Table 1.
Main molecules involved in the initial steps of mammalian autophagosome biogenesis.
| Protein | Complete name | Autophagy related function | Reference |
|---|---|---|---|
| mTOR | Mammalian target of rapamycin | Members of mTOR complex 1 (mTORC1): Autophagy inhibition by phosphorylation of ULK1 complex | Lamb et al., 2013 |
| RAPTOR | Regulatory-associated protein of mTOR | ||
| DEPTOR | DEP domain containing mTOR-interacting protein | ||
| PRAS40 | Proline-rich AKT1 substrate 40 | ||
| mLST8 | Mammalian lethal with SEC13 protein 8 | ||
| AMPK | AMP-activated protein kinase | Autophagy activation by ULK1, mTORC1, and TSC2 phosphorylation | Egan et al., 2011 |
| p62 | Sequestosome-1 (SQSTM1 gene) | Autophagy cargo receptor | Puissant et al., 2012 |
| ULK1 | Unc-51-like kinase 1 | Members of ULK1 complex | Bach et al., 2011; Russell et al., 2013 |
| ATG13 | Autophagy-related protein 13 | ||
| FIP200 | FAK family interacting protein of 200 kDa | ||
| ATG101 | Autophagy-related protein 101 | ||
| BECN1 | Beclin 1 | Members of PI3KC3-C1/2 | Ktistakis and Tooze, 2016 |
| Vps15 | Serine/threonine-protein kinase VPS15 | ||
| Vps34 | Phosphatidylinositol 3-kinase VPS34 | ||
| ATG14L | Autophagy-related protein 14L | Member of PI3KC3-C1 | |
| UVRAG | UV radiation resistance associated protein | Member of PI3KC3-C2 | |
| KAP-1 | E3 SUMO-protein ligase TRIM28 | SUMOylation of Vps34 | Yang et al., 2013 |
| DAPK | Death-associated protein kinase | BECN1 phosphorylation | Zalckvar et al., 2009 |
| CUL3 | Cullin-3 | Poly ubiquitination of ULK1, Vps34, and BECN1 | Liu and Chen, 2016 |
| KLHL20 | Kelch-like protein 20 | Substrate-binding subunit of CUL3 ubiquitin ligase. Recognition of ULK1, Vps34, and BECN1 as substrates | Liu and Chen, 2016 |
| VMP1 | Vacuole Membrane Protein 1 | Recruitment of PI3KC3-C1 by interaction with BECN1 /autophagosomal membrane | Ropolo et al., 2007 |
| EP300 | EP300-interacting inhibitor of differentiation 300 | Vps34 acetylation | Su et al., 2017 |
| DFCP1 | Double FYVE-containing protein 1 | Omegasome marker | Ktistakis and Tooze, 2016 |
| WIPI2b | WD40-repeat phosphoinositide-interacting protein | Isolation membrane marker | Nascimbeni et al., 2017a |
| ATG12 | Autophagy-related protein 12 | Member of ATG12-ATG5-ATG16L complex: E3 like function in LC3 conjugation to phosphatidylethanolamine | Klionsky and Schulman, 2014 |
| ATG5 | Autophagy-related protein 5 | ||
| ATG16L | Autophagy-related protein 16L | ||
| ATG7 | Autophagy-related protein 7 | E1 in LC3 lipidation and ATG12-ATG5 conjugation | |
| ATG10 | Autophagy-related protein 10 | E2 in ATG12-ATG5 conjugation | |
| ATG3 | Autophagy-related protein 3 | E2 like function in LC3 lipidation | Satoo et al., 2009 |
| LC3 | Microtubule-associated proteins 1A/1B light chain 3B | Vesicle maturation/cargo recognition | Lee and Lee, 2016 |
| SIRT1 | NAD-dependent deacetylase sirtuin-1 | LC3 deacetylation | Huang et al., 2015 |
| ATG4B | Autophagy-related protein 4B | Clevage of C-terminal Gly of LC3 | Maruyama and Noda, 2017 |
| ATG9A | Autophagy-related protein 9 A | Isolation membrane extension | Feng and Klionsky, 2017 |
| Esyt 1, 2, 3 | Extended synaptotagmin-1, 2, 3 | ER-PM contact sites | Nascimbeni et al., 2017b |
| AP-4 | Adaptor protein 4 | Isolation membrane extension | Mattera et al., 2017 |
| Sar1 | Sar1 | COPII coat: participation in autophagosome biogenesis | Karanasios et al., 2016 |
| Sec 13, 23, 24, 31 | |||
| Rab11A | Ras-related protein Rab-11A | Recycling endosomes | Puri et al., 2018 |
| AMBRA1 | Activated in BECN1-regulated autophagy protein 1 | ULK1 ubiquitination | Nazio et al., 2013 |
| TRAF6 | TNF receptor (TNFR)-associated factor 6 | ULK1 and BECN1 ubiquitination | Grumati and Dikic, 2018 |