Structural basis for the interaction of SARS-CoV-2 virulence factor nsp1 with Pol α - Primase

  1. Mairi L. Kilkenny
  2. Charlotte E. Veale
  3. Amir Guppy
  4. Steven W. Hardwick
  5. Dimitri Y. Chirgadze
  6. Neil J. Rzechorzek
  7. Joseph D. Maman
  8. Luca Pellegrini

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Abstract

The molecular mechanisms that drive the infection by the SARS-CoV-2 coronavirus – the causative agent of the COVID-19 (Coronavirus disease-2019) pandemic – are under intense current scrutiny, to understand how the virus operates and to uncover ways in which the disease can be prevented or alleviated.

Recent cell-based analyses of SARS-CoV-2 protein - protein interactions have mapped the human proteins targeted by the virus. The DNA polymerase α - primase complex or primosome – responsible for initiating DNA synthesis in genomic duplication – was identified as a target of nsp1 (non structural protein 1), a major virulence factor in the SARS-CoV-2 infection.

Here, we report the biochemical characterisation of the interaction between nsp1 and the primosome and the cryoEM structure of the primosome - nsp1 complex. Our data provide a structural basis for the reported interaction between the primosome and nsp1. They suggest that Pol α - primase plays a part in the immune response to the viral infection, and that its targeting by SARS-CoV-2 aims to interfere with such function.

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  1. ScreenIT

    SciScore for 10.1101/2021.06.17.448816: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Recombinant DNA
    SentencesResources
    Full-length coronavirus nsp1 genes (SARS-CoV-2, SARS-CoV, MERS, HKU1, NL63 and 229E) were ordered as synthetic gBlocks (IDT), and cloned into bacterial expression vector pMAT11 (Peranen et al., 1996).
    pMAT11
    suggested: RRID:Addgene_112592)
    Software and Algorithms
    SentencesResources
    Movie processing was carried out in Relion 3.1 (Scheres, 2012).
    Relion
    suggested: (RELION, RRID:SCR_016274)
    For model building, the crystal structure of human Pol α - primase (PDB ID 5EXR) was fitted manually in the map with ChimeraX (Goddard et al., 2018) and real-space refined in Phenix (Adams et al., 2010), together with local manual rebuilding in Coot (Emsley & Cowtan, 2004).
    Coot
    suggested: (Coot, RRID:SCR_014222)

    Results from OddPub: Thank you for sharing your data.

    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 did not find any issues relating to the usage of bar graphs.

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

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • 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.

    Results from scite Reference Check: We found no unreliable references.

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  2. Version published to 10.1101/2021.06.17.448816v1 on bioRxiv