Table 2. Selected Ert1 target genes.
| Gene | Systematic name | Function | Enrichment (glucose) | Enrichment (ethanol) | Binding of Adr1, Cat8, or Rds2 |
|---|---|---|---|---|---|
| PCK1 | YKR097W | Phosphoenolpyruvate carboxykinase, key enzyme in the gluconeogenesis pathway | 64 | 47 | Adr1, Cat8, Rds2 |
| MAE1 | YKL029C | Mitochondrial malic enzyme, catalyzes the oxidative decarboxylation of malate to pyruvate | 11 | 35 | Rds2 |
| PDC1 | YLR044C | Major of three pyruvate decarboxylase isozymes, key enzyme in alcoholic fermentation | 4.8 | 26 | Rds2 |
| GAT1 | YFL021W | Transcriptional activator of genes involved in nitrogen catabolite repression | NS | 17 | — |
| AQR1 | YNL065W | Plasma membrane transporter of the major facilitator superfamily | 6.1 | 15 | Rds2 |
| ICY1 | YMR195W | Protein of unknown function, required for viability in rich media of cells lacking mitochondrial DNA | 2.7 | 14 | Adr1, Cat8, Rds2 |
| LSC2 | YGR244C | β-Subunit of succinyl-CoA ligase | 3.0 | 14 | Adr1, Rds2 |
| VID24 | YBR105C | GID complex regulatory subunit; regulates fructose-1,6-bisphosphatase targeting to the vacuole | 4.4 | 9.4 | Rds2 |
| PET9 | YBL30C | Major ADP/ATP carrier of the mitochondrial inner membrane; exchanges cytosolic ADP for mitochondrially synthesized ATP; also imports heme and ATP | 2.2 | 7.1 | Rds2 |
| OPI1 | YHL020C | Negative regulator of phospholipid biosynthetic genes | 1.9 | 7.0 | Rds2 |
| FBP1 | YLR377C | Fructose-1,6-bisphosphatase, key regulatory enzyme in the gluconeogenesis pathway | 2.7 | NS | Adr1, Cat8, Rds2 |
| FMP48 | YGR052W | Putative protein of unknown function; the authentic, nontagged protein is detected in highly purified mitochondria in high-throughput studies | NS | 4.7 | Adr1, Rds2 |
| — | YGR050C | Unknown function | |||
| RPM2 | YML091C | Protein subunit of mitochondrial RNase P | NS | 4.6 | Rds2 |
| YPC1 | YBR183W | Alkaline ceramidase/ | NS | 4.5 | — |
| — | Putative protein of unknown function | ||||
| YBR182C-A | |||||
| — | YEL020C-B | Dubious open reading frame | NS | 4.4 | — |
| PTR2 | YKR093W | Integral membrane peptide transporter, mediates transport of di- and tri-peptides | NS | 4.2 | Adr1, Cat8, Rds2 |
| QDR3 | YBR043C | Multidrug transporter of the major facilitator superfamily | NS | 4.2 | Rds2 |
| PHD1 | YLR043W | Transcriptional activator that enhances pseudohyphal growth | NS | 3.3 | — |
| — | YLR044W | Protein of unknown function | |||
| HXT8 | YJL214W | Protein of unknown function with similarity to hexose transporter family members, expression is induced by low levels of glucose and repressed by high levels of glucose | NS | 3.3 | Rds2 |
| IMA5 | YJL216C | Alpha-glucosidase | |||
| PMA1 | YGL008C | Plasma membrane H+-ATPase | NS | 3.2 | — |
| TKL1 | YPR074C | Transketolase of the pentose phosphate pathway | NS | 2.9 | Rds2 |
| DIP5 | YPL265W | Dicarboxylic amino acid permease; mediates high-affinity and high-capacity transport of L-glutamate and L-aspartate | NS | 2.7 | Adr1 |
| ATO2 | YNR002C | Putative transmembrane protein involved in export of ammonia | NS | 2.6 | Adr1, Rds2 |
| HAP4 | YKL109W | Limiting subunit of the heme-activated, glucose-repressed Hap2/3/4/5 complex involved in regulation of respiration genes | NS | 2.6 | Adr1, Rds2 |
| GID8 | YMR135C | Subunit of the GID complex involved in proteasome-dependent catabolite inactivation of fructose-1,6-bisphosphatase | NS | 2.3 | Adr1, Rds2 |
| FMP43 | YGR243W | Highly conserved subunit of the mitochondrial pyruvate carrier; a mitochondrial inner membrane complex comprised of Fmp37p/Mpc1p and either Mpc2p or Fmp43p/Mpc3p mediates mitochondrial pyruvate uptake; more highly expressed in glucose-containing minimal medium than in lactate-containing medium | NS | 2.1 | Adr1 |
| — | YPR036W-A | Protein of unknown function; transcription is regulated by Pdr1 | NS | 2.1 | Adr1, Cat8 |
| QCR6 | YFR033C | Subunit 6 of the ubiquinol cytochrome-c reductase complex | NS | 2.1 | — |
| ADR1 | YDR216W | Carbon source-responsive zinc-finger transcription factor, required for transcription of peroxisomal protein genes, and of genes required for ethanol, glycerol, and fatty acid utilization | NS | 1.9 | Adr1, Cat8 |
| PYC1 | YGL062W | Pyruvate carboxylase isoform involved in the conversion of pyruvate to oxaloacetate | NS | 1.9 | — |
| HXT2 | YMR011W | High-affinity glucose transporter of the major facilitator superfamily; expression is induced by low levels of glucose and repressed by high levels of glucose | NS | 1.8 | Adr1 |
| SFP1 | YLR403W | Regulates transcription of ribosomal protein and biogenesis genes; regulates response to nutrients and stress | NS | 1.8 | — |
| SFC1 | YJR095W | Mitochondrial succinate-fumarate transporter; required for ethanol and acetate utilization | NS | 1.8 | Adr1, Cat8, Rds2 |
Major targets of Ert1 are listed (P < 0.05 and with enrichment values >1.8). Gene functions were taken from the Saccharomyces cerevisiae database (http://www.yeastgenome.org/). Enrichment at a particular promoter is given for cells grown in glucose and ethanol; NS, not significant. ChIP-chip data for Adr1 and Cat8 (obtained under low glucose conditions) were taken from Tachibana et al. (2005) while data for Rds2 (obtained with ethanol) were taken from Soontorngun et al. (2007). For a complete list of targets, see Supporting Information, Table S1.