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 |