Pathway and gates for ATG2A-mediated lipid transport in autophagy

Autophagy is a complex process in which eukaryotic cells degrade cytosolic components by delivering them to lysosomes via double-membrane autophagosomes. The lipid transfer protein ATG2A plays a crucial role in autophagosome formation by tethering the phagophore membrane to the ER and delivering a significant fraction of the required lipids. The mechanism by which ATG2A shuttles lipids from one membrane to the other, however, remains elusive. Here, we combine structural predictions, molecular dynamics simulations and in vitro lipid transfer assays to gain mechanistic insights into ATG2A-mediated lipid transport. Using this integrative approach, we characterize the contact sites of the protein with donor and acceptor membranes. Our simulations capture multiple events of lipid uptake and delivery from and to the bound membrane. Conformational rearrangements of N-terminal amphipathic helices emerge as a critical factor for facile lipid transport. With this insight, we designed an ATG2A mutant that transfers lipids three times faster than the wild type in vitro. In complex with ATG9A, ATG2A forms a bridge between two parallel membranes at 12 nm separation. Overall, our findings suggest that ATG2A is a lipid transporter gated at the N-terminus by blocking helices that, upon release, act as additional membrane tethers.