The translational landscape of SARS-CoV-2 and infected cells

  1. Maritza Puray-Chavez
  2. Nakyung Lee
  3. Kasyap Tenneti
  4. Yiqing Wang
  5. Hung R. Vuong
  6. Yating Liu
  7. Amjad Horani
  8. Tao Huang
  9. Sean P. Gunsten
  10. James B. Case
  11. Wei Yang
  12. Michael S. Diamond
  13. Steven L. Brody
  14. Joseph Dougherty
  15. Sebla B. Kutluay

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Abstract

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 the air-liquid interface to gain a deeper understanding of the translationally regulated events in response to virus replication. We find 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 in comparison to HIV-1, suggesting utilization of distinct structural elements. In the highly permissive cell models, although SARS-CoV-2 infection induced the transcriptional upregulation of numerous chemokines, cytokines and interferon stimulated genes, many of these mRNAs were not translated efficiently. 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.

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  1. Version published to 10.1101/2020.11.03.367516v3 on bioRxiv
  2. Version published to 10.1101/2020.11.03.367516v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.11.03.367516: (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.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Cells were blocked with 1% bovine serum albumin (BSA) and 10% FBS in 0.1% Tween-20 PBS (PBST) for 1 h prior to staining with a rabbit polyclonal anti SARS-CoV-2 nucleocapsid antibody (Sino Biological Inc. catalog # 40588-T62) diluted 1:500 and incubated overnight at 4°C.
    anti SARS-CoV-2 nucleocapsid antibody
    suggested: (BioLegend Cat# 940901, RRID:AB_2888743)
    The following day, cells were stained with an Alexa Fluor 488-conjugated goat anti-rabbit secondary antibody (Invitrogen) at 1:1000 dilution, counter-stained with DAPI and imaged by microscopy.
    anti-rabbit
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    HIV-1 stocks were generated by transfection of Human embryonic kidney cell line, HEK293T, with proviral plasmids and collection of cell culture supernatants two days after.
    HEK293T
    suggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)
    HIV-1 stocks were titered on TZM-bl cells by conventional methods.
    TZM-bl
    suggested: NIH-ARP Cat# 8129-442, RRID:CVCL_B478)
    SARS-CoV-2 strain 2019-nCoV/USA-WA1/2020 was obtained from Natalie Thornburg at the Centers for Disease Control and Prevention (CDC), propagated in Vero CCL-81 cells and titrated on Vero E6 cells by plaque-forming assays.
    Vero CCL-81
    suggested: None
    Vero E6
    suggested: RRID:CVCL_XD71)

    Results from OddPub: Thank you for sharing your code and 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.

    About SciScore

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  4. Version published to 10.1101/2020.11.03.367516v1 on bioRxiv