N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry

  1. Dongxia Wang
  2. Bin Zhou
  3. Theodore R. Keppel
  4. Maria Solano
  5. Jakub Baudys
  6. Jason Goldstein
  7. M. G. Finn
  8. Xiaoyu Fan
  9. Asheley P. Chapman
  10. Jonathan L. Bundy
  11. Adrian R. Woolfitt
  12. Sarah H. Osman
  13. James L. Pirkle
  14. David E. Wentworth
  15. John R. Barr

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Abstract

N-glycosylation plays an important role in the structure and function of membrane and secreted proteins. The spike protein on the surface of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, is heavily glycosylated and the major target for developing vaccines, therapeutic drugs and diagnostic tests. The first major SARS-CoV-2 variant carries a D614G substitution in the spike (S-D614G) that has been associated with altered conformation, enhanced ACE2 binding, and increased infectivity and transmission. In this report, we used mass spectrometry techniques to characterize and compare the N-glycosylation of the wild type (S-614D) or variant (S-614G) SARS-CoV-2 spike glycoproteins prepared under identical conditions. The data showed that half of the N-glycosylation sequons changed their distribution of glycans in the S-614G variant. The S-614G variant showed a decrease in the relative abundance of complex-type glycans (up to 45%) and an increase in oligomannose glycans (up to 33%) on all altered sequons. These changes led to a reduction in the overall complexity of the total N-glycosylation profile. All the glycosylation sites with altered patterns were in the spike head while the glycosylation of three sites in the stalk remained unchanged between S-614G and S-614D proteins.

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  1. Version published to 10.1038/s41598-021-02904-w
  2. ScreenIT

    SciScore for 10.1101/2021.07.26.453787: (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

    Software and Algorithms
    SentencesResources
    Data analysis: MS/MS data were processed using PMi-Byonic (Version 3.7) node within Proteome Discover (Thermo Scientific) Data were searched using the Protein Metrics 182 human N-glycan library (included in the Byonic program) as potential glycan modifications.
    PMi-Byonic
    suggested: (PMI-Byonic, RRID:SCR_016735)
    The model was displayed using PyMOL, the only change being that the O-linked glycans were hidden due to low occupancy [3].
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

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

    About SciScore

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  3. Version published to 10.1101/2021.07.26.453787v1 on bioRxiv