Table 1.
Key reagents used in these studies.
| REAGENT or RESOURCE |
SOURCE |
IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-YFP | Clontech | 632381; RRID: AB_2313808 |
| Anti-peroxidase (anti-protein A) | Jackson ImmunoResearch | 323–005-024; RRID:AB_2315781 |
| Anti-Pgk1 | Dr. Jeremy Thorner | N/A |
| Anti-Atg1 | In house | N/A |
| Goat anti-rabbit IgG, HRP | Fisher Scientific | ICN55676; RRID:AB_2334589 |
| Rabbit anti-mouse IgG, HRP |
Jackson ImmunoResearch |
315–035-003; RRID:AB_2340061 |
| Chemicals, peptides, and recombinant proteins | ||
| Power SYBR Green PCR Master Mix | Applied Biosystems/ThermoFisher Scientific | ILT4367659 |
| p-Nitrophenyl phosphate | Sigma-Aldrich | N4645 |
| Complete EDTA-free protease inhibitor cocktail | Roche | 05056489001 |
| TURBO DNA-free kit | Fisher Scientific | AM1907 |
| RNasin® PLUS Rnase inhibitor | Fisher Scientific | PRN2615 |
| Lipofectamine 3000 |
Invitrogen |
L3000001 |
| Critical commercial assays | ||
| BCA Protein assay | Fisher Scientific | PI23223, PI23224 |
| Dual Luciferase Assay System | Promega | E1910 |
| NucleoSpin® RNA II | Clontech | 740955.50 |
| High-Capacity cDNA Reverse Transcription Kit | Applied Biosystems/ThermoFisher Scientific | ILT4368814 |
| DNA Gel Purification Kit | Qiagen | 28706X4 |
| Q5® Site-Directed Mutagenesis Kit |
New England BioLabs |
E0554S |
| Experimental models: Cell lines | ||
| Human: HEK293-FT | Thermo Fisher Scientific | R70007 |
| Human: HeLa |
American Type Culture Collection |
CCL-2 |
| Experimental models: Organisms/strains | ||
|
S. cerevisiae: strain background: SEY6210 |
See Table S4 |
N/A |
| Oligonucleotides | ||
| Primers for RT-qPCR in yeast | [66] | N/A |
| Primers for RT-qPCR in human | See Table S5 | N/A |
| Primers for plasmid cloning and strains construction |
See Table S6 |
N/A |
| Recombinant DNA | ||
| pRS406-ATG13 5'UTR-ATG13-PA | This study | N/A |
| pRS406-ATG135'UTRmut-ATG13-PA | This study | N/A |
| pRS406-ATG12 5'UTR-ATG12-PA | This study | N/A |
| pRS406-ATG125'UTRmut-ATG12-PA | This study | N/A |
| pRS406-ATG19 5’ UTR-ATG19-PA | This study | N/A |
| pRS406-ATG195'UTRmut-ATG19-PA | This study | N/A |
| pRS416-ATG5 5'UTR-ATG5-PA | This study | N/A |
| pRS416-ATG55'UTRmut1-ATG5-PA | This study | N/A |
| pRS416-ATG55'UTRmut2-ATG5-PA | This study | N/A |
| pRS416-ATG55'UTRmut3-ATG5-PA | This study | N/A |
| pCMV-ATG4B 5'UTR-LUC | This study | N/A |
| pCMV-ATG4B5'UTRmut-LUC | This study | N/A |
| pCMV-ATG12 5'UTR-LUC | This study | N/A |
| pCMV-ATG125'UTRmut1-LUC | This study | N/A |
| pCMV-ATG125'UTRmut2-LUC | This study | N/A |
| pCMV-ATG125'UTRmut3-LUC | This study | N/A |
| pCMV-ATG125'UTRmut4-LUC | This study | N/A |
|
pRL-SV40P |
[67] |
Addgene, 27163; deposited by Ron Prywes |
| Software and algorithms | ||
| CFX Manager Software | Bio-Rad | N/A |
| R studio | R studio® | https://www.rstudio.com/ |
| Bio-Rad Image Lab Software | Bio-Rad | |
| GraphPad Prism 9 | GraphPad | https://www.graphpad.com/ |