Neuraminidase and secretory pathway stress converge to remodel host glycosylation during influenza A virus infection
Glycosylation is critical for viral-host cell interactions in influenza A virus (IAV) infection, but we lack a comprehensive understanding of how IAV infection shapes the host glycoproteome. Here, we performed liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic, glycomic, and glycoproteomic characterisation of the dynamic subcellular responses to an in vitro time course infection of human A549 cells. IAV infection resulted in only modest changes to the subcellular proteome, but robust and significant changes to the host secreted and organelle glycome and glycoproteome. Infection caused reductions in sialylation across the N- and O-glyco(proteo)me; increased oligomannose, paucimannose, and phosphorylated glycans; and shorter hybrid/complex glycans. Desialylation was greater when glycans were fucosylated; for sialic acid linked α2,3 or on the α3 arm; on larger, complex glycans; and on proteins likely to be more accessible to IAV neuraminidase (NA). Subtle activation of the unfolded protein response in infection was associated with a doubling of oligomannose N-glycosylation. Glycans were shorter in infection, implicating IAV-induced disruption of Golgi glycoprotein flux as a mechanism that reduces host glycoprotein sialylation and promotes virion release, independent of NA activity.