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Download Table S1 List of Ert1 targets (P 0.05 with enrichment values >1.8
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Table S1 List of Ert1 targets (P <0.05 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 as the carbon source) were taken from (SOONTORNGUN et al. 2007). Gene Systematic name PCK1 YKR097W MAE1 YKL029C PDC1 YLR044C GAT1 YFL021W AQR1 YNL065W ICY1 YMR195W LSC2 YGR244C VID24 YBR105C PET9 YBL30C OPI1 YHL020C FBP1 YLR377C PRP28 YDR243C 2 SI Function Phosphoenolpyruvate carboxykinase, key enzyme in the gluconeogenesis pathway Mitochondrial malic enzyme, catalyzes the oxidative decarboxylation of malate to pyruvate Major of three pyruvate decarboxylase isozymes, key enzyme in alcoholic fermentation Transcriptional activator of genes involved in nitrogen catabolite repression Plasma membrane transporter of the major facilitator superfamily Protein of unknown function, required for viability in rich media of cells lacking mitochondrial DNA β-subunit of succinyl-CoA ligase GID complex regulatory subunit; regulates fructose-1,6-bisphosphatase targeting to the vacuole Major ADP/ATP carrier of the mitochondrial inner membrane; exchanges cytosolic ADP for mitochondrially synthesized ATP; also imports heme and ATP Negative regulator of phospholipid biosynthetic genes Fructose-1,6-bisphosphatase, key regulatory enzyme in the gluconeogenesis pathway RNA helicase in the DEAD-box family, involved in RNA isomerization at the 5' splice site N. Gasmi et al. Enrichment (glucose) Enrichment (ethanol) Binding of Adr1, Cat8 or Rds2 64 47 Adr1, Cat8, Rds2 11 35 Rds2 4.8 26 Rds2 NS 17 - 6.1 15 Rds2 2.7 14 Adr1, Cat8, Rds2 3.0 14 Adr1, Rds2 4.4 9.4 Rds2 2.2 7.1 Rds2 1.9 7.0 Rds2 2.7 NS Adr1, Cat8, Rds2 NS 6.2 Rds2 PEX5 YDR244W HSP30 YCR021C IXR1 YKL032C FMP4 8 YGR052W - NS 5.6 - NS 5.3 - NS 4.7 Adr1, Rds2 NS 4.6 Rds2 NS 4.5 - NS 4.4 - NS 4.2 Adr1, Cat8, Rds2 NS 4.2 Rds2 NS 3.7 - NS 3.3 - NS 3.3 Rds2 NS 3.2 - NS 2.9 Rds2 NS 2.8 - NS 2.7 Adr1 NS 2.7 - YGR050C RPM2 YML091C YPC1 YBR183W - YBR182C-A YEL020C-B PTR2 YKR093W QDR3 YBR043C HMS1 YOR032C PHD1 YKL043W HXT8 Peroxisomal membrane signal receptor required for peroxisomal matrix protein import Hydrophobic plasma membrane localized, stress-responsive protein that negatively regulates the H(+)-ATPase Pma1p; induced by heat shock, ethanol treatment, weak organic acid, glucose limitation, and entry into stationary phase Transcription factor that mediates aerobic transcriptional repression of COX5b Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies YKL044W YJL214W IMA5 YJL216C PMA1 YGL008C TKL1 YPR074C DSF1 YEL070W DIP5 YPL265W - YGR161W-C Unknown function Protein subunit of RNase P Alkaline ceramidase/ mitochondrial Putative protein of unknown function Dubious open reading frame Integral membrane peptide transporter, mediates transport of di- and tripeptides Multidrug transporter of the major facilitator superfamily Basic helix-loop-helix (bHLH) protein with similarity to myc-family transcription factors Transcriptional activator that enhances pseudohyphal growth Protein of unknown function 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 Alpha-glucosidase Plasma membrane H+-ATPase Transketolase of the pentose phosphate pathway Putative mannitol dehydrogenase Dicarboxylic amino acid permease; mediates high-affinity and highcapacity transport of L-glutamate and L-aspartate Putative protein of unknown function N. Gasmi et al. 3 SI RTS3 YGR161C ATO2 YNR002C HAP4 YKL109W ZEOI YOL109W TAM41 YGR046W RME1 YGR044C AQY1 YPR192W YCF1 YDR135C TPO1 YLL028W YNL179C RPS3 Putative component of the protein phosphatase type 2A complex Putative transmembrane protein involved in export of ammonia Limiting subunit of the heme-activated, glucose-repressed Hap2/3/4/5 complex involve in regulation of respiration genes Peripheral membrane protein of the plasma membrane; regulates the cell integrity pathway mediated by Pkc1p and Slt2p. The authentic protein is detected in a phosphorylated state in highly purified mitochondria Mitochondrial protein required for cardiolipin biosynthesis Zinc finger protein involved in control of meiosis Spore-specific water channel that mediates the transport of water across cell membranes Vacuolar glutathione S-conjugate transporter; member of the ATPbinding cassette family Polyamine transporter of the major facilitator superfamily Protein component of the small (40S) ribosomal subunit NS 2.6 Adr1, Rds2 NS 2.6 Adr1, Rds2 NS 2.6 Adr1, Cat8, Rds2 NS 2.5 Rds2 NS 2.5 Rds2 NS 2.4 - NS 2.4 - NS 2.3 Adr1, Rds2 NS 2.3 Adr1, Rds2 NS 2.3 - NS 2.3 Adr1, Rds2 NS 2.3 Adr1, Rds2 NS 2.3 Rds2 NS 2.2 Rds2 NS 2.2 - YNL180C GID8 YMR135C ERG11 YHR007C SNA2 YDR525W-A HOR7 YMR251W-A MCM1 YMR043W RSC3 YDR303C MLP1 YKR095W 4 SI Subunit of the GID complex involved in proteasome-dependent catabolite inactivation of fructose-1,6bisphosphatase Lanosterol 14-alpha-demethylase Protein of unknown function, has similarity to Pmp3p, which is involved in cation transport Protein of unknown function; overexpression suppresses Ca2+ sensitivity of mutants lacking inositol phosphorylceramide mannosyltransferases Transcription factor involved in celltype-specific transcription and pheromone response Component of the RSC chromatin remodeling complex; required for maintenance of proper ploidy and regulation of ribosomal protein genes and the cell wall/stress response Myosin-like protein associated with the nuclear envelope, connects the nuclear N. Gasmi et al. MGA1 YGR249W SFK1 YKL051W HSP12 YFL014W ROX1 YPR065W SKS1 YPL026C FMP4 3 YGR243W - YPR036W-A QCR6 YFR033C RGI2 YIL057C VHR1 YIL056W BAS1 YKR099W TIP1 YBR067C MTL1 YGR023W - YKL027W pore complex with the nuclear interior Protein similar to heat shock transcription factor Plasma membrane protein that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P Plasma membrane protein involved in maintaining membrane organization in stress conditions; induced by heat shock, oxidative stress, osmostress, stationary phase, glucose depletion, oleate and alcohol Heme-dependent repressor of hypoxic genes Putative serine/threonine protein kinase; involved in the adaptation to low concentrations of glucose independent of the SNF3 regulated pathway 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 Protein of unknown function; transcription is regulated by Pdr1 Subunit 6 of the ubiquinol cytochromec reductase complex Protein of unknown function involved in energy metabolism under respiratory conditions; expression induced under carbon limitation and repressed under high glucose Transcriptional activator; required for the vitamin H-responsive element (VHRE) mediated induction of VHT1 (Vitamin H transporter) Myb-related transcription factor involved in regulating basal and induced expression of genes of the purine and histidine biosynthesis pathways Major cell wall mannoprotein with possible lipase activity Putative plasma membrane sensor, involved in cell integrity signaling and stress response during glucose starvation and oxidative stress Protein of unknown function, localized N. Gasmi et al. NS 2.2 - NS 2.2 Rds2 NS 2.2 Adr1 NS 2.2 - NS 2.1 - NS 2.1 Adr1 NS 2.1 Adr1, Cat8 NS 2.1 - NS 2.1 Adr1, Cat8, Rds2 2,5 2.1 - NS 2.0 Adr1, Rds2 NS 2.0 Adr1 NS 1.9 - 5 SI PEX1 YKL197C ADR1 YDR216W MET13 YGL125W TMA10 YLR327C CYC8 YBR112C PYC1 YGL062W NAF1 YNL124W - YHR080C HXT2 YMR011W MIP6 YHR015W SFP1 YLR403W IGD1 YFR017C FAT3 YKL187C SFC1 YJR095W 6 SI to the mitochondrial outer membrane AAA-peroxin that heterodimerizes with AAA-peroxin Pex6p and participates in the recycling of peroxisomal signal receptor Pex5p from the peroxisomal membrane to the cystosol 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 Major isozyme of methylenetetrahydrofolate reductase Protein of unknown function that associates with ribosomes General transcriptional co-repressor Pyruvate carboxylase isoform involved in the conversion of pyruvate to oxaloacetate RNA-binding protein required for the assembly of box H/ACA snoRNPs and thus for pre-rRNA processing Protein of unknown function; nontagged protein is detected in highly purified mitochondria in highthroughput studies High-affinity glucose transporter of the major facilitator superfamily, expression is induced by low levels of glucose and repressed by high levels of glucose Putative RNA-binding protein Regulates transcription of ribosomal protein and biogenesis genes; regulates response to nutrients and stress Cytoplasmic protein that inhibits Gdb1 glycogen debranching activity Putative protein of unknown function; the authentic, non-tagged protein is detected in a phosphorylated state in highly purified mitochondria in highthroughput studies Mitochondrial succinate-fumarate transporter; required for ethanol and acetate utilization N. Gasmi et al. NS 1.9 - NS 1.9 Adr1, Cat8 NS 1.9 - NS 1.9 Adr1 NS 1.9 - NS 1.9 - NS 1.8 - NS 1.8 - NS 1.8 Adr1 NS 1.8 - NS 1.8 - NS 1.8 - NS 1.8 Adr1 NS 1.8 Adr1, Cat8, Rds2