The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation

  1. Antonin Tidu
  2. Aurélie Janvier
  3. Laure Schaeffer
  4. Piotr Sosnowski
  5. Lauriane Kuhn
  6. Philippe Hammann
  7. Eric Westhof
  8. Gilbert Eriani
  9. Franck Martin

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Abstract

SARS-CoV-2 coronavirus is responsible for the Covid-19 pandemic. In the early phase of infection, the single-strand positive RNA genome is translated into nonstructural proteins (NSP). One of the first proteins produced during viral infection, NSP1, binds to the host ribosome and blocks the mRNA entry channel. This triggers translation inhibition of cellular translation. Despite the presence of NSP1 on the ribosome, viral translation proceeds, however. The molecular mechanism of the so-called viral evasion to NSP1 inhibition remains elusive. Here, we confirm that viral translation is maintained in the presence of NSP1 and we show that the evasion to NSP1-inhibition is mediated by the cis -acting RNA hairpin SL1 in the 5′UTR of SARS-CoV-2. Only the apical part of SL1 is required for viral translation. We further show that NSP1 remains bound on the ribosome during viral translation. We suggest that the interaction between NSP1 and SL1 frees the mRNA accommodation channel while maintaining NSP1 bound to the ribosome. Thus, NSP1 acts as a ribosome gatekeeper, shutting down host translation and fostering SARS-CoV-2 translation in the presence of the SL1 5′UTR hairpin. SL1 is also present and necessary for translation of subgenomic RNAs in the late phase of the infectious program. Consequently, therapeutic strategies targeting SL1 should affect viral translation at early and late stages of infection. Therefore, SL1 might be seen as a genuine “Achilles heel” of the virus.

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  1. Version published to 10.1261/rna.078121.120
  2. ScreenIT

    SciScore for 10.1101/2020.10.14.339515: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Experimental Models: Organisms/Strains
    SentencesResources
    NSP1 overexpression and purification: NSP1 and derivatives (R124A+K125A–Inhibits translation, no mRNA degradation–(Lokugamage et al., 2012a); K164A+H165A—biologically inactive–(Narayanan et al., 2008) were cloned in plasmid pET-His-GST-TEV-LIC-(2GT).
    K164A+H165A—biologically inactive–
    suggested: None
    Software and Algorithms
    SentencesResources
    The statistical analysis based on spectral counts was performed using a homemade R package that calculates fold change and p-values using the quasi-likelihood negative binomial generalized log-linear model implemented in the edgeR package (https://github.com/hzuber67/IPinquiry4).
    edgeR
    suggested: (edgeR, RRID:SCR_012802)
    The size factors used to scale samples were calculated according to the DESeq2 normalization method (i.e., median of ratios method).
    DESeq2
    suggested: (DESeq, RRID:SCR_000154)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2020.10.14.339515v1 on bioRxiv