Antagonizes Innate Antiviral Immunity by Targeting Interferon Regulatory Factor 3

Freitas

Crum

Parvatiyar

2022

Front. Cell. Infect. Microbiol.

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“…Similarly, our antibody to nsp10, an intriguing protein known to form complex with nsp16 that is involved in methylation of a capped RNA strand and necessary for viral immune evasion [25], is the first anti-nsp10 antibody reported for use in flow cytometry and, in particular, on infected cells. Many other antibodies described here cover SARS-CoV-2 non-structural proteins that have been of great interest due to their important role in the immune response: nsp1 that functions as a virulence factor inhibiting host translation [26,27] and resulting in modulation of host immune functions [28], and nsp8 and nsp9 that interfere with IFN response [29]. These SARS-CoV-2 proteins represent promising antiviral drug targets, indicating the need for their further functional and biochemical studies.…”

Section: Discussionmentioning

confidence: 99%

Collection of Monoclonal Antibodies Targeting SARS-CoV-2 Proteins

Matešić

Brlić

Roviš

et al. 2022

Viruses

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In early 2020, the COVID-19 pandemic sparked a global crisis that continues to pose a serious threat to human health and the economy. Further advancement in research is necessary and requires the availability of quality molecular tools, including monoclonal antibodies. Here, we present the development and characterization of a collection of over 40 new monoclonal antibodies directed against different SARS-CoV-2 proteins. Recombinant SARS-CoV-2 proteins were expressed, purified, and used as immunogens. Upon development of specific hybridomas, the obtained monoclonal antibody (mAb) clones were tested for binding to recombinant proteins and infected cells. We generated mAbs against structural proteins, the Spike and Nucleocapsid protein, several non-structural proteins (nsp1, nsp7, nsp8, nsp9, nsp10, nsp16) and accessory factors (ORF3a, ORF9b) applicable in flow cytometry, immunofluorescence, or Western blot. Our collection of mAbs provides a set of novel, highly specific tools that will allow a comprehensive analysis of the viral proteome, which will allow further understanding of SARS-CoV-2 pathogenesis and the design of therapeutic strategies.

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“…The SARS-COV-2 NSP13 protein is well known for its ability to evade the host immune system by binding to TBK1 and inhibiting the phosphorylation of TBK1 and IRF3 from suppressing IFNβ production and signaling. Since several mutations have been observed in NSP13 ( Xia et al, 2020 ; Yuen et al, 2020 ; Guo et al, 2021 ; Vazquez et al, 2021 ), it was necessary to elucidate the effects of different NSP13 mutants on binding with TBK1. Using computational tools, understanding the impact of different mutations is an accurate and traditional approach ( Hussain et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

“…The individual protein of SARS-CoV-2 antagonizes IFNβ production by different mechanisms ( Lei et al, 2020 ; Li et al, 2020 ; Xia et al, 2020 ; Yuen et al, 2020 ; Rashid et al, 2021a , b ; Vazquez et al, 2021 ). Among these viral proteins, non-structural protein 13 (NSP13) was found to antagonize IFNβ production by binding to TBK1 to inhibit its phosphorylation and cause decreased activation of IRF3 and IFNβ ( Xia et al, 2020 ; Yuen et al, 2020 ; Guo et al, 2021 ; Vazquez et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…The mutations P504L and Y541C in NSP13 were important for different disease outcomes ( Cao et al, 2021 ). The function of NSP13 has been reported in several studies to antagonize the production of IFNβ by physically binding to TBK1 and to evade immune response ( Lei et al, 2020 ; Xia et al, 2020 ; Yuen et al, 2020 ; Guo et al, 2021 ; Vazquez et al, 2021 ). Since various VOIs and VOCs were emerging, we were interested in whether the pathogenesis of these variants might also be contributed by the mutations in NSP13 besides the spike protein in terms of its immune evasion.…”

Section: Introductionmentioning

confidence: 99%

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Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System

et al. 2021

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Mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have made this virus more infectious. Previous studies have confirmed that non-structural protein 13 (NSP13) plays an important role in immune evasion by physically interacting with TANK binding kinase 1 (TBK1) to inhibit IFNβ production. Mutations have been reported in NSP13; hence, in the current study, biophysical and structural modeling methodologies were adapted to dissect the influence of major mutations in NSP13, i.e., P77L, Q88H, D260Y, E341D, and M429I, on its binding to the TBK1 and to escape the human immune system. The results revealed that these mutations significantly affected the binding of NSP13 and TBK1 by altering the hydrogen bonding network and dynamic structural features. The stability, flexibility, and compactness of these mutants displayed different dynamic features, which are the basis for immune evasion. Moreover, the binding was further validated using the MM/GBSA approach, revealing that these mutations have higher binding energies than the wild-type (WT) NSP13 protein. These findings thus justify the basis of stronger interactions and evasion for these NSP13 mutants. In conclusion, the current findings explored the key features of the NSP13 WT and its mutant complexes, which can be used to design structure-based inhibitors against the SARS-CoV-2 new variants to rescue the host immune system.

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SARS-CoV-2 viral proteins NSP1 and NSP13 inhibit interferon activation through distinct mechanisms

Cited by 87 publications

References 43 publications

SARS-CoV-2 Spike Antagonizes Innate Antiviral Immunity by Targeting Interferon Regulatory Factor 3

SARS-CoV-2 Spike Antagonizes Innate Antiviral Immunity by Targeting Interferon Regulatory Factor 3

Collection of Monoclonal Antibodies Targeting SARS-CoV-2 Proteins

Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System

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