Table 2.
Proteins which were differentially translated in the glucose repressed, glucose derepressed and xylose-grown cells, identified from the 2-DE gels [Additional files 14 and 15].
| log2 X72/G24 | log2 X72/G5 | log2 G24/G5 | |||||||
| Swiss Prot Id | Proteina | ORF | Function | 2D | array | 2D | array | 2D | array |
| P32316 | Ach1p | YBL015W | acetyl-CoA hydrolase | 0.0 | -1.0 | 3.4 | 2.7 | 3.4 | 3.7 |
| P00330 | Adh1p_a | YOL086C | alcohol dehydrogenase | 1.4 | 0.9 | 0.2 | 0.3 | -1.2 | -0.6 |
| P00330 | Adh1p_b | YOL086C | alcohol dehydrogenase | 2.1 | 0.9 | 0.5 | 0.3 | -1.6 | -0.6 |
| P00331 | Adh2p | YMR303C | alcohol dehydrogenase | 4.8 | -2.6 | 5.7 | 1.4 | 0.9 | 4.0 |
| P47143 | Ado1p_a | YJR105W | adenosine kinase | -1.1 | 0.4 | -1.4 | -1.3 | -0.2 | -1.7 |
| P47143 | Ado1p_b | YJR105W | adenosine kinase | -1.4 | 0.4 | -1.9 | -1.3 | -0.5 | -1.7 |
| P38013 | Ahp1p | YLR109W | thioredoxin peroxidase | -0.4 | 0.0 | 0.5 | -0.2 | 1.0 | -0.2 |
| P54114 | Ald3p | YMR169C | aldehyde dehydrogenase | 0.4 | 0.8 | 1.8 | 1.8 | 1.4 | 1.0 |
| P46367 | Ald4p | YOR374W | aldehyde dehydrogenase (NAD+) | 1.7 | -0.2 | 3.6 | 1.0 | 1.9 | 1.1 |
| P54115 | Ald6p_a | YPL061W | aldehyde dehydrogenase (NADP+) | -0.9 | -2.6 | 0.2 | -1.9 | 1.0 | 0.7 |
| P54115 | Ald6p_b | YPL061W | aldehyde dehydrogenase (NADP+) | -2.0 | -2.6 | -2.8 | -1.9 | -0.8 | 0.7 |
| P28777 | Aro2p | YGL148W | chorismate synthase | -0.7 | 0.4 | -1.4 | -1.4 | -0.7 | -1.8 |
| P53090 | Aro8p | YGL202W | aromatic-amino-acid transaminase | -1.7 | 1.5 | -0.6 | -1.0 | 1.1 | -2.5 |
| P38011 | Asc1p | YMR116C | molecular function unknown | -0.6 | 1.8 | -2.4 | -1.1 | -1.8 | -3.0 |
| P07251 | Atp1p | YBL099W | hydrogen-transporting ATP synthase | 0.1 | -0.2 | 1.8 | 0.7 | 1.7 | 0.9 |
| P00830 | Atp2p | YJR121W | hydrogen-transporting ATP synthase | 0.2 | -0.4 | 1.6 | 0.9 | 1.4 | 1.2 |
| P38891 | Bat1p | YHR208W | branched-chain-amino-acid transaminase | 1.9 | 3.9 | 0.4 | 0.7 | -1.5 | -3.2 |
| P07256 | Cor1p_a | YBL045C | ubiquinol-cytochrome-c reductase | 0.6 | -0.2 | 1.3 | 1.0 | 0.8 | 1.2 |
| P07256 | Cor1p_b | YBL045C | ubiquinol-cytochrome-c reductase | 0.3 | -0.2 | 1.3 | 1.0 | 1.0 | 1.2 |
| P07256 | Cor1p_c | YBL045C | ubiquinol-cytochrome-c reductase | -0.1 | -0.2 | 1.3 | 1.0 | 1.5 | 1.2 |
| P06115 | Ctt1p | YGR088W | catalase | 1.4 | 1.8 | 3.4 | 2.4 | 2.0 | 0.6 |
| P31373 | Cys3p | YAL012W | cystathionine gamma-lyase | -2.3 | -0.6 | -2.9 | -3.1 | -0.6 | -2.4 |
| P32582 | Cys4p_a | YGR155W | cystathionine beta-synthase | -2.5 | -0.8 | -0.2 | -1.1 | 2.3 | -0.3 |
| P32582 | Cys4p_b | YGR155W | cystathionine beta-synthase | -0.9 | -0.8 | -1.7 | -1.1 | -0.9 | -0.3 |
| P06634 | Ded1p | YOR204W | RNA helicase | 0.5 | 0.3 | -2.2 | 0.5 | -2.7 | 0.2 |
| P14306 | Dka1p | YLR178C | carboxypeptidase Y inhibitor | -1.2 | -0.6 | 1.7 | 0.8 | 2.9 | 1.4 |
| P39976 | Dld3p | YEL071W | D-lactate dehydrogenase (cytochrome) | -2.0 | -0.2 | -2.4 | -0.6 | -0.3 | -0.4 |
| P00924 | Eno1p_a | YGR254W | phosphopyruvate hydratase | 1.5 | 0.6 | 5.2 | 0.5 | 3.7 | -0.1 |
| P00924 | Eno1p_b | YGR254W | phosphopyruvate hydratase | 3.5 | 0.6 | 5.7 | 0.5 | 2.2 | -0.1 |
| P00924 | Eno1p_c | YGR254W | phosphopyruvate hydratase | 1.2 | 0.6 | 2.6 | 0.5 | 1.3 | -0.1 |
| P14065 | Gcy1p | YOR120W | aldo-keto reductase | 2.0 | 0.3 | 3.7 | 3.1 | 1.7 | 2.8 |
| Q00055 | Gpd1p | YDL022W | glycerol-3-phosphate dehydrogenase | 0.7 | 0.0 | 1.9 | 0.2 | 1.2 | 0.2 |
| P00950 | Gpm1p | YKL152C | phosphoglycerate mutase | 1.7 | 0.5 | 1.6 | -0.1 | 0.0 | -0.7 |
| P38625 | Gua1p | YMR217W | GMP synthase | -0.8 | 1.3 | -1.8 | -1.0 | -1.0 | -2.3 |
| P15454 | Guk1p | YDR454C | guanylate kinase | -1.7 | 0.3 | -1.4 | -1.3 | 0.3 | -1.6 |
| P15992 | Hsp26p_a | YBR072W | heat shock protein | 0.1 | -0.2 | 3.0 | 2.0 | 2.9 | 2.2 |
| P15992 | Hsp26p_b | YBR072W | heat shock protein | -0.6 | -0.2 | 2.2 | 2.0 | 2.8 | 2.2 |
| P04807 | Hxk2p_a | YGL253W | hexokinase | 2.6 | 2.9 | 10.7 | -0.5 | 8.1 | -3.4 |
| P04807 | Hxk2p_b | YGL253W | hexokinase | 0.7 | 2.9 | -1.1 | -0.5 | -1.8 | -3.4 |
| P28241 | Idh2p | YOR136W | isocitrate dehydrogenase (NAD+) | -0.9 | -0.5 | 0.7 | 0.2 | 1.7 | 0.7 |
| P00817 | Ipp1p | YBR011C | inorganic diphosphatase | -1.7 | -0.5 | -1.5 | -0.9 | 0.3 | -0.5 |
| P53598 | Lsc1p | YOR142W | succinate-CoA ligase (ADP-forming) | -0.5 | -0.4 | 0.6 | 0.1 | 1.1 | 0.4 |
| P36060 | Mcr1p | YKL150W | cytochrome-b5 reductase | 1.8 | 0.1 | 3.3 | 1.5 | 1.4 | 1.4 |
| P05694 | Met6p | YER091C | methionine synthase | -2.5 | -1.3 | -2.9 | -1.0 | -0.4 | 0.3 |
| P04147 | Pab1p | YER165W | poly(A) binding protein | 0.4 | 0.2 | -1.1 | -0.3 | -1.6 | -0.5 |
| P06169 | Pdc1p_ab | YLR044C | pyruvate decarboxylase | -1.7 | 2.0 | -1.8 | -0.2 | 0.0 | -2.2 |
| P06169 | Pdc1p_bb | YLR044C | pyruvate decarboxylase | -2.1 | 2.0 | -1.2 | -0.2 | 0.9 | -2.2 |
| P17967 | Pdi1p | YCL043C | protein disulfide isomerase | -0.7 | -0.1 | -2.6 | -0.5 | -1.9 | -0.4 |
| P00560 | Pgk1p_a | YCR012W | phosphoglycerate kinase | 1.1 | 0.6 | 1.8 | 0.1 | 0.7 | -0.5 |
| P00560 | Pgk1p_b | YCR012W | phosphoglycerate kinase | 1.9 | 0.6 | 2.6 | 0.1 | 0.7 | -0.5 |
| P34227 | Prx1p | YBL064C | thioredoxin peroxidase | -0.2 | -0.9 | 1.7 | 0.7 | 1.9 | 1.6 |
| Q12335 | Pst2p | YDR032C | molecular function unknown | -0.6 | -0.1 | 0.8 | -0.4 | 1.5 | -0.3 |
| P07703 | Rpc5p | YPR110C | DNA-directed RNA polymerase | -0.3 | 0.5 | -1.5 | -1.3 | -1.2 | -1.8 |
| P26783 | Rps5p | YJR123W | structural constituent of ribosome | -0.6 | 0.7 | -3.0 | -0.6 | -2.4 | -1.2 |
| P19358 | Sam2p | YDR502C | methionine adenosyltransferase | -2.2 | -2.0 | -2.5 | -2.6 | -0.3 | -0.6 |
| P07283 | Sec53p_a | YFL045C | phosphomannomutase | -0.1 | 0.2 | -2.5 | -1.6 | -2.4 | -1.8 |
| P07283 | Sec53p_b | YFL045C | phosphomannomutase | -1.1 | 0.2 | -2.0 | -1.6 | -0.8 | -1.8 |
| P33330 | Ser1p | YOR184W | phosphoserine transaminase | -0.8 | -0.3 | -0.9 | -1.0 | -0.1 | -0.8 |
| P37291 | Shm2p | YLR058C | glycine hydroxymethyltransferase | 0.1 | -0.1 | -1.5 | 0.6 | -1.6 | 0.7 |
| Q03144 | Sno1p | YMR095C | molecular function unknown | 0.3 | 0.4 | -0.8 | 2.0 | -1.1 | 1.6 |
| P00447 | Sod2p | YHR008C | manganese superoxide dismutase | -0.5 | -0.2 | 1.9 | 1.1 | 2.4 | 1.2 |
| P15705 | Sti1p | YOR027W | Hsp90 cochaperone | 0.6 | 0.2 | 1.7 | 0.3 | 1.1 | 0.1 |
| P23254 | Tkl1p | YPR074C | transketolase | -0.6 | 1.1 | -1.0 | -0.6 | -0.5 | -1.7 |
| P00942 | Tpi1p | YDR050C | triose-phosphate isomerase | -1.1 | 0.2 | 0.5 | -0.1 | 1.5 | -0.3 |
| P17649 | Uga1p | YGR019W | 4-aminobutyrate transaminase | -0.8 | -0.1 | 1.4 | 0.2 | 2.2 | 0.3 |
| Q12363 | Wtm1p_a | YOR230W | transcriptional modulator | 0.1 | -0.1 | 1.7 | 0.2 | 1.6 | 0.3 |
| Q12363 | Wtm1p_b | YOR230W | transcriptional modulator | -0.1 | -0.1 | 1.3 | 0.2 | 1.4 | 0.3 |
| P23180 | Yhl021p | YHL021C | molecular function unknown | -0.5 | -0.8 | 1.6 | 0.6 | 2.1 | 1.3 |
| P35691 | Ykl056cp | YKL056C | molecular function unknown | -1.0 | 0.5 | -1.8 | -1.4 | -0.9 | -1.9 |
| Q04869 | Ymr315wp | YMR315W | molecular function unknown | 2.5 | 2.3 | 3.1 | 1.8 | 0.6 | -0.4 |
Log2 values of the protein abundance ratios, and the expression ratios for the corresponding gene of cells grown on xylose for 72 h (X72) to cells grown on glucose for 24 h (G24), or 5 h (G5), and of cells grown on glucose for 24 h to cells grown on glucose for 5 h are given. Proteins whose encoding genes showed a statistically significant expression difference in the samples studied are marked with bold text.
aDifferent pI forms of a protein indicated by a, b and c
bThese spots of Pdc1p had substantially lower molecular weight compared with the major Pdc1p protein spot identified earlier [15] and are likely either degraded or post-translationally processed forms of the enzyme.