The following primary antibodies were used (key: IB, immunoblot concentration; IF, immunofluorescence concentration): rabbit anti-ATG16L1 (PM040: IB, 1:1,000; IF, 1:400; MBL); mouse anti-ATG3 (M1333: IB, 1:1,000; MBL); rabbit anti-ATG7 (2631: IB, 1:1,000; Cell Signaling); mouse anti-FLAG (A00187: IB, 1:1,500; IF, 1:300; GenScript); rabbit anti-GAPDH (G8796: IB, 1:2,000; Sigma-Aldrich); mouse anti-GFP (MMS-118R: IB, 1:2,000; Covance); goat anti-Lamin B (sc-6216: IB, 1:500; Santa Cruz); rabbit anti-LC3A/B (L8918: IB, 1:1,000; Sigma-Aldrich); rabbit anti-LC3B (L7543: IF, 1:400; IP; Sigma-Aldrich); rabbit anti-LMX1A (AB10533: IB, 1:1,000; IF, 1:1,000; IP; Millipore); rabbit anti-LMX1A (51-606: IP; ProSci); rabbit anti-LMX1B (18278: IB, 1:1,000; IF, 1:250; IP; Proteintech); rabbit anti-LMX1B (Witzgall lab: IB, 1:2,000; IF, 1:350); mouse anti-p62 (H0008878: IB, 1:1,000; IF, 1:400; Abnova); rabbit anti-TH (AB152: IB, 1:1,000; IF, 1:300; Millipore); mouse anti-TH (sc-25269: IB, 1:1,000; IF, 1:100; Santa Cruz); mouse anti-TUJ1 (801201: IB, 1:1,000; IF, 1:1,000; BioLegend); mouse anti-WIPI2 (MCA5780GA: IF, 1:400; BioRad). Secondary antibodies for immunoblotting: chicken anti-mouse HRP (G32-62DC-SGC: 1:10,000; Stratech); goat anti-rabbit HRP (G33-62G-SGC: 1:10,000; Stratech); chicken anti-goat HRP (G34-62DC-SGC; Stratech). Secondary antibodies for immunofluorescence: goat anti-mouse Alexa Fluor 488 (A-11029: 1:400; Invitrogen); goat anti-rabbit Alexa Fluor 488 (A-11034: 1:400; Invitrogen) goat anti-mouse Alexa Fluor 568 (A-11031: 1:400; Invitrogen); goat anti-rabbit Alexa Fluor 568 (A-11036: 1:400; Invitrogen); goat anti-mouse Alexa Fluor 647 (A-21236: 1:400; Invitrogen); goat anti-rabbit Alexa Fluor 647 (A-21244: 1:400; Invitrogen).

The following reagents were used in cell-based assays: MitoSOX (M36008; Thermo Fisher Scientific); carbonyl cyanide chlorophenylhydrazone (C2759; Sigma-Aldrich); BafA1 (Enzo, BML-CM110); MG132 (M7449; Sigma-Aldrich); CHX (TOKU-E, C084); DOX (Clontech, 631311); rotenone (R8875; Sigma-Aldrich). The following kits were used: EnzChek caspase-3 assay kit (Z-DEVD-AMC; E13183; Thermo Fisher Scientific); high-capacity RNA-to-cDNA kit (4387406; Thermo Fisher Scientific); LightSwitch luciferase assay kit (LS010; SwitchGear Genomics); RNA isolation kit (74104; Qiagen); Seahorse Mito Stress Test (103010-100; Agilent).