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Table 1 Significantly induced genes of Saccharomyces cerevisiae by HMF during the lag phase

From: Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae

Systematic Name Standard Name Description Fold change
    0.2 h 0.5 h 1 h 2 h
Reductase
YCR105W ADH7 NADPH-dependent medium chain alcohol dehydrogenase with broad substrate specificity +38.4 +60.3 +81.3 +39.5
YGL157W ARI1 NADPH-dependent aldehyde reductase +12.3 +21.3 +29.2 +27.2
YOL151W GRE2 3-methylbutanal reductase and NADPH-dependent methylglyoxal reductase (D-lactaldehyde dehydrogenase) +8.0 +7.6 +10.4 +12.0
YOR374W ALD4 NAD(P)-dependent mitochondrial aldehyde dehydrogenase +4.3 +3.2 +2.7 +3.2
PDR family
YOR153W PDR5 Plasma membrane ATP-binding cassette (ABC) transporter +30.0 +19.0 +30.6 +23.7
YPL058C PDR12 Plasma membrane ATP-binding cassette (ABC) transporter +7.1 +4.1 +6.2 +3.3
YDR406W PDR15 Plasma membrane ATP binding cassette (ABC) transporter +9.5 +3.5 +5.4 +7.3
YDR011W SNQ2 Plasma membrane ATP-binding cassette (ABC) transporter +4.7 +3.8 +6.4 +4.1
YGR281W YOR1 Plasma membrane ATP-binding cassette (ABC) transporter +4.7 +3.0 +4.4 +3.5
YOR049C RSB1 Suppressor of sphingoid long chain base (LCB) sensitivity of an LCB-lyase mutation +15.7 +6.9 +9.5 +8.6
YLR099C ICT1 Lysophosphatidic acid acyltransferase +3.4 +2.9 +4.8 +6.2
YER142C MAG1 3-methyl-adenine DNA glycosylase involved in protecting DNA against alkylating agents +4.3 +4.5 +5.1 +3.7
YER143W DDI1 DNA damage-inducible v-SNARE binding protein +2.4 +2.2 +2.4 +1.7
YLL028W TPO1 Polyamine transporter that recognizes spermine, putrescine, and spermidine +4.5 +3.3 +5.1 +4.3
YOR273C TPO4 Polyamine transporter that recognizes spermine, putrescine, and spermidine +2.7 +2.0 +3.0 +2.6
YDL020C RPN4 Transcription factor that stimulates expression of proteasome genes +1.9 +2.5 +2.8 +3.3
YGR035C YGR035C Putative protein of unknown function +3.1 +3.8 +4.1 +5.9
YLL056C YLL056C Putative protein of unknown function +2.0 +2.0 +5.8 +6.2
YMR102C YMR102C Putative protein of unknown function +1.8 +1.6 +2.2 +2.9
Proteasome and ubiquitin
YER012W PRE1 Beta 4 subunit of the 20 S proteasome +2.7 +2.4 +2.1 +1.8
YJL001W PRE3 Beta 1 subunit of the 20 S proteasome +3.0 +3.0 +2.6 +2.1
YOL038W PRE6 Alpha 4 subunit of the 20 S proteasome +2.0 +2.2 +2.8 +2.3
YBL041W PRE7 Beta 6 subunit of the 20 S proteasome +3.5 +2.6 +2.6 +1.9
YOR362C PRE10 Alpha 7 subunit of the 20 S proteasome +2.4 +2.2 +2.2 +1.9
YER094C PUP3 Beta 3 subunit of the 20 S proteasome involved in ubiquitin-dependent catabolism +2.4 +2.2 +2.9 +2.1
YDR427W RPN9 Non-ATPase regulatory subunit of the 26 S proteasome +2.7 +2.4 +2.4 +2.1
YFR052W RPN12 Subunit of the 19 S regulatory particle of the 26 S proteasome lid +2.8 +2.4 +2.6 +2.5
YHL030W ECM29 Major component of the proteasome +4.6 +3.3 +3.6 +2.6
YDL007W RPT2 One of six ATPases of the 19 S regulatory particle of the 26 S proteasome involved in the degradation of ubiquitinated substrates +3.3 +2.6 +2.6 +2.4
YDR394W RPT3 One of six ATPases of the 19 S regulatory particle of the 26 S proteasome involved in the degradation of ubiquitinated substrates +2.9 +2.0 +2.5 +2.5
YOR259C RPT4 One of six ATPases of the 19 S regulatory particle of the 26 S proteasome involved in the degradation of ubiquitinated substrates +3.1 +2.6 +3.2 +2.5
YBL058W SHP1 UBX (ubiquitin regulatory X) domain-containing protein that regulates Glc7p phosphatase activity and interacts with Cdc48p +2.5 +2.0 +2.1 +2.8
YFL044C OTU1 Deubiquitylation enzyme that binds to the chaperone-ATPase Cdc48p +2.3 +1.9 +3.3 +2.3
Amino acids
YLR142W PUT1 Proline oxidase +4.8 +6.9 +10.8 +43.0
YHR037W PUT2 Delta-1-pyrroline-5-carboxylate dehydrogenase +3.7 +3.7 +4.7 +3.3
YJR010W MET3 ATP sulfurylase +2.5 +2.7 +3.3 +3.6
YKL001C MET14 Adenylylsulfate kinase +1.7 +2.6 +2.8 +3.2
YCL064C CHA1 Catabolic L-serine (L-threonine) deaminase, catalyzes the degradation of both L-serine and L-threonine +13.3 +17.7 +15.8 +7.3
YLR089C ALT1 Alanine transaminase +2.9 +3.1 +4.1 +4.9
YPL111W CAR1 Arginase, responsible for arginine degradation +3.4 +2.2 +1.9 +1.6
Stress
YBR072W HSP26 Small heat shock protein (sHSP) with chaperone activity +10.8 +1.8 +2.0 +8.0
YER103W SSA4 Heat shock protein that is highly induced upon stress +13.2 +1.5 +2.0 +2.6
Transcription factors
YML007W YAP1 Basic leucine zipper (bZIP) transcription factor required for oxidative stress tolerance +3.3 +2.1 +2.5 +2.2
YDL020C RPN4 Transcription factor that stimulates expression of proteasome genes +1.9 +2.5 +2.8 +3.3
Others
YPL171C OYE3 Conserved NADPH oxidoreductase containing flavin mononucleotide (FMN) +5.9 +3.9 +5.3 +17.7
YOR306C MCH5 Plasma membrane riboflavin transporter +2.6 +4.9 +7.8 +7.2
YAR073W IMD1 Nonfunctional protein with homology to IMP dehydrogenase +2.2 +2.1 +3.4 +2.7
YBL078C ATG8 Component of autophagosomes and Cvt vesicles +4.5 +3.3 +2.7 +3.5
YBR062C YBR062C Hypothetical protein +2.5 +2.4 +2.4 +2.1
YML130C ERO1 Thiol oxidase required for oxidative protein folding in the endoplasmic reticulum +2.3 +2.4 +2.8 +2.3
YBR114W RAD16 Protein that recognizes and binds damaged DNA in an ATP-dependent manner (with Rad7p) during nucleotide excision repair +2.8 +2.1 +2.8 +1.7
YBR170C NPL4 Endoplasmic reticulum and nuclear membrane protein +2.4 +2.7 +2.2 +1.5
YDL021W GPM2 Homolog of Gpm1p phosphoglycerate mutase +3.5 +1.6 +1.7 +2.8
YBL101W-A YBL101W-A Retrotransposon TYA Gag gene co-transcribed with TYB Pol +1.4 +1.6 +2.6 +6.4
YDR210W-B YDR210W-B Retrotransposon TYA Gag and TYB Pol genes +1.9 +1.7 +2.6 +4.4
YDR316W-B YDR316W-B Retrotransposon TYA Gag and TYB Pol genes +1.8 +1.8 +2.6 +3.2
YDR365W-B YDR365W-B Retrotransposon TYA Gag and TYB Pol genes +1.7 +1.7 +2.2 +4.3
YDR515W SLF1 RNA binding protein that associates with polysomes +2.7 +2.7 +2.4 +2.7
YOR009W TIR4 Cell wall mannoprotein of the Srp1p/Tip1p family of serine-alanine-rich proteins -1.3 +1.3 +4.6 +5.9
YPL156C PRM4 Pheromone-regulated protein proposed to be involved in mating +3.4 +2.8 +3.5 +3.5
YGL062W PYC1 Pyruvate carboxylase isoform +2.3 +2.6 +3.1 +2.1
YOR007C SGT2 Glutamine-rich cytoplasmic protein of unknown function +2.8 +2.5 +2.9 +3.0
YOR052C YOR052C Nuclear protein of unknown function +4.1 +2.6 +1.8 +2.4
YDR034W-B YDR034W-B Protein of unknown function +7.2 +5.0 +3.6 +4.5
YML125C PGA3 Putative cytochrome b5 reductase +1.6 +2.7 +3.0 +2.4
YBL107C YBL107C Putative protein of unknown function +2.4 +2.6 +2.1 +2.9
YBR255C-A YBR255C-A Putative protein of unknown function +4.0 +2.0 +1.8 +2.1
YER137C YER137C Putative protein of unknown function +2.9 +2.4 +2.5 +3.6
YGR111W YGR111W Putative protein of unknown function +2.1 +2.2 +4.3 +7.1
YHR138C YHR138C Putative protein of unknown function +4.2 +2.8 +2.4 +2.8
YKR011C YKR011C Putative protein of unknown function +4.6 +2.3 +1.9 +1.3
YNL155W YNL155W Putative protein of unknown function +3.7 +2.4 +2.2 +1.9
YOR059C YOR059C ORF, Uncharacterized +2.1 +2.6 +2.2 +2.2