I. Phase I (initiation): mTOR (mammalian target of rapamycin)-dependent and mTOR-independent pathways can induce autophagy. mTOR works via Ulk1 and 2 (mammalian Atg1 orthologs) that in turn directs (most likely on the ER) appropriate protein and lipid transactions to allow formation of a nascent pre-phagophore () possibly corresponding to the well defined structure in yeast termed pre-autophagosomal structure (or phagophore assembly site; PAS). The pre-phagophore in mammalian cells may emerge from an ER structure termed omegasome (Ω). Contributions of the secretory pathway [ER-Golgi-trans Golgi network (ER-G-TGN)], plasma membrane (PM)-derived organelles and mitochondria (MT) have also been reported: PM, acts possibly as additional source of lipid bilayers or a source of regulatory effects within the endosomal system with which autophagosomes merge during maturation; MT may contribute as a major source of phosphatidylethanolamine (PE) where phosphatydilserine (PS) decarboxylase is located on the MT inner membrane to generate PE from PS for conjugation of LC3 (LC3-II) and as a source of regulatory reactive oxygen intermediates that may promote autophagosome formation; ER-G-TGN contributions are probably complex and affecting the process directly and indirectly at multiple stages. Another major system regulating autophagy is the phosphatidylinositol 3-kinase hVPS34, which generates phosphatidylinositol 3-phopshate (PI3P). DFCP is a protein with two FYVE (PI3P-binding) domains and serves as a marker for the merger of the hVPS34/PI3P systems and TOR/Ulk at the point of autophagy initiation at the ER. hVPS34 is in a complex (often referred to as complex I) with multiple proteins, with Beclin 1 being key for autophagy altogether, and mAtg14 being key specifically for autophagy initiation. WIPI1 and 2 (mammalian Atg18) bind to PI3P and likely facilitate anteretrograde (and retrograde for recycling) membrane and protein flow to the nascent phagosomes. PI3P phosphatases, such as Jumpy/MTMR14, modulate progression of autophagy by tempering PI3P-dependent processes. II. Phase II (elongation and closure): Autophagic membrane is elongated to from a structure known as sensu stricto phagophore (or isolation membrane) based on two conjugation systems: (a) Atg5-Atg12 in complex with Atg16L, which acts as an E3 enzyme (nomenclature borrowed form the ubiquitination system) topologically restricting and enzymatically facilitating (b) conversion of LC3 to LC3-II (lipidated at the C-terminus by PE). Atg16 is a Crohn's disease risk locus in human populations and has also been found in complexes with clathrin at the plasma membrane (not shown). Elongating phagophore, also known as isolation membrane () wraps around its targets and eventually closes to form a sealed double membrane organelle known as sensu stricto autophagosome (). III. Phase III (maturation). Autophagosomes fuse with late endosomal and lysosomal organelles or intermediates in a process dependent on hVPS34 (in complex with Beclin 1 and UVRAG; referred to as complex II). This process is also subject to inhibition/modulation by PI3P phosphatases such as Jumpy/MTMR14. The fusion with lysosomal organelles heralds the dissolution of the inner membrane and formation of autolysosomes, where the degradation of the captured material occurs.
