Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifier | Additional information |
|---|---|---|---|---|
| Gene (kanr) | kanr | Yeast Knockout Collection; Horizon Discovery | kanMX | |
| Gene (Klebsiella pneumoniae) | hph | pAG26; Goldstein AL, McCusker JH | hphMX | |
| Gene (Streptomyces noursei) | nat1 | pPKI | natMX | |
| Gtrain (Saccharomyces cerevisiae) | YPS1009 Mat a Euploid, hoΔ::HYG | this study | AGY731 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009 Mat alpha Euploid, hoΔ::HYG | this study | AGY732 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009_Chr12 Mat a Disome12, hoΔ::HYG | this study | AGY735 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009_Chr12 Mat alpha Disome12, hoΔ::HYG | this study | AGY736 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009 Mat a Euploid, hoΔ::HYG, ssd1Δ::KAN | this study | AGY1444 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009_Chr12 Mat a Disome12, hoΔ::HYG, ssd1Δ::KAN | this study | AGY1445 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009 Mat a Euploid, hoΔ::HYG, ssd1-Δ2 (KANMX removed) | this study | AGY1503 | Haploid, marker rescued for plasmid expression, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009_Chr12 Mat a Disome12, hoΔ::HYG, ssd1-Δ2 (KANMX removed) | this study | AGY1517 | Haploid, marker rescued for plasmid expression, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009 Mat a Euploid, hoΔ::HYG, SSD1-GFP-SSD1YPS1009-terminator-NATMX | this study | AGY1446 | Haploid, GFP tagged Ssd1, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009_Chr12 Mat a Disome12, hoΔ::HYG, SSD1-GFP-SSD1YPS1009-terminator-NATMX | this study | AGY1447 | Haploid, GFP tagged Ssd1, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009 Mat a Euploid, hoΔ::HYG, his3Δ::KAN | this study | AGY1504 | Haploid, his3 deletion enabling HIS3 selection, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009_Chr12 Mat a Disome12, hoΔ::HYG, his3Δ::KAN | this study | AGY1505 | Haploid, his3 deletion enabling HIS3 selection, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009 Mat a Euploid, hoΔ::HYG, his3Δ::KAN, ssd1Δ::KAN | this study | AGY1506 | Haploid, his3 deletion enabling HIS3 selection, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009_Chr12 Mat a Disome12, hoΔ::HYG, his3Δ::KAN, ssd1Δ::KAN | this study | AGY1507 | Haploid, his3 deletion enabling HIS3 selection, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009 Mat a Euploid, hoΔ::HYG, his3Δ::KAN, PET123-GFP-ADH1terminator-HIS3M × 6 | this study | AGY1513 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009_Chr12 Mat a Disome12, hoΔ::HYG, his3Δ::KAN, PET123-GFP-ADH1terminator-HIS3M × 6 | this study | AGY1514 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009 Mat a Euploid, hoΔ::HYG, his3Δ::KAN, HSP104-GFP-ADH1terminator-HIS3M × 6 | this study | AGY1518 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009_Chr12 Mat a Disome12, hoΔ::HYG, his3Δ::KAN, HSP104-GFP-ADH1terminator-HIS3M × 6/HSP104 | this study | AGY1519 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009 Mat a Euploid, hoΔ::HYG, his3Δ::KAN, ssd1Δ::KAN, HSP104-GFP-ADH1terminator-HIS3M × 6 | this study | AGY1520 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009_Chr12 Mat a Disome12, hoΔ::HYG, his3Δ::KAN, ssd1Δ::KAN, HSP104-GFP-ADH1terminator-HIS3M × 6/HSP104 | this study | AGY1521 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | d-YPS1009_Chr12.2n Euploid | Hose et al. | AGY613 | Diploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | d-YPS1009_Chr12.4n Aneuploid | Hose et al. | AGY614 | Diploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | d-YPS1009_Chr12.2n Euploid, ssd1Δ::KAN/ssd1Δ::KAN | this study | AGY1560 | Diploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | d-YPS1009_Chr12.4n Aneuploid, ssd1Δ::KAN/ssd1Δ::KAN | this study | AGY1561 | Diploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | W303 Mat a Euploid ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 Gal+ ade16Δ::KAN | this study | AGY1387 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | W303_Chr12 Mat a Disome12 ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 Gal+ ade16Δ::KAN/ade16Δ::HYG | this study | AGY768 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | W303 Mat a Euploid ADE2+ his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 Gal+ ade16Δ::KAN | this study | AGY1388 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | W303_Chr12 Mat a Disome12 ADE2+ his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 Gal+ ade16Δ::KAN/ade16Δ::HYG | this study | AGY1389 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | W303 Mat a Euploid ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 Gal+ | this study | AGY103 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | W303_Chr8 Mat a Disome8 ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 Gal+ | this study | AGY1495 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | W303_Chr8-15 Mat a Disome8,15 ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 Gal+ | this study | AGY1496 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | W303_Chr8-10-16 Mat a Disome8,10,16 ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 Gal+ | this study | AGY1497 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009xW303 (sp100) Mat alpha Disome12 trp1-1 ade16Δ::KAN HYG+ | this study | AGY1548 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | d-NCYC110 Euploid | Hose et al. | AGY729 | Diploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | d-NCYC110_Chr8-4n Aneuploid | Hose et al. | AGY703 | Diploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | d-NCYC110 Euploid, ssd1Δ::KAN/ssd1Δ::KAN | this study | AGY1493 | Diploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | d-NCYC110_Chr8-4n Aneuploid, ssd1Δ::KAN/ssd1Δ::KAN | this study | AGY1494 | Diploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | KCY40 (or VC580) Euploid, hoΔ::MFAprom-HYGMX-NATMX | Hose et al. | AGY806 | Haploid |
| Strain (Saccharomyces cerevisiae) | KCY40 (or VC580) Disome8, hoΔ::MFAprom-HYGMX-NATMX | Hose et al. | AGY1105 | Haploid |
| Strain (Saccharomyces cerevisiae) | KCY40 (or VC580) Euploid, hoΔ::MFAprom-HYGMX-NATMX, ssd1Δ::KAN | this study | AGY1385 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | KCY40 (or VC580) Disome8, hoΔ::MFAprom-HYGMX-NATMX, ssd1Δ::KAN | this study | AGY1386 | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009_Chr12 Mat a Disome12, hoΔ::HYG + pPKI | this study | AGY735 transformed with plasmid | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009_Chr12 Mat a Disome12, hoΔ::HYG, ssd1Δ::KAN + pPKI | this study | ABY1445 transformed with plasmid | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009_Chr12 Mat a Disome12, hoΔ::HYG, ssd1Δ::KAN + pJH1-SSD1-W303 | this study | ABY1445 transformed with plasmid | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | YPS1009_Chr12 Mat a Disome12, hoΔ::HYG, ssd1Δ::KAN + pJH1-SSD1-YPS1009 | this study | ABY1445 transformed with plasmid | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | d-NCYC110_Chr8-4n Aneuploid + pJH1 | this study | AGY703 tranformed with plasmid | Diploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | d-NCYC110_Chr8-4n Aneuploid, ssd1Δ::KAN/ssd1Δ::KAN + pJH1 | this study | AGY1494 transformed with plasmid | Diploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | d-NCYC110_Chr8-4n Aneuploid, ssd1Δ::KAN/ssd1Δ::KAN + pJH1-SSD1-W303 | this study | AGY1494 transformed with plasmid | Diploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | d-NCYC110_Chr8-4n Aneuploid, ssd1Δ::KAN/ssd1Δ::KAN + pJH1-SSD1-YPS1009 | this study | AGY1494 transformed with plasmid | Diploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | W303 Mat a Euploid ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 Gal+ ade1::HIS3, lys2::KAN | Torres et al. | AGY487 | Haploid |
| Strain (Saccharomyces cerevisiae) | W303_Chr12 Mat a Disome12 ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 Gal+ ade16::HIS3 ade16::KAN | Torres et al. | AGY488 | Haploid |
| Strain (Saccharomyces cerevisiae) | W303 Mat a Euploid ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 Gal+ ade1::HIS3, lys2::KAN + pJH1 | this study | AGY487 transformed with plasmid | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | W303_Chr12 Mat a Disome12 ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 Gal+ ade16::HIS3 ade16::KAN + pJH1 | this study | AGY488 transformed with plasmid | Haploid, available on request from the Gasch Lab |
| Strain (Saccharomyces cerevisiae) | W303_Chr12 Mat a Disome12 ade2-1 his3-11,15 leu2-3,112 trp1-1 ura3-1 can1-100 Gal+ ade16::HIS3 ade16::KAN + pJH1-SSD1-YPS1009 | this study | AGY488 transformed with plasmid | Haploid, available on request from the Gasch Lab |
| Antibody | Rabbit polyclonal Anti-GFP | Abcam | Abcam catalog #ab290 | Rabbit polyclonal; 1:2000 |
| Antibody | Mouse monoclonal Anti-Actin | Thermo Fisher Scientific | Thermo Fisher Scientific catalog #MA1-744 | Mouse monoclonal; 1:1000 |
| Antibody | Mouse monoclonal Anti-COX2 | Abcam | Abcam catalog #ab110271 | Mouse monoclonal; 1:500 |
| Antibody | Mouse monoclonal Anti-DPM1 | Abcam | Abcam catalog #ab113686 | Mouse monoclonal; 1:250 |
| Antibody | Mouse monoclonal Anti-VPH1 | Abcam | Abcam catalog #ab113683 | Mouse monoclonal; 1:1000 |
| Recombinant DNA reagent | pXIPHOS | GenBank accession MG897154 | PAM sgRNA sequence (GAATCGAATG CAACCGGCGC) that targeted KanMX | Higgins et al., Wrobel et al. |
| Recombinant DNA reagent | pPKI | this study | AGB185 | CEN plasmid with the natMX selection marker. |
| Recombinant DNA reagent | pJH1 | this study | AGB090 | CEN plasmid derived from pKI that has natMX selection marker. pJH is equivalent to pKI except for a fragment of unexpressed DNA that was removed during generation. |
| Recombinant DNA reagent | pJH1-SSD1-YPS1009 | this study | ORF + 1000 bp upstream and 337 bp downstream of SSD1 from YPS1009 genomic DNA. Plasmid has natMX selection marker | |
| Recombinant DNA reagent | pJH1-SSD1-W303 | this study | ORF + 1000 bp upstream and 337 bp downstream of SSD1 from aW303 genomic DNA. Plasmid has natMX selection marker | |
| Recombinant DNA reagent | Molecular Barcoded Yeast (MoBY) v2.0 ORF Library | other | obtained from Great Lakes Bioenergy Research Center (GLBRC) | Ho, CH. et al. A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nat. Biotech. 27 (Holland and Cleveland, 2012), 369–377 (2009). |
| Sequence-based reagent | MMR1 FISH probes | Stellaris | designed against MMR1 mRNA | |
| Sequence-based reagent | Mitochondrial rRNA FISH probes | Stellaris | designed against 15 s and 21 s rRNA | |
| Peptide, recombinant protein | von Hippel-Lindau (VHL) tumor suppressor | Kaganovich et al. | Addgene catalog #21053 | Kaganovich D, Kopito R, Frydman J. Misfolded proteins partition between two distinct quality control compartments. Nature. 2008 Aug 28. 454 (7208):1088–95. |
| Peptide, recombinant protein | Aequorea victoria GFP (S65T) | Huh et al. | Huh W, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, and O'Shea EK (2003) Global Analysis of Protein Localization in Budding Yeast Nature 425:686–691. | |
| Commercial assay or kit | Mitochondrial Yeast Isolation Kit | Abcam | Abcam catalog #ab178779 | |
| Commercial assay or kit | Illumina TruSeq Total RNA Stranded | Illumina | Illumina catalog #20020597; previously RS-122–2203 | |
| Commercial assay or kit | NEBNext Ultra DNA Library Prep Kit for Illumina | New England Biolabs | NEB catalog #E7370L | |
| Commercial assay or kit | Yeast Mitochondrial Stain Sampler Kit | Thermo Fisher Scientific | Thermo Fisher Scientific catalog #Y7530 | |
| Chemical compound, drug | Nourseothricin-dihydrogen sulfate(clonNAT) | Werner BioAgents | Werner BioAgents catalog #5.005.000 | |
| Chemical compound, drug | 4',6-Diamidino-2-phenylindole, dihydrochloride (DAPI) | Thermo Fisher Scientific | Thermo Fisher Scientific catalog #PI62247 | |
| Chemical compound, drug | Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) | Sigma-Aldrich | Sigma catalog #C2759 | |
| Chemical compound, drug | Radicicol, Humicola fuscoatra | A.G. Scientific | A.G. Scientific catalog #R-1130 | |
| Chemical compound, drug | GFP-Trap Magnetic Agarose | Chromotek | Chromotek catalog #gtma-20 |