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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
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