TABLE 1.
Autophagy core machinery and their functions
| Autophagy core machinery | Protein name | Functions | References |
|---|---|---|---|
| The ULK1 complex | ULK1/ATG1 | Serine/threonine kinase; phosphorylates different components of the autophagy machinery to initiate autophagy. | 18 , 19 |
| ATG13 | Interacts with ULK1; bridges ULK1 to RB1CC1. | 19 , 20 , 21 | |
| ATG101 | Heterodimerizes with ATG13 via their HORMA domain to stabilize the binding of ATG13 to ULK1; enhances ULK1 activity. | 20 , 22 | |
| RB1CC1/FIP200 | Scaffold protein; possibly serves as scaffold for ULK1 and ATG13. | 21 , 23 | |
| The class III lipid kinase complex I (PI3KC3–C1) | PIK3C3/VPS34 | PtdIns3 kinase; generates PtdIns3P. | 24 |
| PIK3R4/VPS15 | Scaffold and protein kinase; binds to PIK3C3 to form the catalytic arm of PI3KC3–C1. | 25 , 26 | |
| BECN1 | Forms the regulatory arm of PI3KC3–C1 via binding to ATG14. | 24 , 27 | |
| ATG14 | Directs PI3KC3–C1 to PAS. | 28 , 29 | |
| The WIPI family and WIPI–ATG2A complex | WIPI1 | PtdIns3P binding protein. | 30 |
| WIPI2 | PtdIns3P binding protein; recruits ATG12–ATG5‐ATG16L1 complex to conjugate LC3/GABARAP to PE. | 30 , 31 | |
| WIPI3 | PtdIns3P binding protein; associates with TSC complex to regulate mTOR activity; complexes with ATG2A to regulate phagophore expansion. | 32 , 33 | |
| WIPI4 | PtdIns3P binding protein; complexes with ATG2A to regulate phagophore expansion. | 32 , 33 , 34 | |
| ATG2A | Complexes with WIPI3/WIPI4 to regulate phagophore expansion. | 33 , 34 , 35 | |
| The two ubiquitin‐like conjugation systems | ATG4 | Cysteine protease to cleave pro‐ATG8s; deconjugation of ATG8s from PE (phosphatidylethanolamine). | 36 , 37 |
| ATG7 | E1‐like enzyme for both the ATG8s conjugation system and ATG12 conjugation system. | 4 , 38 | |
| ATG3 | E2‐like enzyme for the ATG8s conjugation system. | 4 , 38 | |
| ATG10 | E2‐like enzyme that conjugates ATG12 to ATG5. | 38 , 39 | |
| ATG5 | Conjugated by ATG12. | 38 , 39 | |
| ATG12 | The ubiquitin‐like molecule in the ATG12 conjugation system. | 38 , 39 | |
| ATG16L1 | Interacts with the ATG12–ATG5 conjugate to form the ATG12–ATG5‐ATG16L1 complex, which acts as the E3‐like enzyme to conjugate mATG8 to PE. | 40 | |
| mATG8 | The ubiquitin‐like molecule in the ATG8s conjugation system. | 41 , 42 | |
| ATG9 vesicles | ATG9 | Contributes membrane source to the forming phagophore. | 43 , 44 , 45 |