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Table 1 Relative changes in the yeast protein abundance when cultured in succinate versus glucose

From: Proteomic and metabolomic analysis of the carotenogenic yeast Xanthophyllomyces dendrorhous using different carbon sources

   c Fold-change succinate/glucose
a SSP b Assignment L EE EL S
  Cellular Processes: Transport and Motor Proteins     
6813 Putative coatomer subunit alpha 2.22 3.53 2.99 2.32
8703 Myosin -associated protein 26.33 2.34 3.83 2.58
8711 Myosin -associated protein 16.31 2.01 3.47 2.13
7403 KIP1 kinesin- related protein 4.68 −1.20 1.01 1.42
2503 Alpha-tubulin 3.92 −3.12 2.70 2.38
  Environmental Information Processing and Signal Transduction   
5515 Negative regulator of the PHO system. Ser-thr kinase −5.15 −1.20 −2.03 −1.04
3808 Serine/threonine-protein phosphatase PP1-1 1.09 5.86 1.48 1.49
9206 Ribosomal_L15 −9.72 −10.86 −6.31 −30.40
8104 Protein PXR1 −18.08 −21.03 −22.68 −24.75
5417 Eukaryotic translation initiation factor 3 subunit H −18.02 −1.63 2.41 −3.29
4411 Pre-mRNA-splicing factor −49.64 −5.13 −3.64 1.09
7815 Mediator of RNA polymerase II transcription sub.14 3.62 3.10 2.24 2.05
5602 Hypothetical protein. ATP-binding, Chaperone −5.05 1.17 −2.18 −1.25
2603 HSP60 5.25 −1.50 −1.09 −1.01
6411 Transcription factor RfeF, putative 22.00 3.95 2.84 3.20
7109 GTP-binding nuclear protein RAN −2.19 −1.69 −1.26 −1.07
  Metabolism     
3715 HSP 70 1.04 2.37 1.00 1.18
7812 Vacuolar membrane ATPase subunit a precursor 2.66 2.61 4.24 1.83
8504 Glutathione S-transferase Gst3 5.43 −1.65 1.88 3.71
  Metabolism: Lipid and Carbohydrate    
2523 CQ798506 NID. Acetyl-CoA carboxylase, cytosolic −4.12 −1.57 −2.23 −2.88
4603 ADR052 Wp. Simil acyl-CoA synthetase 3.96 3.75 3.98 7.02
6604 Fatty acid synthase 14.69 2.32 19.30 2.64
2319 Acetyl-CoA synthetase −6.54 −2.51 −19.85 −1.18
6503 Citrate synthase 1.07 6.07 3.12 2.24
6609 Glucokinase −5.48 −3.12 −4.63 −8.47
4201 Phosphoglycerate kinase 3.02 −2.30 −1.04 1.74
5314 GAPDH 11.61 −1.46 1.51 −2.33
2213 Transaldolase 1.03 −2.83 −2.42 −2.21
6610 Succinate dehydrogenase (ubiquinone) −4.25 1.55 3.22 1.74
6403 Pyruvate dehydrogenase −27.44 −1.20 2.54 −1.55
5509 Succinyl-CoA synthetase beta subunit −1.15 16.26 17.02 6.02
3206 NADP+ malate dehydrogenase 36.04 1.90 38.06 3.81
4605 Pyruvate decarboxylase 5.43 3.29 3.21 2.90
4519 Glucose-6-phosphate isomerase −5.39 −26.97 −1.06 3.10
0604 6-phosphogluconate dehydrogenase 6.28 −1.42 1.76 2.69
3331 Enolase 1.07 −3.59 −1.64 −1.75
4717 Aldehyde dehydrogenase [NAD(P)+] 4.27 2.02 −1.93 6.80
7110 Ribose-5-phosphate isomerase 1.42 −2.02 9.29 −2.32
5617 Glucose-6-P dehydrogenase −5.94 −5.64 −10.98 −2.08
7206 Malate dehydrogenase 7.82 1.70 3.24 4.74
6516 Acyl-CoA carboxylate CoA-transferase 6.07 7.73 8.02 4.43
6109 Endo-1,3(4)-beta-glucanase -glucanase −4.62 −1.23 −2.28 −2.36
  Metabolism: Secondary metabolite/carotenoid biosynthesis   
4609 Mevalonate kinase 13.23 3.51 71.38 10.07
5717 Squalene synthase −2.19 1.28 1.01 −1.26
5303 Prenyltransferase 1.46 −1.17 −5.57 −1.11
6308 Diphosphomevalonate decarboxylase 1.62 1.25 −1.27 −1.30
3517 Phosphomevalonate kinase 1.14 4.42 1.99 2.43
7501 Astaxanthin synthase −1.15 1.50 3.62 2.30
7311 Cytochrome P450 reductase (crtR) gene 1.62 1.40 −1.11 −2.87
  Metabolism: Redox     
4713 Monooxygenase 1.68 2.28 2.20 1.78
5703 Monooxygenase 2.18 3.91 1.45 2.05
5208 Alcohol dehydrogenase −3.91 −2.74 −5.20 −8.99
5202 Dehydrogenases with different specificities SDR 3.53 1.62 1.67 1.24
7108 Mn superoxide dismutase −27.58 −6.57 −40.12 −1.10
7105 Peroxiredoxin TSA2. −41.82 −18.13 −57.80 −2.93
4310 Oxidoreductase 1.10 3.09 3.60 1.57
5320 Monooxygenase, putative 19.98 1.81 26.11 22.52
7618 Glutathione-disulfide reductase 33.21 3.49 1.86 1.42
2210 Short-chain dehydrogenase/reductase SDR −10.14 −2.70 21.55 1.26
5313 Probable thioredoxin peroxidase −8.84 1.07 −4.86 −4.04
  Metabolism: Amino acid     
7811 Mitochondrial isoleucyl-tRNA synthetase 1.94 2.25 −1.13 1.66
7210 RIB40 genomic DNA. Methionyl-tRNA formyltransferase 10.14 −1.18 1.78 2.03
7816 Kynurenine 3-monooxygenase 6.59 4.93 2.74 2.80
7307 Aspartate aminotransferase putative 4.58 1.60 1.03 −2.50
2628 Adenosylhomocysteinase −27.35 1.36 −3.14 −2.53
3515 Delta-1-pyrroline-5-carboxylate dehydrogenase −2.66 −2.32 5.77 1.93
  Unknown     
7715 UPF0553 protein C589.05c. 5.54 4.35 1.38 −1.51
5304 Conserved hypothetical protein −6.74 −1.43 −2.32 −2.82
3615 YALI0F00616p −5.60 1.39 32.23 2.13
0310 Predicted protein 3.56 −4.53 −4.39 −1.57
3002 Hypothetical protein −2.89 −2.51 3.24 2.19
6111 Hypothetical protein −14.03 1.15 4.27 −1.05
  1. aSSP numbers were assigned using the PDQuest software analysis. bIdentifications were obtained using the Swiss-Prot and KEGG Pathways databases and contigs of X. dendrorhous genomic DNA. cMean fold changes in succinate compared with glucose. Statistical significance was estimated by t-test (p <0.02) that is shown in italics and the Benjamini-Hochberg (p <0.05) correction shown as bold values. Abbreviations: L: lag phase, EE: Early exponential, EL: Late exponential, S: Stationary.