Coronavirus nsp6 proteins generate autophagosomes from the endoplasmic reticulum via an omegasome intermediate

Abstract

Autophagy is a cellular response to starvation which generates autophagosomes to carry cellular organelles and long-lived proteins to lysosomes for degradation. Degradation through autophagy can provide an innate defence against virus infection, or conversely autophagosomes can promote infection by facilitating assembly of replicase proteins. We demonstrate that the avian coronavirus, Infectious Bronchitis Virus (IBV) activates autophagy. A screen of individual IBV non-structural proteins (nsps) showed that autophagy was activated by IBV nsp6. This property was shared with nsp6 of mammalian coronaviruses Mouse Hepatitis Virus, and Severe Acute Respiratory Syndrome Virus, and the equivalent nsp5-7 of the arterivirus Porcine Reproductive and Respiratory Syndrome Virus. These multiple-spanning transmembrane proteins located to the endoplasmic reticulum (ER) where they generated Atg5 and LC3II-positive vesicles, and vesicle formation was dependent on Atg5 and class III PI3 kinase. The vesicles recruited double FYVE-domain containing protein (DFCP) indicating localised concentration of phosphatidylinositol 3 phosphate, and therefore shared many features with omegasomes formed from the ER in response to starvation. Omegasomes induced by viral nsp6 matured into autophagosomes that delivered LC3 to lysosomes and therefore recruited and recycled the proteins needed for autophagosome nucleation, expansion, cellular trafficking and delivery of cargo to lysosomes. The coronavirus nsp6 proteins activated omegasome and autophagosome formation independently of starvation, but activation did not involve direct inhibition of mTOR signalling, activation of sirtuin1 or induction of ER stress.

Porcine Epidemic Diarrhea Virus Induces Autophagy to Benefit Its Replication

“…However, autophagosome-like vesicles were rarely observed in the mock-infected cells (Figure 1A). It is well known that coronavirus infection can induce a large number of double-membrane vesicles (DMVs), and the functional link between autophagic DMVs and coronavirus-induced replication-associated DMVs remains controversial [22,23,24]. In this study, these two different DMVs might co-exist in PEDV-infected cells [25].…”

How phosphoinositide 3-phosphate controls growth downstream of amino acids and autophagy downstream of amino acid withdrawal

“…Live imaging experiments suggested that at least some autophagosomes are formed within omegasomes. Subsequent work suggested that several pathogens known to induce autophagy also induce omegasomes, whereas depletion of WIPI2 (a mammalian equivalent of Atg18) increases omegasome numbers [40,43,44]. Finally, DFCP1 and WIPI2 co-localize on omegasomes and neither becomes part of mature autophagosomes [40].…”

Early events in the generation of autophagosomes are required for the formation of membrane structures involved in hepatitis C virus genome replication

“…Further to this, another recent study (Cottam et al, 2011) demonstrated that the nsp6 protein of various coronaviruses (including the SARS coronavirus), or the nsp5-7 protein of the arterivirus, porcine reproductive and respiratory syndrome virus (PPRSV), located to the ER where they recruited Vps34 and DFCP1, leading to omegasome formation. Our data complement this study and we propose therefore that the similarities between HCV and coronavirus or arterivirus membrane rearrangements may, at least in part, be explained by a common mechanism of biogenesis of these membrane structures.…”