Viral inhibition of ER-phagy is critical to membrane remodelling for biogenesis of (+)RNA virus replication organelles

Infection by (+)RNA viruses are accompanied by induction of ER-expansion and membrane remodelling to form viral replication organelles, followed by assembly and secretion of viral progenies. We previously identified that virus triggered lipophagy was critical for the process of flaviviral assembly, driven by the lipid droplet associated protein Ancient ubiquitin protein 1 (Aup1). A ubiquitin conjugating protein Ube2g2 that functions as a co-factor for Aup1 was also identified as a host dependency factor in our study. Here we characterized its function: Ube2g2-deficient cells displayed a dramatic reduction in production of flavi- and coronaviruses, which could be rescued by reconstituting the wild-type but not the catalytically deficient (C89K) mutant of Ube2g2, suggesting that its enzymatic activity is necessary. Ube2g2 deficiency did not affect entry of virus particles but resulted in a profound loss in formation of replication organelles, and production of infectious progenies. This phenomenon resulted from its dual activity in (i) triggering lipophagy in conjunction with Aup1, and (ii) degradation of ER chaperones such as Herpud1, SEL1L, Hrd1 to restrict ER-phagy upon Xbp1-IRE1 triggered ER expansion. Ube2g2-deficient cells were impaired in lipophagy, while undergoing wide-spread Sec62 and Chmp4 dependent ER-phagy, inhibiting membrane remodelling required for biogenesis of viral replication organelles. Our results therefore underscore a virus-driven exquisite fine-tuning of selective autophagy of organelles that drive host membrane reorganization during +RNA virus infection to enable biogenesis of viral replication organelles.