Conserved role of spike S2 domain N-glycosylation across beta-coronavirus family

Qi Yang; Anju Kelkar; Balaji Manicassamy; Sriram Neelamegham

doi:10.1101/2024.09.05.611372

Besides acting as an immunological shield, the N-glycans of SARS-CoV-2 are also critical for viral life cycle. As the S2 subunit of spike is highly conserved across beta-coronaviruses, we determined the functional significance of the five 'stem N-glycans' located in S2 between N1098-N1194. Studies were performed with 31 Asn-to-Gln mutants, beta-coronavirus virus-like particles and single-cycle viral replicons. Deletions of stem N-glycans enhanced S1 shedding from trimeric spike, reduced ACE2 binding and abolished syncytia formation. When three or more N-glycans were deleted, spike expression on cell surface and incorporation into virions was both reduced. Viral entry function was progressively lost upon deleting the N1098 glycan in combination with additional glycosite modifications. In addition to SARS-CoV-2, deleting stem N-glycans in SARS-CoV and MERS-CoV spike also prevented viral entry into target cells. These data suggest multiple functional roles for the stem N-glycans, and evolutionarily conserved properties for these complex carbohydrates across human beta-coronaviruses.Besides acting as an immunological shield, the N-glycans of SARS-CoV-2 are also critical for viral life cycle. As the S2 subunit of spike is highly conserved across beta-coronaviruses, we determined the functional significance of the five 'stem N-glycans' located in S2 between N1098-N1194. Studies were performed with 31 Asn-to-Gln mutants, beta-coronavirus virus-like particles and single-cycle viral replicons. Deletions of stem N-glycans enhanced S1 shedding from trimeric spike, reduced ACE2 binding and abolished syncytia formation. When three or more N-glycans were deleted, spike expression on cell surface and incorporation into virions was both reduced. Viral entry function was progressively lost upon deleting the N1098 glycan in combination with additional glycosite modifications. In addition to SARS-CoV-2, deleting stem N-glycans in SARS-CoV and MERS-CoV spike also prevented viral entry into target cells. These data suggest multiple functional roles for the stem N-glycans, and evolutionarily conserved properties for these complex carbohydrates across human beta-coronaviruses.Previous work shows that the N-linked glycans of SARS-CoV-2 are essential for viral life cycle. Few natural mutations have been observed in the S2-subunit of the viral spike glycoprotein in GISAID data, and mutations are absent in the five 'stem N-glycans' located between N1098-N1194. In the post-fusion spike structure these glycans lie equidistant, ~4 nm apart, suggesting functional significance. Upon testing the hypothesis that these glycans are critical for SARS-CoV-2 function, we noted multiple roles for the complex carbohydrates including regulation of S1-subunit shedding, spike expression on cells and virions, syncytial formation/cell-cell fusion and viral entry. Besides SARS-CoV-2, these glycans were also critical for other human beta-coronaviruses. Thus, these carbohydrates represent targets for the development of countermeasures against future outbreaks.Author SummaryPrevious work shows that the N-linked glycans of SARS-CoV-2 are essential for viral life cycle. Few natural mutations have been observed in the S2-subunit of the viral spike glycoprotein in GISAID data, and mutations are absent in the five 'stem N-glycans' located between N1098-N1194. In the post-fusion spike structure these glycans lie equidistant, ~4 nm apart, suggesting functional significance. Upon testing the hypothesis that these glycans are critical for SARS-CoV-2 function, we noted multiple roles for the complex carbohydrates including regulation of S1-subunit shedding, spike expression on cells and virions, syncytial formation/cell-cell fusion and viral entry. Besides SARS-CoV-2, these glycans were also critical for other human beta-coronaviruses. Thus, these carbohydrates represent targets for the development of countermeasures against future outbreaks.

Conserved role of spike S2 domain N-glycosylation across beta-coronavirus family

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