Autophagy pathway in mammals. The formation of autophagosomes appears to follow a pathway conserved across species and most findings made in yeast or other organisms also apply to mammalian autophagy. a.) Autophagy can be induced via mTOR dependent or independent pathways (for more information, see text and Fig. 3) which stimulate the nucleation and expansion of the phagophore/isolation membrane. b.) A multi-protein complex surrounding BECN1 with PI3K activity (mediated by PIK3C3) is important for the formation of the autophagosomal membrane. c.) Two ubiquitin-like modification systems are essential for mammalian autophagy; ATG12 is activated by ATG7 (E1 step), transferred to ATG10 (E2 step), conjugated to ATG5 and subsequently forms a complex with ATG16. This step is necessary early in autophagy for the formation of the phagophore or isolation membrane. MAP1LC3 (LC3) is cleaved by ATG4, activated by ATG7 (E1 step), transferred to ATG3 (E2 step), and conjugated to the phospholipid phosphoethanolamine (PE). This form known as MAP1LC3-II (LC3-II), localizes to the autophagosome membrane and is subsequently degraded in the lysosome. ATG4 cleaves off a C-terminal arginine (R) to expose a glycine residue that is then being linked to PE. Rapamycin (Rap) inhibits mTOR and activates macroautophagy, while 3-methyladenin (3-MA) and wortmannin (WM) inhibit the PI3K activity and de-activate macroautophagy.