The SARS-CoV-2 Envelope and Membrane proteins modulate maturation and retention of the Spike protein, allowing optimal formation of VLPs in presence of Nucleoprotein

  1. Bertrand Boson
  2. Vincent Legros
  3. Bingjie Zhou
  4. Cyrille Mathieu
  5. François-Loïc Cosset
  6. Dimitri Lavillette
  7. Solène Denolly

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Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a β-coronavirus, is the causative agent of the COVID-19 pandemic. Like for other coronaviruses, its particles are composed of four structural proteins, namely Spike S, Envelope E, Membrane M and Nucleoprotein N proteins. The involvement of each of these proteins and their interplays during the assembly process of this new virus are poorly-defined and are likely β-coronavirus-type different. Therefore, we sought to investigate how SARS-CoV-2 behaves for its assembly by expression assays of S, in combination with E, M and/or N. By combining biochemical and imaging assays, we showed that E and M regulate intracellular trafficking of S and hence its furin-mediated processing. Indeed, our imaging data revealed that S remains at ERGIC or Golgi compartments upon expression of E or M, like for SARS-CoV-2 infected cells. By studying a mutant of S, we showed that its cytoplasmic tail, and more specifically, its C-terminal retrieval motif, is required for the M-mediated retention in the ERGIC, whereas E induces S retention by modulating the cell secretory pathway. We also highlighted that E and M induce a specific maturation of S N-glycosylation, which is observed on particles and lysates from infected cells independently of its mechanisms of intracellular retention. Finally, we showed that both M, E and N are required for optimal production of virus-like-proteins. Altogether, our results indicated that E and M proteins influence the properties of S proteins to promote assembly of viral particles. Our results therefore highlight both similarities and dissimilarities in these events, as compared to other β-coronaviruses.

Author Summary

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Its viral particles are composed of four structural proteins, namely Spike S, Envelope E, Membrane M and Nucleoprotein N proteins, though their involvement in the virion assembly remain unknown for this particular coronavirus. Here we showed that presence of E and M influence the localization and maturation of S protein, in term of cleavage and N-glycosylation maturation. Indeed, E protein is able to slow down the cell secretory pathway whereas M-induced retention of S requires the retrieval motif in S C-terminus. We also highlighted that E and M might regulate the N glycosylation maturation of S independently of its intracellular retention mechanism. Finally, we showed that the four structural proteins are required for optimal formation of virus-like particles, highlighting the involvement of N, E and M in assembly of infectious particles. Altogether, our results highlight both similarities and dissimilarities in these events, as compared to other β-coronaviruses.

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  1. ScreenIT

    SciScore for 10.1101/2020.08.24.260901: (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
    Antibodies: Mouse anti-actin (clone AC74, Sigma-Aldrich), rabbit anti-SARS-CoV2 S2, mouse anti-SARS-CoV2 S1 and mouse anti-SARS-CoV2 N (Sino Biological), mouse anti-GFP (Roche), anti-VSV-G 41A1 and rabbit anti-GM130 (clone EP892Y, Abcam) were used according to the providers’ instructions.
    anti-actin
    suggested: None
    anti-SARS-CoV2
    suggested: None
    S1
    suggested: None
    anti-SARS-CoV2 N
    suggested: None
    anti-GFP
    suggested: None
    anti-VSV-G
    suggested: None
    After a saturation step with 3% BSA/PBS, cells were incubated for 1 hour with rabbit anti-GM130 and mouse anti-SARS-CoV2 S1 antibodies at 1/200 dilution in 1% BSA/PBS, washed 3 times with 1%BSA/PBS, and stained for 1 hour with donkey anti-rabbit AlexaFluor-488 and donkey anti-mouse AlexaFluor-555 secondary antibodies (Molecular Probes) diluted 1/2,000 in 1% BSA/PBS.
    anti-GM130
    suggested: None
    anti-SARS-CoV2 S1
    suggested: None
    anti-rabbit
    suggested: None
    anti-mouse
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Supernatant fluids were collected after two days at 37°C, clarified by centrifugation (400xg, 5min), aliquoted and titrated in plaque forming unit by classic dilution limit assay on the same Vero E6 cells.
    Vero E6
    suggested: RRID:CVCL_XD71)
    VSV-Gts analysis: Huh7.5 cells were seeded 16h prior to transfection with pEGFP-N3-VSV-Gts and p7-encoding plasmid using GeneJammer transfection reagent (Agilent).
    Huh7.5
    suggested: RRID:CVCL_7927)
    Analysis of expression different proteins in cell lysate and pellet: HEK293T cells were seeded 24h prior to transfection with the different plasmids (2μg of each plasmid for a 10cm dish) using calcium phosphate precipitation.
    HEK293T
    suggested: None
    Software and Algorithms
    SentencesResources
    Images were analyzed with the ImageJ software (imagj.nih.gov) and the Manders’ overlap coefficients were calculated by using the JACoP plugin.
    ImageJ
    suggested: (ImageJ, RRID:SCR_003070)
    Statistical analysis: Significance values were calculated by applying the Kruskal-Wallis test and Dunn’s multiple comparison test using the GraphPad Prism 6 software (GraphPad Software, USA).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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 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

    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.

  2. Version published to 10.1101/2020.08.24.260901 on bioRxiv