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Table 3 Functional categories and comparative expression fold changes of candidate and key genes for ethanol tolerance and ethanol fermentation for tolerant Saccharomyces cerevisiae NRRL Y-50316 and its parental strain Y-50049 over time under the ethanol challenge

From: Quantitative transcription dynamic analysis reveals candidate genes and key regulators for ethanol tolerance in Saccharomyces cerevisiae

Gene and Category Function description Y-50316 Y-50049 Msn4p/Msn2p Yap1p Hsf1p Pdr1p/Pdr3p
   0 h 1 h 6 h 24 h 48 h 0 h 1 h 6 h 24 h 48 h     
Heat shock proteins
HSP12 Plasma membrane localized heat shock protein 0.7 5.2 7.8 6.7 5.6 1.0 4.3 2.1 1.3 1.2 7 0 1 0
HSP26 Small heat shock protein with chaperone activity 0.9 55.2 30.0 31.7 54.4 1.0 59.5 34.8 17.8 15.3 4 0 7 0
HSP30 Hydrophobic plasma membrane localized heat shock protein 1.0 7.6 3.3 7.1 23.9 1.0 48.8 4.6 3.2 3.0 0 3 0 0
HSP31* Member of the DJ-1/ThiJ/PfpI superfamily, chaperone and cysteine protease 2.1 3.6 7.9 10.2 9.3 1.0 1.3 5.5 2.1 1.8 1 2 4 0
HSP32 Possible chaperone and cysteine protease 0.8 1.0 2.4 2.1 2.3 1.0 1.5 2.1 1.4 1.0 4 0 6 0
HSP42 Small heat shock protein with chaperone activity 0.8 3.8 1.5 1.6 1.6 1.0 6.9 2.8 1.2 0.7 3 0 8 0
HSP78 Heat shock protein of ATP-dependent proteases, mitochondrial 0.6 3.0 2.2 2.8 2.9 1.0 4.3 2.0 0.9 0.3 3 1 8 0
HSP82* Heat shock protein,Hsp90 chaperone required for pheromone signaling 1.7 7.6 2.6 2.2 2.4 1.0 3.4 3.4 1.3 0.6 2 1 4 0
HSP104 Heat shock protein 0.5 3.7 1.6 1.7 1.9 1.0 8.8 2.6 1.0 0.4 3 1 10 0
HSP150 O-mannosylated heat shock protein 1.4 1.0 1.9 1.7 1.7 1.0 1.0 1.0 0.7 0.4 2 1 0 0
Trehalose and glycogen metablism
PGM1* Phosphoglucomutase, minor isoform 1.6 0.6 0.6 0.6 0.4 1.0 0.4 0.7 0.3 0.2 3 0 2 0
PGM2 Phosphoglucomutase, major isoform 0.4 3.6 2.6 3.8 2.3 1.0 1.4 2.4 0.9 0.5 7 1 0 0
UGP1 UDP-glucose pyrophosphorylase 1.1 2.4 1.5 1.9 1.2 1.0 2.6 1.5 0.6 0.3 5 0 2 0
GPH1 Glycogen phosphorylase 1.0 5.2 14.3 19.9 17.7 1.0 2.4 6.6 4.5 3.5 3 1 0 0
GSY1 Glycogen synthase 0.6 3.4 2.2 2.0 1.0 1.0 1.6 2.5 1.1 0.5 2 0 0 0
GSY2 UDP-glucose--starch glucosyltransferase 0.6 1.2 3.2 3.2 2.4 1.0 1.4 2.1 1.5 0.6 2 1 4 0
TSL1 alpha-trehalose-phosphate synthase 0.6 3.2 3.5 3.1 2.3 1.0 1.8 2.3 1.1 0.4 7 0 7 0
TPS1 alpha-trehalose-phosphate synthase 0.6 1.5 1.9 1.9 1.1 1.0 1.3 1.7 0.7 0.4 6 2 2 0
TPS3 Regulatory subunit of trehalose-6-phosphate synthase/phosphatase complex 0.7 0.7 0.9 1.1 0.9 1.0 0.8 1.2 0.6 0.3 2 0 2 0
ATH1 Acid trehalase, vacuolar 1.1 1.6 2.1 2.2 2.0 1.0 1.7 1.2 0.6 0.4 1 1 4 0
NTH1 Neutral trehalase 0.9 1.3 2.3 2.7 2.5 1.0 0.6 2.0 1.2 0.5 3 0 2 0
NTH2 alpha-trehalase 1.0 1.4 2.1 2.8 2.8 1.0 0.9 1.4 0.9 0.5 1 1 2 0
Glycolysis
HXK1 Hexokinase I 0.5 16.8 6.9 13.1 15.8 1.0 14.1 8.1 3.8 2.2 5 0 4 0
GLK1 Glucokinase 0.4 4.0 2.7 2.4 1.8 1.0 2.5 6.3 2.3 0.8 4 0 0 0
PGI1 Glycolytic enzyme phosphoglucose isomerase 1.4 0.8 0.8 0.8 0.8 1.0 0.8 1.0 0.5 0.3 0 0 2 0
PFK1* Alpha subunit of heterooctameric phosphofructokinase involved in glycolysis 1.6 0.9 0.8 0.7 0.5 1.0 0.9 1.3 0.3 0.2 0 0 2 0
FBA1 Fructose 1,6-bisphosphate aldolase 1.2 1.0 0.8 0.9 0.7 1.0 0.9 1.0 0.4 0.3 0 1 1 0
TDH1 Glyceraldehyde-3-phosphate dehydrogenase 1 0.6 25.8 16.4 17.8 20.2 1.0 11.4 17.3 9.8 5.9 2 2 0 0
TDH2 Glyceraldehyde-3-phosphate dehydrogenase 2 1.3 1.3 1.0 0.7 0.5 1.0 1.1 1.1 0.4 0.2 0 0 0 0
TDH3 Glyceraldehyde-3-phosphate dehydrogenase 3 1.1 0.9 0.8 0.7 0.4 1.0 0.8 0.6 0.2 0.2 3 2 1 0
GPM2* Homolog of Gpm1p phosphoglycerate mutase 1.6 10.4 6.1 10.2 5.6 1.0 34.6 16.9 5.2 1.8 1 3 4 0
ERR1 Enolase related protein 0.9 1.1 1.0 0.8 0.9 1.0 1.1 0.6 0.4 0.5 4 0 4 0
PYK2 Pyruvate kinase 0.7 0.9 0.9 0.9 0.5 1.0 0.5 1.1 0.5 0.3 1 1 0 0
IRC15* Putative dihydrolipoamide dehydrogenases 2.1 1.9 1.6 2.2 1.8 1.0 2.0 1.6 1.2 0.8 2 1 2 0
LPD1* Dihydrolipoamide dehydrogenase 1.5 0.7 1.0 1.7 1.3 1.0 0.7 1.2 0.6 0.4 2 3 0 2
PDA1* E1 alpha subunit of the pyruvate dehydrogenase (PDH) complex 1.9 0.8 1.2 1.2 0.9 1.0 0.7 1.7 0.6 0.3 2 1 2 0
ALD4 Mitochondrial aldehyde dehydrogenase, utilizes NADP+ or NAD+ equally as coenzymes 0.9 5.3 7.8 7.0 6.1 1.0 11.3 5.3 2.8 1.4 3 3 0 0
ALD6* Cytosolic aldehyde dehydrogenase 1.9 0.4 0.4 0.2 0.1 1.0 0.3 0.1 0.1 0.1 4 1 0 2
ADH1* Alcohol dehydrogenase I 2.9 4.2 4.0 2.9 2.0 1.0 4.3 5.8 2.5 1.8 4 1 2 0
ADH2* Alcohol dehydrogenase II 2.9 4.4 4.8 3.9 2.4 1.0 4.8 7.1 3.4 1.9 2 0 2 0
ADH3* Alcohol dehydrogenase III 2.0 0.8 2.5 2.6 2.3 1.0 0.6 4.0 1.7 1.0 0 1 0 0
ADH7* NADP(H)-dependent alcohol dehydrogenase 2.9 2.6 2.3 2.4 3.2 1.0 3.9 2.9 1.4 1.1 1 2 2 0
SFA1 Long-chain alcohol dehydrogenase 1.2 1.7 2.0 2.4 2.3 1.0 1.9 2.3 1.0 0.6 1 0 2 0
Pentose phosphate pathway
ZWF1* Glucose-6-phosphate dehydrogenase 1.8 1.2 1.5 1.3 0.9 1.0 0.8 1.2 0.7 0.3 5 1 0 0
YDR248C* Sequence similarity to bacterial and human gluconokinase 1.7 0.7 1.5 3.0 2.4 1.0 0.7 1.4 0.7 0.5 3 1 0 0
SOL3* Possible 6-phosphogluconolactonase 1.8 0.3 0.6 1.3 0.4 1.0 0.4 0.9 0.4 0.3 1 3 0 0
SOL4 putative 6-phosphogluconolactonase 0.3 1.8 8.2 9.9 7.5 1.0 6.7 7.0 1.5 1.1 1 0 6 0
GND1* 6-phosphogluconate dehydrogenase 1.8 0.3 0.3 0.9 0.5 1.0 0.3 0.6 0.3 0.1 1 0 0 0
GND2 6-phosphogluconate dehydrogenase 0.9 8.6 23.1 26.2 23.0 1.0 2.1 4.0 1.2 1.0 3 1 7 0
NQM1 Transaldolase of unknown function 1.1 0.8 10.2 3.4 6.1 1.0 1.2 1.1 0.6 0.6 3 1 2 0
TKL1* Transketolase 1 1.6 0.2 0.6 1.0 0.6 1.0 0.2 0.8 0.3 0.1 1 1 2 0
TKL2 Transketolase 2 0.9 0.8 1.3 0.7 1.1 1.0 1.0 0.5 0.5 0.5 2 2 1 0
PRS1* 5-phospho-ribosyl-1(alpha)-pyrophosphate synthetase 2.2 0.3 0.5 1.0 0.9 1.0 0.3 1.1 0.4 0.3 0 2 6 0
PDR family
PDR1* zinc finger transcription factor for pleiotropic drug response 1.7 0.9 1.0 0.9 1.0 1.0 0.7 1.0 0.4 0.3 0 1 0 0
PDR5* Plasma membrane ATP-binding cassette (ABC) transporter 4.4 0.5 0.4 0.3 0.4 1.0 0.2 0.6 0.3 0.1 1 2 6 8
PDR12* Plasma membrane ATP-binding cassette (ABC) transporter 1.5 1.3 0.7 0.7 0.9 1.0 1.0 0.6 0.3 0.2 0 1 2 0
PDR15 ATP binding cassette (ABC) transporter of the plasma membrane 1.3 1.7 1.5 2.3 1.7 1.0 1.0 0.9 0.4 0.3 5 0 0 3
YOR1* ATP binding cassette (ABC) transporter of the plasma membrane 2.2 0.8 0.8 0.5 0.4 1.0 0.6 0.9 0.1 0.1 2 1 0 2
SNQ2* ATP binding cassette (ABC) transporter of the plasma membrane 2.3 0.6 0.4 0.7 0.5 1.0 0.3 0.5 0.2 0.1 1 2 0 7
ICT1* Lysophosphatidic acid acyltransferase 2.0 0.6 0.6 0.4 0.6 1.0 1.0 1.2 0.7 0.4 1 0 2 2
DDI1* DNA damage-inducible v-SNARE binding protein 1.7 1.7 2.0 1.7 2.4 1.0 1.1 2.0 1.0 0.6 1 1 0 0
TPO1* Vacuolar polyamine-H+ antiporter 1.7 1.0 2.0 3.1 3.5 1.0 1.4 2.6 1.9 1.0 2 3 0 2
GRE2* Methylglyoxal reductase (NADPH-dependent) 4.1 1.4 1.5 1.6 1.8 1.0 1.3 1.5 0.6 0.5 0 1 2 2
YMR102C* Protein of unknown function 1.6 1.2 1.1 1.2 1.0 1.0 1.2 0.9 0.7 0.6 1 0 0 3
Fatty acid metabolism
ETR1 Mitochondrial respiratory function protein 0.9 1.0 1.5 2.1 1.7 1.0 1.6 1.3 0.7 0.5 2 2 2 0
ELO1* Elongase I, Fatty acid elongation protein 1.6 0.8 1.3 1.8 1.0 1.0 0.5 0.7 0.4 0.3 0 1 2 0
HTD2 Mitochondrial 3-hydroxyacyl-thioester dehydratase involved in fatty acid biosynthesis 1.1 0.9 1.1 1.1 1.0 1.0 0.7 1.1 0.5 0.5 0 0 0 0
Egosterol biosynthesis
ERG4* C-24(28) sterol reductase 1.5 0.5 0.6 0.5 0.3 1.0 0.7 0.4 0.2 0.2 0 0 2 2
ERG20 Farnesyl-pyrophosphate synthetase 0.9 0.7 0.9 0.9 0.6 1.0 0.6 1.3 0.6 0.4 1 1 0 0
ERG26 C-3 sterol dehydrogenase 1.0 0.4 0.9 0.8 0.8 1.0 0.4 0.8 0.5 0.4 0 1 5 0
Proline metabolism
PUT1 Proline oxidase 0.6 0.8 2.7 1.8 4.9 1.0 5.1 3.8 6.0 2.6 0 0 0 0
PRO1* Gamma-glutamyl kinase, catalyzes the first step in proline biosynthesis 1.6 1.0 0.7 0.9 0.7 1.0 0.7 1.0 0.5 0.3 0 0 2 0
Tryptophan biosynthesis
TRP5* Tryptophan synthase 1.5 0.5 1.0 1.4 0.7 1.0 0.4 1.3 0.5 0.2 4 2 0 0
Glycerol metabolism
DAK1 Dihydroxyacetone kinase 1.2 2.2 2.0 1.9 1.8 1.0 1.6 2.0 0.7 0.3 0 0 0 0
GCY1 Putative NADP(+) coupled glycerol dehydrogenase 1.1 0.9 4.3 5.4 4.8 1.0 1.1 4.1 2.2 1.7 1 1 2 0
GPD1 NAD-dependent glycerol-3-phosphate dehydrogenase 1.3 0.8 1.0 1.1 0.5 1.0 1.4 1.0 0.3 0.2 4 1 0 0
GUP1 Multimembrane-spanning protein essential for proton symport of glycerol 1.2 1.0 0.9 1.2 0.8 1.0 0.6 1.0 0.5 0.3 0 0 0 0
GUP2* Putative glycerol transporter involved in active glycerol uptake 1.8 0.8 0.6 1.0 0.6 1.0 0.7 1.0 0.6 0.5 1 0 0 0
Transcription factors
MSN2 Transcriptional activator related to Msn4p 1.0 0.8 0.7 0.8 0.5 1.0 1.2 0.7 0.4 0.2 1 0 2 0
MSN4 Transcriptional activator related to Msn2p 1.0 0.8 1.3 2.5 3.2 1.0 1.0 0.7 0.5 0.4 4 0 2 0
YAP1* Transcriptional activator involved in oxidative stress response 1.5 0.9 0.8 1.0 0.7 1.0 1.7 1.0 0.5 0.3 1 2 2 0
HSF1 Heat shock transcription factor 1.4 1.3 1.2 1.5 1.3 1.0 1.6 1.1 0.7 0.4 1 3 2 0
  1. * Genes showing significantly enriched transcription abundance in Y-50316 prior to ethanol challenge (p < 0.01).
  2. Genes in bold indicate new reports by this study and the expression fold changes in bold indicate an increase of greater than 1.5-fold (p < 0.01) compared with a wild type control.
  3. Numbers of protein binding motifs related to transcription factors Msn4p/Msn2p, Yap1p, Hsf1p and Pdr1p/Pdr3p for each gene were marked under each transcription factor