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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]

From: Systems-level organization of yeast methylotrophic lifestyle

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
  1. aIn some cases, P. pastoris has two homologs of the same S. cerevisiae gene (i.e. TAL1-1 and TAL1-2)
  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.)
  3. c n.a. not available on microarray
  4. d n.i. not identified; n.q. identified but could not be quantified
  5. e n.i. not identified in the peroxisome fraction
  6. 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)