The molecular mechanisms of autophagy. The autophagy (Atg) proteins can be divided into 4 functional groups, including (A) a protein kinase autophagy regulatory complex that responds to upstream signals, including nutrient limitation; (B) a lipid kinase signaling complex that mediates vesicle nucleation; (C) ubiquitin-like protein conjugation pathways that are required for vesicle expansion and completion; and (D) a retrieval pathway required for the disassembly of Atg protein complexes from matured autophagosomes. Shown are the yeast Atg proteins that participate in each functional group. Yeast Atg proteins with known orthologs in higher eukaryotes are underlined. PI, phosphatidylinositol; PI3-P, phosphatidylinositol 3-phosphate; PE, phosphatidylethanolamine.