Table 3.
Identification and quantification of methanol metabolic enzymes and control proteins in peroxisomal preparations (Pex) and homogenates (Hom) of P. pastoris grown on methanol. MASCOT scores indicate identification of the respective proteins in the samples while peak areas of the identified peptides were used for quantification. To normalize the dataset, average ratios of the summarized peak areas of Aox1 peptides of peroxisomal samples vs homogenates were set to 1, and all ratios were calculated in relation to this. Peroxisomal proteins serve as positive control, while methanol dissimilation, pentose phosphate pathway (PPP), and glycolysis-related enzymes are negative controls localized to the cytosol
| Short name | Function/localization | Description | MASCOT Score Pex1 | MASCOT Score Pex2 | MASCOT Score Hom1 | MASCOT Score Hom2 | ratio peak area Pex/Hom |
|---|---|---|---|---|---|---|---|
| AOX1 | Methanol assimilation | Alcohol oxidase 1 | 1542.8 | 1157.2 | 1021.4 | 1061 | 1.00 |
| DAS1 | Methanol assimilation | Dihydroxyacetone synthase 1 | 1918.9 | 1503 | 971.2 | 970.4 | 14.79 |
| DAS2 | Methanol assimilation | Dihydroxyacetone synthase 2 | 1797.9 | 1473.2 | 986.3 | 961.1 | 7.10 |
| DAK2 | Methanol assimilation | Dihydroxyacetone kinase | 226.9 | 0 | 666.2 | 550.4 | 0.26 |
| FBA1-2 | Methanol assimilation | Fructose-bisphosphate aldolase | 464.8 | 185.7 | 287 | 291.5 | 0.96 |
| FBP1 | Methanol assimilation | Fructose-1,6-bisphosphatase | 623.8 | 419.8 | 585 | 576.8 | 2.42 |
| SHB17 | Methanol assimilation | Sedoheptulose-1,7-bisphosphatase | 357.4 | 314 | 191 | 145.2 | 3.05 |
| RKI1-2 | Methanol assimilation | Ribose-5-phosphate ketol-isomerase | 217.1 | 0 | 0 | 139.8 | 2.97 |
| TAL1-2 | Methanol assimilation | Transaldolase | 374.3 | 279.8 | 0 | 0 | > > 1 |
| CTA1 | Peroxisomal protein | Catalase | 907.3 | 434.4 | 414.3 | 304.3 | 1.26 |
| PEX3 | Peroxisomal protein | Peroxisomal biogenesis factor | 119.2 | 109.9 | 0 | 0 | > > 1 |
| PEX5 | Peroxisomal protein | Peroxisomal targeting signal 1 receptor | 86.1 | 62.5 | 127.8 | 36.3 | 1.09 |
| PEX11 | Peroxisomal protein | Peroxisomal membrane protein | 523.4 | 262.1 | 221.5 | 151.8 | 4.26 |
| PEX14 | Peroxisomal protein | Peroxisomal membrane protein | 145.2 | 103.7 | 0 | 0 | > > 1 |
| PMP20 | Peroxisomal protein | Peroxiredoxin | 536 | 437.3 | 260.7 | 274.2 | 1.49 |
| PMP47 | Peroxisomal protein | Peroxisomal membrane protein | 539.5 | 345.7 | 165.9 | 162.5 | 8.02 |
| FLD | Methanol dissimilation | Formaldehyde dehydrogenase | 0 | 0 | 577.9 | 424.4 | 0.00 |
| FGH1 | Methanol dissimilation | S-formylglutathione hydrolase | 0 | 0 | 455.4 | 432.4 | 0.00 |
| FDH1 | Methanol dissimilation | Formate dehydrogenase | 491.1 | 303.5 | 910.5 | 856.7 | 0.12 |
| TAL1-1 | PPP | Transaldolase | 220.2 | 0 | 376.7 | 206.5 | 0.38 |
| TKL1 | PPP | Transketolase | 0 | 0 | 85 | 166 | 0.00 |
| ZWF1 | PPP | Glucose-6-phosphate 1-dehydrogenase | 0 | 0 | 0 | 46.7 | 0.00 |
| GND2 | PPP | 6-phosphogluconate dehydrogenase | 247.1 | 66.6 | 626.8 | 522.9 | 0.26 |
| FBA1-1 | Glycolysis | Fructose-bisphosphate aldolase | 0 | 0 | 347.3 | 379.1 | 0.00 |
| HXK1 | Glycolysis | Hexokinase | 0 | 0 | 100.6 | 195.6 | 0.00 |
| TDH3 | Glycolysis | Glyceraldehyde-3-phosphate dehydrogenase | 0 | 0 | 629.6 | 705.5 | 0.00 |
| PGK1 | Glycolysis | Phosphoglycerate kinase | 0 | 0 | 372.1 | 224.3 | 0.00 |
| GPM1 | Glycolysis | Phosphoglycerate mutase | 0 | 0 | 121.7 | 108.4 | 0.00 |