Table 2.
Expression levels of genes associated with the response to oxidative stress in cells shifted to growth on glycerol
| Systematic name | Common name | Fold-changea | Saccharomyces Genome Database gene description (abbreviated) |
|---|---|---|---|
| YDR256C | CTA1 | 40.22 | Catalase A, breaks down hydrogen peroxide in the peroxisome formed during fatty acid beta-oxidation |
| YFL014W | HSP12 | 18.36 | Plasma membrane protein; induced by heat shock, oxidative stress, glucose depletion |
| YGR088W | CTT1 | 7.18 | Cytosolic catalase T, has a role in protection from oxidative damage by hydrogen peroxide |
| YBL064C | PRX1 | 5.47 | Mitochondrial peroxiredoxin; induced during respiratory growth and under conditions of oxidative stress |
| YKL150W | MCR1 | 5.04 | Mitochondrial NADH-cytochrome b5 reductase, involved in ergosterol biosynthesis |
| YKL026C | GPX1 | 4.57 | Phospholipid glutathione peroxidase; induced by glucose starvation; protection from oxidative stress |
| YLL039C | UBI4 | 4.50 | Ubiquitin; marks proteins for selective degradation; essential for the cellular stress response |
| YNL036W | NCE103 | 3.62 | Carbonic anhydrase; poorly transcribed under aerobic conditions |
| YCL035C | GRX1 | 3.38 | Hydroperoxide and superoxide-radical responsive oxidoreductase; protection from oxidative damage |
| YMR250W | GAD1 | 3.11 | Glutamate decarboxylase (glutamate to gamma-aminobutyric acid); response to oxidative stress |
| YPL196W | OXR1 | 2.97 | Protein of unknown function required for resistance to oxidative damage |
| YOR338W | YOR338W | 2.94 | Hypothetical protein |
| YKR066C | CCP1 | 2.89 | Mitochondrial cytochrome-c peroxidase; degrades reactive oxygen species; response to oxidative stress |
| YHR140W | YHR140W | 2.71 | Putative integral membrane protein of unknown function |
| YDR453C | TSA2 | 2.61 | Inducible cytoplasmic thioredoxin peroxidase; removal of reactive oxygen, nitrogen and sulfur species |
| YIR037W | HYR1 | 2.43 | Thiol peroxidase; senses intracellular hydroperoxide levels, transduces a redox signal to Yap1p |
| YCR083W | TRX3 | 2.24 | Mitochondrial thioredoxin; maintains cellular redox homeostasis with Trr2p and Glr1p |
| YBR037C | SCO1 | 2.20 | Mitochondrial inner membrane copper-binding protein required for cyt c oxidase activity and respiration |
| YCL033C | MSRB | 2.19 | Putative protein-methionine-R-oxide reductase; involved in response to oxidative stress |
| YDR513W | GRX2 | 2.18 | Cytoplasmic glutaredoxin; involved in maintaining redox state of target proteins; induced by stress |
| YLL056C | YLL056C | 2.11 | Putative protein of unknown function; activated along with genes involved in pleiotropic drug resistance |
| YJR104C | SOD1 | 2.06 | Copper, Zinc-containing superoxide dismutase |
| YKL086W | SRX1 | 2.02 | Sulfiredoxin, contributes to oxidative stress resistance by reducing peroxiredoxins Tsa1p and Ahp1p |
| YBR006W | UGA2 | 1.95 | Succinate semialdehyde dehydrogenase; utilization of gamma-aminobutyrate as a nitrogen source |
| YHR008C | SOD2 | 1.93 | Manganese-containing superoxide dismutase; protects cells against oxygen toxicity |
| YNL241C | ZWF1 | 1.75 | Glucose-6-phosphate dehydrogenase (pentose phosphate pathway); adaption to oxidative stress |
| YML007W | YAP1 | 1.74 | Transcription factor required for oxidative stress tolerance; mediates pleiotropic drug, metal resistance |
| YHR106W | TRR2 | 1.63 | Mitochondrial thioredoxin reductase; oxidative stress protection; with Glr1p maintains Trx3p redox status |
| YHR126C | YHR126C | 1.47 | Hypothetical protein |
| YML028W | TSA1 | 1.46 | Ubiquitous housekeeping thioredoxin peroxidase, reduces reactive oxygen, nitrogen and sulfur species |
| YMR037C | MSN2 | 1.46 | Transcriptional activator related to Msn4p; activated in stress conditions |
| YPL059W | GRX5 | 1.42 | Mitochondrial hydroperoxide, superoxide-radical responsive oxidoreductase; iron-sulfur center synthesis |
| YGR209C | TRX2 | 1.39 | Cytoplasmic thioredoxin isoenzyme; protects cells against both oxidative and reductive stress |
| YNL259C | ATX1 | 1.35 | Cytosolic copper metallochaperone; copper eventually inserted into Fet3p (high-affinity iron uptake) |
| YPL188W | POS5 | 1.34 | Mitochondrial NAD(H) kinase; required for the response to oxidative stress |
| YER042W | MXR1 | 1.33 | Reverses oxidation of methionine residues; involved in repair and resistance to oxidative stress |
| YFL033C | RIM15 | 1.28 | Glucose-repressible protein kinase; signal transduction during cell proliferation in response to nutrients |
| YBL043W | ECM13 | 1.21 | Nonessential protein of unknown function |
| YER174C | GRX4 | 1.19 | Hydroperoxide, superoxide-radical responsive oxidoreductase; protection from oxidative damage |
| YBR216C | YBP1 | 1.17 | Oxidation of transcription factor Yap1p, resulting in nuclear localization of Yap1p in response to stress |
| YNL331C | AAD14 | 1.15 | Putative aryl-alcohol dehydrogenase; mutational analysis has not yet revealed a physiological role |
| YDR533C | HSP31 | 1.12 | Possible chaperone and cysteine protease with similarity to Hsp32p, Hsp33p, and Sno4p |
| YPR065W | ROX1 | 1.11 | Heme-dependent repressor of hypoxic genes |
| YGR097W | ASK10 | 1.11 | Component of the RNA polymerase II holoenzyme, phosphorylated in response to oxidative stress |
| YLR108C | YLR108C | 1.03 | Protein of unknown function; green fluorescent-fusion protein localizes to the nucleus; non-essential |
| YNL099C | OCA1 | 1.03 | Putative protein tyrosine phosphatase; induces cell cycle arrest in response to oxidative DNA damage |
| YLL028W | TPO1 | −1.04 | Polyamine transporter; catalyzes uptake of polyamines at alkaline pH and excretion at acidic pH |
| YIL010W | DOT5 | −1.08 | Nuclear thiol peroxidase; functions as an alkyl-hydroperoxide reductase during post-diauxic growth |
| YCR021C | HSP30 | −1.12 | Plasma membrane stress response protein; negatively regulates H(+)-ATPase Pma1p |
| YOL165C | AAD15 | −1.15 | Putative aryl-alcohol dehydrogenase; mutational analysis has not yet revealed a physiological role |
| YHR111W | UBA4 | −1.16 | Urmylates thioredoxin peroxidase Ahp1p, suggesting a role of urmylation in oxidative stress response |
| YPL202C | AFT2 | −1.16 | Iron-regulated transcriptional activator, required for iron homeostasis and resistance to oxidative stress |
| YLR109W | AHP1 | −1.21 | Thiol-specific peroxiredoxin, reduces hydroperoxides to protect against oxidative damage |
| YJR155W | AAD10 | −1.22 | Putative aryl-alcohol dehydrogenase; mutational analysis has not yet revealed a physiological role |
| YHR053C | CUP1-1 | −1.23 | Metallothionein, binds copper and mediates resistance to high concentrations of copper and cadmium |
| YHR055C | CUP1-2 | −1.26 | Metallothionein, binds copper and mediates resistance to high concentrations of copper and cadmium |
| YMR173W | DDR48 | −1.26 | DNA damage-responsive protein, induced in response to heat-shock stress or DNA lesions |
| YDR011W | SNQ2 | −1.29 | ABC transporter protein involved in multidrug resistance and resistance to singlet oxygen species |
| YKR052C | MRS4 | −1.31 | Mitochondrial iron transporter; functions under low-iron conditions; may transport other cations |
| YDL039C | PRM7 | −1.38 | Pheromone-regulated protein, predicted to have a transmembrane segment; regulated by Gcn4p |
| YLR043C | TRX1 | −1.40 | Cytoplasmic thioredoxin isoenzyme; protects cells against both oxidative and reductive stress |
| YML086C | ALO1 | −1.44 | Catalyzes the final step of erythroascorbic acid biosynthesis, protective against oxidative stress |
| YNL134C | YNL134C | −1.48 | Uncharacterized ORF; alcohol dehydrogenase (NADP+) activity; biological process unknown |
| YMR102C | YMR102C | −1.51 | Protein of unknown function; activated along with genes involved in multidrug resistance |
| YDR346C | SVF1 | −1.53 | Protein with a potential role in cell survival pathways, required for the diauxic growth shift |
| YPL091W | GLR1 | −1.58 | Cytosolic and mitochondrial glutathione oxidoreductase; reduces oxidized glutathione |
| YLR346C | YLR346C | −1.61 | Putative mitochondrial protein of unknown function; regulated by drug resistance transcription factors |
| YOL118C | YOL118C | −1.64 | Hypothetical protein |
| YGR234W | YHB1 | −1.75 | Nitric oxide oxidoreductase; flavohemoglobin; role in the oxidative and nitrosative stress responses |
| YOR153W | PDR5 | −1.82 | Membrane ATP-binding cassette transporter; involved in transport and cellular detoxification |
| YDR098C | GRX3 | −1.83 | Hydroperoxide and superoxide-radical responsive oxidoreductase; protection from oxidative damage |
| YHR029C | YHI9 | −1.95 | Protein of unknown function possibly involved in a membrane regulation metabolic pathway |
| YPL239W | YAR1 | −2.09 | Cytoplasmic protein; proposed to link 40S ribosomal subunit biogenesis to adaption to oxidative stress |
| YML131W | YML131W | −2.13 | Putative protein of unknown function; increased after osmotic shock; non-essential gene |
| YOL151W | GRE2 | −2.15 | NADPH-dependent methylglyoxal reductase; stress induced (osmotic, ionic, oxidative, heat, metals) |
| YPL095C | EEB1 | −2.17 | Acyltransferase; major part of short-chain fatty acid ethyl ester production during fermentation |
| YPL171C | OYE3 | −2.38 | Widely conserved NADPH oxidoreductase; may be involved in sterol metabolism |
| YKL143W | LTV1 | −2.39 | Protein required for growth at low temperature |
| YCR107W | AAD3 | −2.40 | Putative aryl-alcohol dehydrogenase; mutational analysis has not yet revealed a physiological role |
| YDL166C | FAP7 | −2.51 | Essential NTPase required for small ribosome subunit synthesis |
| YIL008W | URM1 | −2.57 | Ubiquitin-like protein; molecular function of Urm1p pathway is unknown; required for normal growth |
| YNL231C | PDR16 | −2.71 | Phosphatidylinositol transfer protein; controls levels of various lipids, may regulate lipid synthesis |
| YLL060C | GTT2 | −2.75 | Glutathione S-transferase capable of homodimerization; functional overlap with Gtt2p, Grx1p, Grx2p |
| YJL101C | GSH1 | −2.95 | Catalyzes the first step of glutathione biosynthesis; induced by oxidants, cadmium, and mercury |
| YLR214W | FRE1 | −2.98 | Ferric and cupric reductase; reduces iron and copper prior to uptake; induced by low copper, iron levels |
| YDL182W | LYS20 | −3.20 | Homocitrate synthase isozyme; catalyzes first step in the lysine biosynthesis pathway |
| YOR226C | ISU2 | −3.29 | Conserved mitochondrial matrix protein; synthesis of mitochondrial and cytosolic iron-sulfur proteins |
| YHR179W | OYE2 | −3.39 | Widely conserved NADPH oxidoreductase; may be involved in sterol metabolism |
| YNR074C | AIF1 | −3.42 | Mitochondrial cell death effector that translocates to the nucleus in response to apoptotic stimuli |
| YOL058W | ARG1 | −3.44 | Catalyzes the formation of L-argininosuccinate in the arginine biosynthesis pathway |
| YHR183W | GND1 | −3.47 | Regenerates NADPH in the pentose phosphate pathway; required for adaptation to oxidative stress |
| YDR353W | TRR1 | −4.05 | Cytoplasmic thioredoxin reductase; protects cells against both oxidative and reductive stress |
| YIL167W | SDL1 | −4.47 | Open reading frame, unlikely to produce a functional protein in S288C |
| YFL056C | AAD6 | −5.55 | Putative aryl-alcohol dehydrogenase; involved in the oxidative stress response |
| YBR244W | GPX2 | −5.68 | Glutathione peroxidase; protects cells from hydroperoxides and peroxides during oxidative stress |
| YFL057C | AAD16 | −6.74 | Putative aryl-alcohol dehydrogenase; mutational analysis has not yet revealed a physiological role |
| YML116W | ATR1 | −7.41 | Multidrug efflux pump; required for resistance to aminotriazole, 4-nitroquinoline-N-oxide |
| YMR318C | ADH6 | −7.67 | NADPH-dependent alcohol dehydrogenase; possibly involved in fusel alcohol synthesis or aldehyde tolerance |
| YDL243C | AAD4 | −7.91 | Putative aryl-alcohol dehydrogenase; involved in the oxidative stress response |
aEach of these genes were significantly differentially expressed with a P-value of ≤10−4, determined using Rosetta Resolver (see Materials and Methods section).