Table 2.
Transcriptional and post-transcriptional regulation of genes related to the methanol metabolism, the pentose phosphate pathway, and the glyoxylate cycle. Presence of the corresponding protein in the peroxisomal fraction (of methanol- or glucose-grown P. pastoris) is indicated as well as prediction of peroxisomal targeting based on the C-terminal amino residues of the proteins using the PTS1 predictor [43]
| Pathway | Short name a | ORF name b | Description | Transcript (methanol/glycerol vs glucose) c | Protein (methanol/glycerol vs glucose) d | Presence in the peroxisome fraction (methanol) e | Presence in the peroxisome fraction (glucose) e | Prediction of peroxisomal targeting f | Last 12 C-terminal amino acid residues |
|---|---|---|---|---|---|---|---|---|---|
| Methanol assimilation | AOX1 | PP7435_Chr4-0130/ PAS_chr4_0821 | Alcohol oxidase | up | n.i. | yes | no | yes | LGTYEKTGLARF |
| AOX2 | PP7435_Chr4-0863/ PAS_chr4_0152 | Alcohol oxidase | up | up | n.i. | n.i. | yes | LGTYEKTGLARF | |
| DAS1 | PP7435_Chr3-0352/ PAS_chr3_0832 | Dihydroxyacetone synthase variant 1 | up | up | yes | no | no | HDLKGKPKHDKL | |
| DAS2 | PP7435_Chr3-0350/ PAS_chr3_0834 | Dihydroxyacetone synthase variant 2 | up | up | yes | no | no | TDLKGKPKHDKL | |
| DAK2 | PP7435_Chr3-0343/ PAS_chr3_0841 | Dihydroxyacetone kinase | up | up | yes | no | Twilight zone | ITDAYFKSETKL | |
| FBA1-2 | PP7435_Chr1-0639/ PAS_chr1-1_0319 | Fructose-1,6-bisphosphate aldolase | up | up | yes | no | yes | HAAGTFKSESKL | |
| FBP1 | PP7435_Chr3-0309/ PAS_chr3_0868 | Fructose-1,6-bisphosphatase | up | up | yes | no | no | LTKKIKIQSVNL | |
| SHB17 | PP7435_Chr2-0185/ PAS_chr2-2_0177 | Sedoheptulose-1,7-bisphosphatase | up | up | yes | no | no | VVPVEEAEADRA | |
| RKI1-2 | PAS_chr4_0212 | Ribose-5-phosphate ketol-isomerase | up | up | yes | no | yes | ITSLSVSVPARL | |
| TAL1-2 | PAS_chr2-2_0338 | Transaldolase | up | up | yes | no | yes | VPSLFRRVLSKL | |
| RPE1-2 | PP7435_Chr3-0772 | D-ribulose-5-phosphate 3-epimerase | up | n.i. | n.i. | n.i. | Twilight zone | QKKAKAKPKPNL | |
| Peroxisomal protein | CTA1 | PP7435_Chr2-0137/ PAS_chr2-2_0131 | Catalase A | up | n.q. | yes | no | yes | QLSPRGDSAARL |
| PMP20 | PP7435_Chr1-1351/ PAS_chr1-4_0547 | Peroxiredoxin | up | up | yes | no | yes | KHSSADRVLAKL | |
| Methanol dissimilation | FLD | PP7435_Chr3-0140/ PAS_chr3_1028 | Bifunctional alcohol dehydrogenase and formaldehyde dehydrogenase | up | n.q. | no | no | no | AGNCIRAVITMH |
| FGH1 | PP7435_Chr3-0312/ PAS_chr3_0867 | Esterase that can function as an S-formylglutathione hydrolase | up | n.q. | no | no | no | HAAHHAKYLGLN | |
| FDH1 | PP7435_Chr3-0238/ PAS_chr3_0932 | NAD(+)-dependent formate dehydrogenase | up | up | yes | no | no | KTKAYGNDKKVA | |
| Pentose phosphate pathway oxidative branch | ZWF1 | PP7435_Chr2-0993/ PAS_chr2-1_0308 | Glucose-6-phosphate dehydrogenase | not changed | not changed | no | no | no | WPVTRPDVLHKM |
| SOL3 | PP7435_Chr3-0037/ PAS_chr3_1126 | 6-phosphogluconolactonase | not changed | n.q. | no | no | Twilight zone | ALSGVSVSTSKY | |
| GND2 | PP7435_Chr3-0944/ PAS_chr3_0277 | 6-phosphogluconate dehydrogenase | not changed | not changed | yes | yes | no | KGGNVSASTYDA | |
| Pentose phosphate pathway non-oxidative branch | RPE1-1 | PP7435_Chr3-0771 | D-ribulose-5-phosphate 3-epimerase | n.a. | up | n.i. | n.i. | no | QDSLKKKGLLDE |
| RKI1-1 | PAS_chr4_0213 | Ribose-5-phosphate ketol-isomerase | up | n.q. | n.i. | n.i. | no | GNEDGSVATLTL | |
| TKL1 | PP7435_Chr1-0919/ PAS_chr1-4_0150 | Transketolase | not changed | not changed | no | no | no | SPLNKAFESVHA | |
| TAL1-1 | PP7435_Chr2-0357/ PAS_chr2-2_0337 | Transaldolase | not changed | not changed | yes | yes | no | TLLNLLKEKVQA | |
| Glyoxylate cycle | CIT1 | PP7435_Chr1-0426/ PAS_chr1-1_0475 | Citrate synthase | not changed | n.q. | yes | no | no | EKYIELVKGLGK |
| ACO1 | PP7435_Chr1-0105/ PAS_chr1-3_0104 | Aconitase | not changed | not changed | yes | no | no | ALNNMAAVKASK | |
| ACO2 | PP7435_Chr3-0541/ PAS_chr3_0659 | Aconitase | not changed | n.q. | no | no | no | INYIGRLKREQQ | |
| ICL1 | PP7435_Chr1-1123/ PAS_chr1-4_0338 | Isocitrate lyase | not changed | n.q. | no | no | no | GAGVTEDQFKDH | |
| MLS1 | PP7435_Chr4-0820/ PAS_chr4_0191 | Malate synthase | not changed | up | n.i. | n.i. | no | LESSPVDLDSLK | |
| MDH3 | PP7435_Chr4-0136/ PAS_chr4_0815 | Peroxisomal malate dehydrogenase | up | up | yes | no | no | NIAKGTAFIAGN | |
| MLS2 | PP7435_Chr1-1255/ PAS_chr1-4_0459 | Malate synthase | up | n.i. | n.i. | n.i. | Twilight zone | STIPINIHQQKL | |
| AAT1 | PP7435_Chr1-0511/ PAS_chr1-1_0200 | Aspartate aminotransferase | up | n.q. | yes | no | no | YLANAIHEVTTN | |
| AAT2 | PAS_chr4_0974 | Aspartate aminotransferase | not changed | n.q. | yes | no | no | RVAAAIDQVVRV | |
| ODC1 | PP7435_Chr3-1205/ PAS_chr3_0040 | Oxoglutarate-malate shuttle | up | up | yes | no | no | FTTCMDFFRTLQ | |
| OSM1 | PP7435_Chr3-1001/ PAS_chr3_0225 | Fumarate reductase | up | n.i. | n.i. | n.i. | Twilight zone | YLLKSLSNYHKL |
aIn some cases, P. pastoris has two homologs of the same S. cerevisiae gene (i.e. TAL1-1 and TAL1-2)
bORF names of two P. pastoris strains: P. pastoris CBS7435/P. pastoris GS115 (the sequences are identical in the two strains; however, in a few cases only the ORF name of one strain is reported because the sequence of the other strain is not or wrongly annotated.)
c n.a. not available on microarray
d n.i. not identified; n.q. identified but could not be quantified
e n.i. not identified in the peroxisome fraction
f Prediction of peroxisomal targeting with PTS1 predictor [43] (classification according to [42]: yes: predicted; twilight zone: questionable but with reasonable estimated false-positive rate; no: not predicted)