SARS-CoV-2 protein ORF3a induces Atg8ylation of lysosomal membranes

Autophagy Conjugation machinery forms a center piece of autophagy and is essential for sequestration of a broad range of cargo destined for degradation. Apart from its role in canonical autophagy, recent evidence suggests an unconventional role of conjugation machinery. Membrane Atg8ylation is one of the manifestations of autophagy, wherein ATG8 conjugation machinery recruit mammalian ATG8s (mATG8s) to the damaged membranes for repair or removal. Herein, we show that SARS-CoV-2 factor ORF3a induces membrane Atg8ylation and selectively inflicts lysophagy, a cellular response to evade apoptotic cell death. mATG8s and SNARE protein syntaxin 17 (STX17) interact with ORF3a and are required for Atg8ylation induced by ORF3a. ORF3a displaces mTOR from the lysosomes and affects nuclear translocation of TFEB, which is dependent on mATG8s and STX17. Despite mTOR inhibition, its conventional target ULK1 is dispensable for ORF3a induced Atg8ylation. In addition, mATG8s and STX17 protected against the cell death induced by ORF3a. Overall, our findings demonstrate ORF3a induced lysosomal membrane Atg8ylation while identifying the unexpected role of STX17 in Atg8ylation.