KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-GFP clones 7.1 and 13.1 | Roche | RRID:AB_390913; Cat # 11814460001 |
| Mouse monoclonal anti-PGK1 clone 22C5D8 | Abcam | RRID:AB_10861977; Cat # ab113687 |
| Rabbit polyclonal anti-Aco1 | Roland Lill Lab (Marburg) | N/A |
| Rabbit polyclonal anti-Rip1 | Dennis Winge Lab (Utah) | N/A |
| Rabbit polyclonal anti-Sdh2 | Dennis Winge Lab (Utah) | N/A |
| Rabbit polyclonal anti-F1β | Alexander Tzagoloff Lab (Columbia) | N/A |
| Mouse monoclonal anti-Por1 clone 16G9E6BC4 | Abcam | RRID:AB_10865182; Cat # ab110326 |
| Rabbit polyclonal anti-HSP70 | Kostas Tokatlidis Lab (Glasgow) | N/A |
| Mouse monoclonal anti-CpY (Prc1) clone 10A5B5 | Thermo Fisher | RRID:AB_2536203; Cat # A-6428 |
| Mouse monoclonal anti-Pep12 clone 2C3G4 | Thermo Fisher | RRID:AB_2535823; Cat # A-21273 |
| Mouse monoclonal anti-2 Cys Peroxiredoxin clone 6E5 | Abcam | RRID:AB_443456; Cat # ab16765 |
| Rabbit polyclonal anti-Peroxiredoxin-SO3 | Abcam | RRID:AB_443491; Cat # ab16830 |
| Bacterial and Virus Strains | ||
| Yeast Genomic Tiling Collection | Dharmacon | Cat # YSC4613 |
| E. coli: DH5α | Jared Rutter Lab (Utah) | N/A |
| Chemicals | ||
| Lyticase from Anthrobacter luteus | Sigma-Aldrich | Cat # L4025; CAS: 1032350-13-2 |
| Concanamycin A | Santa Cruz | Cat # 202111; CAS: 80890-47-7 |
| Ammonium Iron(II) Sulfate Hexahydrate | Sigma-Aldrich | Cat # 215406; CAS: 7783-85-9 |
| Iron(III) chloride | Sigma-Aldrich | Cat # 157740; CAS: 7705-08-0 |
| Concanavalin A | Sigma-Aldrich | Cat # L7647; CAS: 11028-71-0 |
| DiOC6 (3, 3’ Dihexyloxacarbocyanine Iodide) | Thermo Fisher | Cat # D273; CAS: 53213-82-4 |
| BPS (Bathophenanthrolinedisulfonic Acid Disodium Salt Hydrate) | Sigma-Aldrich | Cat # 146617; CAS: 52746-49-3 |
| RNase Free DNase | Qiagen | Cat # 79254 |
| β-Estradiol | Sigma-Aldrich | Cat # E8875; CAS: 50-28-2 |
| MG-132 | Cayman Chemical | Cat # 10012628; CAS: 133407-82-6 |
| Cycloheximide | Sigma-Aldrich | Cat # C1988; CAS: 66-81-9 |
| EZ Link Sulfo-NHS-LC-Biotin | Thermo Fisher | Cat # 21335 |
| µMACS Streptavidin MicroBeads | Miltenyi Biotec | Cat # 120-001-017 |
| Alexa Fluor 660 NHS Ester (Succinimidyl Ester) | Thermo Fisher | Cat # A20007 |
| Fluorescent Brightener 28 (Calcofluor White MR2) | Sigma-Aldrich | Cat # F3543; CAS: 4404-43-7 |
| Digitonin special-grade (water-soluble) | Gold Biotechnology | Cat # D-180; CAS: 11024-24-1 |
| NativePAGE 20X Running Buffer | Thermo Fisher | Cat # BN2001 |
| NativePAGE 20X Cathode Buffer Additive | Thermo Fisher | Cat # BN2002 |
| 20X Bolt MES SDS Running Buffer | Thermo Fisher | Cat # B000202 |
| cOmplete Protease Inhibitor Cocktail | Sigma-Aldrich | Cat # 11697498001 |
| Peptone (Granulated) | Thermo Fisher | Cat # BP9725; CAS: 73049-73-7 |
| Casamino acids (Acid hydrolyzed casein) | US Biological | Cat # 0012501A; CAS: 65072-00-6 |
| D-Threonine | Thermo Fisher | Cat # AC346970250; CAS: 632-20-2 |
| L-Glutathione, reduced | Sigma-Aldrich | Cat # G4251; CAS: 70-18-8 |
| L-Homocysteine | Chem-Impex Int’l Inc. | Cat # 21338; CAS: 6027-13-0 |
| S-Methyl-L-cysteine | Sigma-Aldrich | Cat # M6626; CAS: 1187-84-4 |
| Hydrogen peroxide | Sigma-Aldrich | Cat # H1009; CAS: 7722-84-1 |
| Paraquat dichloride hydrate | Sigma-Aldrich | Cat # 36541; CAS: 75365-73-0 |
| Methoxypolyethylene glycol maleimide (PEG-maleimide) | Sigma-Aldrich | Cat # 63187; CAS: 99126-64-4 |
| U-13C/U-15N stable isotope labeled amino acids | Cambridge Isotope Laboratories | Cat # CNLM-6696-1 |
| Methoxylamine Hydrochloride (MOX) | MP Biomedicals | Cat # 02155405; CAS: 593-56-6 |
| Pyridine | EMD Millipore | Cat # PX2012–7; CAS: 110-86-1 |
| N-methyl-N-trimethylsilyltrifluoracetamide (MSTFA) | Thermo Fisher | TS-48913 |
| Critical Commercial Assays | ||
| Gibson Assembly Master Mix | New England Biolabs | Cat # E2611 |
| Gateway BP Clonase II Enzyme Mix | Thermo Fisher | Cat # 11789020 |
| Gateway LR Clonase II Enzyme Mix | Thermo Fisher | Cat # 11791020 |
| RNeasy Mini Kit | Qiagen | Cat # 74104 |
| SuperScript IV First-Strand Synthesis | Thermo Fisher | Cat # 18091050 |
| KAPA SYBR FAST ROX Low qPCR Kit | Kapa Biosystems | Cat # KK4621 |
| Ribo-Zero Gold rRNA Removal Kit (yeast) | Illumina | Cat # MRZY1306 |
| TruSeq Stranded Total Rna Kit | Illumina | Cat # RS-122–2302 |
| D1000 ScreenTape Assay | Agilent | Cat # 5067–5582 |
| Pierce BCA Protein Assay Kit | Thermo Fisher | Cat # 23225 |
| Amplex Red Hydrogen Peroxide/Peroxidase Assay Kit | Thermo Fisher | Cat # A22188 |
| OxyBlot Protein Oxidation Kit | Millipore Sigma | Cat # S7150 |
| Deposited Data | ||
| See Table S1, RNA sequencing deposited at GEO | This study | Accession # GSE133214 |
| Experimental Models: Organisms/Strains | ||
| Yeast Homozygous Diploid Collection | (Winzeler et al., 1999); Dharmacon | Cat # YSC1056 |
| S. cerevisiae: wild type: BY4741 MATa his3Δ1 leu2Δ0 ura3Δ0 met15Δ0 | (Brachmann et al., 1998); ATCC | Cat # 201388 |
| S. cerevisiae: wild type: BY4742 MATα his3Δ1 leu2Δ0 ura3Δ0 lys2Δ0 | (Brachmann et al., 1998); ATCC | Cat # 201389 |
| S. cerevisiae: wild type; BY4743 MATa/α his3Δ1/his3Δ1 leu2Δ0/leu2Δ0 ura3Δ0/ura3Δ0 met15Δ0/+ lys2Δ0/+ | (Brachmann et al., 1998); ATCC | Cat # 201390 |
| S. cerevisiae: vph2Δ: BY4741 vph2Δ::KanMX | (Winzeler et al., 1999); Dharmacon | MATa deletion collection |
| S. cerevisiae: Tim50-GFP: BY4743 Tim50-yeGFP: His3MX/Tim50-yeGFP:His3MX Tom70-mCherry: KanMX/Tom70-mCherry:KanMX | This study | AHY7356 |
| S. cerevisiae: Tim50-mCherry: BY4743 Tim50-mCherry: KanMX/Tim50-mCherry:KanMX | This study | AHY8455 |
| S. cerevisiae: wild type Aft1 reporter: BY4741 chrI(199456–199457)::PFIT2-yeGFP-TermADH1:KanMX | This study | AHY2993 |
| S. cerevisiae: vma1Δ Aft1 reporter: BY4741 chrI(199456–199457)::PFIT2-yeGFP-TermADH1:KanMX vma1Δ::URA3 | This study | AHY5012 |
| S. cerevisiae: vph2Δ Aft1 reporter: BY4741 chrI(199456–199457)::PFIT2-yeGFP-TermADH1:KanMX vph2Δ::URA3 | This study | AHY5010 |
| S. cerevisiae: rox1Δ: BY4741 rox1Δ::URA3 | This study | AHY1776 |
| S. cerevisiae: rox1Δ fet4Δ: BY4741 rox1Δ::URA3 fet4Δ::LEU2 | This study | AHY2926 |
| S. cerevisiae: Aft1-GFP: BY4742 AFT1-yeGFP:HphMX SRM1-mCherry:KanMX | This study | AHY2977 |
| S. cerevisiae: wild type Aft1 reporter: chrI(199456–199457)::PFIT2-yeGFP-TermADH1:HphMX | This study | AHY5005 |
| S. cerevisiae: aft1Δ: BY4741 aft1Δ::KanMX | (Winzeler et al., 1999); Dharmacon | MATa deletion collection |
| S. cerevisiae: aft1Δ Aft1 reporter: chrI(199456–199457)::PFIT2-yeGFP-TermADH1:HphMX aft1Δ::KanMX | This study | AHY5007 |
| S. cerevisiae: Lys4-GFP: BY4741 LYS4-GFP:His3MX | Thermo Fisher | GFP clone collection |
| S. cerevisiae: Dre2-GFP: BY4741 DRE2-GFP:His3MX | Thermo Fisher | GFP clone collection |
| S. cerevisiae: Elp3-GFP: BY4741 ELP3-GFP:His3MX | Thermo Fisher | GFP clone collection |
| S. cerevisiae: Tyw1-GFP: BY4741 TYW1-GFP:His3MX | Thermo Fisher | GFP clone collection |
| S. cerevisiae: Grx6-GFP: BY4741 GRX6-GFP:His3MX | Thermo Fisher | GFP clone collection |
| S. cerevisiae: Bio2-GFP: BY4741 BIO2-GFP:His3MX | Thermo Fisher | GFP clone collection |
| S. cerevisiae: RITE-tag parent: BY4742 TermCYC1:URA3-PGPD/TDH3-cre-EBD78:TermCYC1 | Dan Gottschling Lab (Calico) | UCC6886 |
| S. cerevisiae: Lys4-RITE: UCC6886 LYS4-V5-loxP-HA-GFP:HphMX-loxP-T7-mRFP:KanMX | This study | AHY1758 |
| S. cerevisiae: Tyw1-RITE: UCC6886 TYW1-V5-loxP-HA-GFP:HphMX-loxP-T7-mRFP:KanMX | This study | AHY1759 |
| S. cerevisiae: Pgk1-RITE: UCC6886 PGK1-V5-loxP-HA-GFP:HphMX-loxP-T7-mRFP:KanMX | This study | AHY1761 |
| S. cerevisiae: rho0: BY4741 rho0 | This study | AHY1772 |
| S. cerevisiae: atg5Δ Aft1 reporter: BY4741 chrI(199456–199457)::PFIT2-yeGFP-TermADH1-KanMX atg5::URA3 | This study | AHY5014 |
| S. cerevisiae: pep4Δ Aft1 reporter: BY4741 chrI(199456–199457)::PFIT2-yeGFP-TermADH1-KanMX pep4::URA3 | This study | AHY5016 |
| S. cerevisiae: pdr5Δ Aft1 reporter: BY4741 chrI(199456–199457)::PFIT2-yeGFP-TermADH1-KanMX pdr5::URA3 | This study | AHY6133 |
| S. cerevisiae: cys3Δ Aft1 reporter: BY4741 chrI(199456–199457)::PFIT2-yeGFP-TermADH1-KanMX cys3::URA3 | This study | AHY5020 |
| S. cerevisiae: gly1Δ Aft1 reporter: BY4741 chrI(199456–199457)::PFIT2-yeGFP-TermADH1-KanMX gly1::URA3 | This study | AHY8052 |
| S. cerevisiae: gly1Δ: BY4741 gly1::KanMX | (Winzeler et al., 1999); Dharmacon | Yeast MATa Collection |
| S. cerevisiae: Tsa1-GFP: BY4741 TSA1-GFP-His3MX | Thermo Fisher | GFP clone collection |
| S. cerevisiae: tsa1Δ: BY4741 tsa1::KanMX | (Winzeler et al., 1999); Dharmacon | Yeast MATa Collection |
| S. cerevisiae: sod1Δ: BY4741 sod1::URA3 | This study | AHY1762 |
| S. cerevisiae: skn7Δ Aft1 reporter: BY4741 chrI(199456–199457)::PFIT2-yeGFP-TermADH1-KanMX skn7::URA3 | This study | AHY6316 |
| S. cerevisiae: AVT1 OE Aft1 reporter: BY4741 chrI(199456–199457)::PFIT2-yeGFP-TermADH1-KanMX avt1Δ::PGPD1-AVT1-TermCYC1-URA3 | This study | AHY4577 |
| S. cerevisiae: Tom70-GFP: BY4743 hoΔ::PSCW11-cre-EBD78-NatMX/hoΔ::PSCW11-cre-EBD78- NatMX loxP-CDC20-Intron-loxP-HphMX/loxP-CDC20-Intron-loxPHphMX loxP-UBC9-loxp-LEU2/loxP-UBC9-loxp-LEU2 TOM70-yeGFP-KanMX/+ | Hughes et al., 2016 | AHY548 |
| Oligonucleotides | ||
| See Table S2 | This study | N/A |
| Recombinant DNA | ||
| Plasmid: pKT127 | (Sheff and Thorn, 2004); Addgene | Plasmid # 8728 |
| Plasmid: pKT127-mCherry | Dan Gottschling Lab (Calico) | N/A |
| Plasmid: pRS306 | (Brachmann et al., 1998); ATCC | N/A |
| Plasmid: pGP564 | Dharmacon | N/A |
| Plasmid: pGP564 FET4 | This study | N/A |
| Plasmid: pLV015 | Fred van Leeuwen Lab (Netherlands Cancer Institute); (Verzijlbergen et al., 2010) | N/A |
| Plasmid: p2FG2.0 | This study | N/A |
| Plasmid: pHLUM | (Mulleder et al., 2012); Addgene | Plasmid #40276 |
| Plasmid: pDONR221 | Thermo Fisher | Cat # 12536017 |
| Plasmid: pAG426 GPD ccdb | (Alberti et al., 2007); Addgene | Plasmid # 14156 |
| Plasmid: pAG426 GPD-FET4 | This study | N/A |
| Plasmid: pAG426 GPD-GLY1 | This study | N/A |
| Plasmid: pAG426 GPD-CYS3 | This study | N/A |
| Plasmid: pAG426 GPD-TSA1 | This study | N/A |
| Plasmid: pAG425 GPD ccdb | (Alberti et al., 2007); Addgene | Plasmid # 14154 |
| Plasmid: pAG425 GPD-SOD1 | This study | N/A |
| Plasmid: pAG415 GPD ccdb | (Alberti et al., 2007); Addgene | Plasmid # 14146 |
| Plasmid: pAG415 GPD HyPer-3 (yeast codons) | This study | N/A |
| Plasmid: pAG415 GPD HyPer-3 C199S (yeast codons) | This study | N/A |
| Plasmid: pAG306 GPD chrI ccdb | (Hughes and Gottschling, 2012) | N/A |
| Plasmid: pAG306 GPD-AVT1 chrI | (Hughes and Gottschling, 2012) | N/A |
| Plasmid: pAG306 GPD-MRS3 chrI | This study | N/A |
| Plasmid: pAG306 GPD-MRS4 chrI | This study | N/A |
| Software and Algorithms | ||
| FIJI | (Schindelin et al., 2012) | Version 1 |
| FlowJo | FlowJo | Version 10.3 |
| Prism | Graphpad Software | Version 7 |
| SnapGene | GSL Biotech | Version 4.2 |
| Image Lab | BioRad | Version 2 |
| QuantStudio | Applied Biosystems | Version 1.3 |
| EVOS FL Auto software | Thermo Fisher | Version 1.6 |
| Zen Blue | Carl Zeiss | Version 2.6 |
| Zen Black | Carl Zeiss | Version 2.3 |
| FACSDiva | BD Biosciences | Version 8.0.1.1 |
| MassHunter Qual | Agilent | Version B.07.00 |
| MassHunter Quant | Agilent | Version B.07.00 |
| STAR Aligner | (Dobin et al., 2013) | Version 2.5.2b |
| featureCounts | (Liao et al., 2014) | Version 1.5.1 |
| XPRESSplot | (Berg, 2019) | Version 0.0.4beta |
| matplotlib | (Hunter, 2007) | Version 3.1.0 |
| Other | ||
| NativePAGE 4–16% Bis-Tris Gel (15 well) | Thermo Fisher | Cat # BN2112BX10 |
| Bolt 4–12% Bis-Tris Plus Gel (15 well) | Thermo Fisher | Cat # NW04125BOX |