KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti-LC3 clone APG8C | Sigma-Aldrich | SAB1301850 |
| Rabbit anti-LC3B | Cell Signaling Technology | 3868 |
| Mouse anti-β-Actin | Sigma-Aldrich | A5441; RRID:AB_476744 |
| Rabbit anti-NDP52 | Abcam | ab68588; RRID:AB_1640255 |
| Mouse anti-p62 | Abcam | ab109012; RRID:AB_2810880 |
| Mouse anti-V5 | Abcam | ab27671; RRID:AB_471093 |
| FK2 anti-ubiquitin | Enzo Life Sciences | BML-PW8810; RRID:AB_10541840 |
| Rabbit anti-SACM1L | Abnova | H00022908-D01P; RRID:AB_10632266 |
| Rabbit anti-SACM1L | Thermo Fisher | 13033-1-AP; RRID:AB_2301284 |
| Mouse anti-TOMM20 | Santa Cruz Biotechnology | sc-17764; RRID:AB_628381 |
| Alexa Fluor-conjugated secondary antibodies | Thermo Fisher | A31571; RRID:AB_162542, A21206; RRID:AB_2535792, A32744; RRID:AB_2762826 |
| Sheep anti-TGN46 | Bio-Rad | AHP500; RRID:AB_324049 |
| Mouse anti-GM130 | BD | 610822; RRID:AB_398141 |
| Mouse anti-WIPI2 | Abcam | ab105459; RRID:AB_10860881 |
| Mouse anti-PtdIns(4)P IgM | Echelon | Z-P004–2 |
| Rabbit anti-LAMP1 | Cell Signaling Technology | 9091; RRID:AB_2687579 |
| Bacterial and virus strains | ||
| S. Typhimurium SL1344 | Hoiseth and Stocker, 1981 | N/A |
| S. Typhimurium SL1344 Xen26 | Conway et al., 2013 | N/A |
| S. Typhimurium SL1344 DsRed | Rioux et al., 2007 | N/A |
| S. Typhimurium SL14028s ΔsteA | Laboratory of Dr. Luís Jaime Mota | N/A |
| S. Typhimurium SL14028s ΔsteA reconstituted with PsteA-SteA | This study | N/A |
| S. Typhimurium SL14028s ΔsteA reconstituted with PrpsM-SteA | This study | N/A |
| S. Typhimurium SL14028s ΔsteA reconstituted with PsteA-SteA K36A | This study | N/A |
| S. Typhimurium SL14028s ΔsteA reconstituted with PsteA-SteA-V5 | This study | N/A |
| S. Typhimurium SL1344 x-light-mCherry | This study | N/A |
| S. Typhimurium SL1344 mCerulean | This study | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Torin1 | MedChemExpress | Hy-13003 |
| Bafilomycin A1 | Selleckchem | S1413 |
| Hoechst 33342 | Thermo Fisher | H3570 |
| Puromycin | InvivoGen | ant-pr-1 |
| Isopropyl β-D-1-thiogalactopyranoside | Sigma-Aldrich | 367-93-1 |
| Chloroquine | Sigma-Aldrich | C6628 |
| Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) | Sigma-Aldrich | C2759 |
| Oligomycin | Sigma-Aldrich | 75351 |
| Antimycin A | Sigma-Aldrich | A8674 |
| Lipofectamine 2000 | Thermo Fisher | 11668027 |
| Lipofectamine RNAiMAX | Thermo Fisher | 13778150 |
| Paraformaldehyde | Electron Microscopy Sciences | 15714S |
| VectaShield | Vector Laboratories | H-1000-10 |
| Critical commercial assays | ||
| LysoTracker Red DND-99 | Thermo Fisher | L7528 |
| DQ Green BSA | Thermo Fisher | D12050 |
| Ovalbumin AF647 | Thermo Fisher | O34784 |
| CellTracker Deep Red Dye | Thermo Fisher | C34565 |
| BODIPY FL-pepstatin A | Thermo Fisher | P12271 |
| Magic Red Cathepsin B | ImmunoChemistry Technologies | 938 |
| LysoView 633 | Biotium | 70058 |
| Gibson Assembly Master Mix | New England Biolabs | E2611 |
| Experimental models: Cell lines | ||
| Human: HeLa | ATCC | Cat #CCL-2; RRID:CVCL_0030 |
| Human: HeLa SACM1L KO | This paper | N/A |
| Human: HeLa SACM1L KO reconstituted with BFP-V5 | This paper | N/A |
| Human: HeLa SACM1L KO reconstituted with SACM1L-V5 WT | This paper | N/A |
| Human: HeLa SACM1L KO reconstituted with SACM1L-V5 C389S | This paper | N/A |
| Human: HeLa NDP52 KO | This paper | N/A |
| Human: HeLa mCherry-GFP-LC3 | This paper | N/A |
| Human: HeLa GFP-LC3 | This paper | N/A |
| Human: HeLa GFP-LC3; LAMP1-mCherry | This paper | N/A |
| Human: HeLa GFPLC3; BFP-2xP4M | This paper | N/A |
| Human: HeLa SACM1L KO mCherry-GFP-LC3 | This paper | N/A |
| Human: HeLa SACM1L KO GFP-LC3 | This paper | N/A |
| Human: HeLa SACM1L KO GFP-LC3; LAMP1-mCherry | This paper | N/A |
| Human: HeLa SACM1L KO GFP-LC3; BFP-2xP4M | This paper | N/A |
| Human: H4 | ATCC | Cat#HTB-148; RRID:CVCL_1239 |
| Oligonucleotides | ||
| Silencer Select siRNA | Thermo Fisher | See Table S2 |
| Recombinant DNA | ||
| CGSW-mCherry-GFP-LC3 | Laboratory of Dr. Christian Münz | N/A |
| CSGW-GFP-LC3 | Laboratory of Dr. Christian Münz | N/A |
| pKB269 IPTG inducible x-light-mCherry | Laboratory of Dr. Serge Mostowy | Sirianni et al., 2016 |
| pBMN-mCherry-Parkin | Addgene | (Yamano et al., 2014); RRID:Addgene_59419 |
| pEGFP-hGal3 | Addgene | Maejima et al., 2013; RRID:Addgene_73080 |
| LAMP1-mRFP-FLAG | Addgene | (Zoncu et al., 2011); RRID:Addgene_34611 |
| pFPV25.1 | Addgene | Valdivia and Falkow, 1996 |
| pFPV25.1_rpsM_mCerulean3 | Addgene | Lane et al., 2019; RRID:Addgene_124904 |
| pXPR-BRD023 | Broad Institute | N/A |
| pXPR-BRD003 | Broad Institute | N/A |
| pLX317-BFP | Broad Institute | N/A |
| pLX317-SACM1L-V5 | This paper | N/A |
| pLX317-SACM1L(C389S)-V5 | This paper | N/A |
| pSFFV-P4M(SidM)x2-BFP | This paper | N/A |
| pFPV25.1-PrpsM-SteA | This paper | N/A |
| pFPV25.1-PSteA-SteA | This paper | N/A |
| pFPV25.1-PsteA-SteA(K36A) | This paper | N/A |
| pFPV25.1-PSteA-SteA-V5 | This paper | N/A |
| pFPV25.1-PsteA-SteA(K36A)-V5 | This paper | N/A |
| pLX304-EF1a-SteA-V5 | This paper | N/A |
| Software and algorithms | ||
| NIS-Elements | Nikon | N/A |
| Harmony High-Content Imaging and Analysis Software | Perkin Elmer | N/A |
| GraphPad Prism8 | GraphPad Software, Inc. | N/A |
| Flowjo | FLOWJO | https://www.flowjo.com/ |