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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)
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ISSN: 1741-7007

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