Mechanism of bridge-type phospholipid transfer by Atg2 for autophagosome biogenesis

Autophagy requires de novo autophagosome formation, which depends on supplying millions of phospholipids from membrane-source organelles. In Saccharomyces cerevisiae, Atg2, a lipid transfer protein (LTP), collaborates with the phosphoinositide-binding protein Atg18 in this process. However, it remains largely unknown how the Atg2-Atg18 complex achieves bulk lipid transport and how much it contributes to autophagosome biogenesis. Here, by combining in silico, in vitro, and in vivo approaches, we explored the possibility that Atg2 mediates a bridge-type lipid transfer mechanism. All-atom molecular dynamics (MD) simulations based on the AlphaFold-predicted structure of the Atg2-Atg18 complex indicate that the hydrophobic cavity of Atg2 accommodates ~25 phospholipids in a water-excluding arrangement, aligning them side-by-side while maintaining bilayer-like fluidity. During simulations, Atg2 continuously bridged two membranes via its two termini and transferred a cavity-resident phospholipid to a membrane, contingent on Atg18-phosphoinositide interactions. Importantly, narrowing the cavity on the way disrupted side-by-side lipid alignment in silico, impaired bridge-type lipid transfer in vitro, and inhibited autophagosomal membrane expansion in vivo. Together, these findings demonstrate that Atg2 mediates bulk lipid transport through a bridge model, which serves as the primary mechanism for supplying membrane building blocks to autophagosomes.