Flow-chart showing the three principal steps of the (macro)autophagy process. The first step starts with the vesicle nucleation from a pre-existing isolation membrane and terminates with the formation of an autophagosome that entraps cellular materials. The core complex of the autophagy interactome, and some other beclin 1 interactors, are shown in the inset. The kinase activity of PI3k class III can be inhibited by Wortmannin, LY294002 or 3-methyadenine (3MA). The interaction of bcl-2 with beclin 1 precludes the formation of the beclin 1-PI3k III complex. JNK-mediated phosphorylation of bcl-2 or DAPk-mediated phosphorylation of beclin 1 disrupts the bcl-2/beclin 1 interaction, and thus favors the formation of the autophagy interactome. During vesicle nucleation and expansion, a lipidated LC3-II isoform is included in both the internal and external membrane of the autophagosome. Atg4 plays a crucial role in the generation of LC3 II from LC3 I. Other Atg proteins (namely, atg3, atg5, atg7 and atg12) participate in the process of lipidation (i.e., conjugation with phosphatydil choline) and membrane insertion of LC3 II. The second step consists in the docking and fusion of the autophagosome with several endosomes and lysosomes to form the autophagolysosome. This step can be inhibited by drugs that increase the lysosome pH (e.g. Chloroquine, Bafilomycin A1). The third step consists in the degradation of the autophagic vesicle and of its cargo by acid hydrolases, and subsequent release of substrates (essentially AA, aminoacids; FFA, free fatty acids) for reutilization. The lysosomal degradation step can be inhibited by protease inhibitors (e.g., Leupeptin, Pestatin A) or by raising the internal pH.