Table 2.
P. pastoris proteins identified in culture supernatants of the glycerol batch (B1), glycerol fed‐batch (G2) and methanol (M3‐M8) or glucose (F3‐F8) fed‐batch (1, 27, 67 h after changing the carbon source). Detected proteins are indicated with ‘1’.
| Short Name P. pastoris | Core proteome | Accession | Glycerol batch/fed‐batch | Methanol fed‐batch | Glucose fed‐batch | Description | Predicted protein parameters | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| B1 | G2 | M3 | M5 | M8 | F3 | F5 | F8 | Protein function | MW/pIa | Signal peptideb | GPI anchorc | Localizationd | |||
| Acs2 | F2QWI5 | 1 | 1 | 1 | 1 | 1 | Acetyl‐coA synthetase isoform which is the nuclear source of acetyl‐coA for histone acetylation | 74.0/5.5 | N | cyto: 14.5, cyto_nucl: 1 | |||||
| Atp2 | F2QR41 | 1 | Beta subunit of the F1 sector of mitochondrial F1F ATP synthase | 54.0/5.2 | N | mito: 27 | |||||||||
| Bgl2 | core | F2QPL8 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Endo‐beta‐1,3‐glucanase, major protein of the cell wall, involved in cell wall maintenance | 31.9/4.0 | Y | Highly probable | extr: 25, mito: 1 |
| Cda2 | F2QMB5 | 1 | 1 | 1 | Chitin deacetylase, involved in the biosynthesis of the ascospore wall component chitosan | 32.4/5.1 | Y | Highly probable | extr: 17, cyto_nucl: 3.5 | ||||||
| Cld1‐2 | F2QTL2 | 1 | 1 | 1 | 1 | 1 | 1 | Mitochondrial cardiolipin‐specific phospholipase | 48.7/7.7 | N | mito: 2.5, cyto_mito: 12.5 | ||||
| CpB | product | PDKT_3 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Porcine pancreatic carboxypeptidase | 34.5/6.0 | n.d. | n.d. | n.d. |
| Cpr5 | F2QNY8 | 1 | 1 | 1 | 1 | Peptidyl‐prolyl cis‐trans isomerase of the ER | 22.2/4.7 | Y | Highly probable | E.R.: 13, extr: 7 | |||||
| Crh1 | F2QYV4 | 1 | 1 | 1 | 1 | 1 | Chitin transglycosylase that functions in the transfer of chitin to beta(1‐6) and beta(1‐3) glucans in the cell wall | 47.4/4.3 | Y | Highly probable | extr: 21, mito: 2 | ||||
| Cts1 | core | F2QUR1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Endochitinase, required for cell separation after mitosis | 71.7/4.1 | Y | extr: 27 | |
| Dse4 | core | F2QME5 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Daughter cell‐specific secreted protein with similarity to glucanases | 17.2/4.7 | Y | Highly probable | extr: 24, cyto: 2 |
| Epx1 | core | F2QXH5 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Pichia pastoris extracellular protein X1 | 3.0/5.1 | Y | extr: 27 | |
| Exg1 | core | F2QSZ6 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Major exo‐1,3‐beta‐glucanase of the cell wall, involved in cell wall beta‐glucan assembly | 47.8/4.5 | Y | extr: 2, golg: 3 | |
| Fdh1 | F2QUY2 | 1 | NAD(+)‐dependent formate dehydrogenase | 4.3/6.6 | N | cyto: 24, mito: 2 | |||||||||
| Flo11 | F2QRD4 | 1 | 1 | 1 | 1 | GPI‐anchored cell surface glycoprotein (flocculin) | 83.9/3.7 | Y | Highly probable | extr: 11, mito: 7 | |||||
| Flo5‐1 | core | F2QQ27 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Lectin‐like protein (flocculin) involved in flocculation | 48.4/4.3 | Y | extr: 24, E.R.: 2 | |
| Flo5‐2 | F2QXP | 1 | 1 | 1 | 1 | 1 | 1 | Lectin‐like cell wall protein (flocculin) involved in flocculation | 76.0/4.3 | Y | Highly probable | mito: 1, plas: 8, extr: 5 | |||
| Fpr2 | F2QUB4 | 1 | 1 | 1 | 1 | 1 | ER peptidyl‐prolyl cis‐trans isomerase (PPIase) | 12.9/4.8 | Y | extr: 21, golg: 3 | |||||
| Gas1‐1 | core | F2QNF8 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Beta‐1,3‐glucanosyltransferase, required for cell wall assembly | 55.3/4.0 | Y | Highly probable | extr: 22, plas: 3, mito: 1 |
| Gas3 | F2QQJ2 | 1 | 1 | 1 | 1 | 1 | Putative 1,3‐beta‐glucanosyltransferase | 53.8/4.1 | Y | Highly probable | extr: 13, E.R.: 6 | ||||
| Gcs1 | F2QUT9 | 1 | 1 | 1 | 1 | 1 | 1 | ADP‐ribosylation factor GTPase activating protein (ARF GAP), involved in ER‐Golgi transport | 4.0/5.8 | N | nucl: 15.5, cyto_nucl: 11.5 | ||||
| Hsp12 | F2QYN4 | 1 | 1 | 1 | 1 | 1 | Plasma membrane protein involved in maintaining membrane organization in stress conditions | 12.5/4.8 | N | nucl: 14, cyto_nucl: 9.8 | |||||
| Hyp2 | F2QUL4 | 1 | 1 | Translation elongation factor eIF‐5A | 17.0/5.0 | N | cyto: 14.5, cyto_nucl: 14.5 | ||||||||
| Kar2 | core | F2QTW5 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Molecular chaperone of the endoplasmic reticulum lumen | 7.8/4.7 | Y | extr: 15, E.R.: 9 | |
| Lhs1 | F2QLU | 1 | 1 | 1 | 1 | Molecular chaperone of the endoplasmic reticulum lumen | 99.5/5.0 | Y | extr: 1, E.R.: 8 | ||||||
| Msb2 | F2QNL1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Mucin family member involved in signalling | 86.5/3.8 | Y | Highly probable | extr: 1, cyto: 8 | ||
| Pdi1 | core | F2QY5 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Protein disulphide isomerase, multifunctional protein of ER lumen | 55.4/4.6 | Y | cyto: 11, E.R.: 7 | |
| Pep4 | core | F2QUG8 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Vacuolar aspartyl protease (proteinase A) | 42.0/4.7 | Y | extr: 13, cyto: 8.5 | |
| Pir1 | core | F2QS11 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Cell wall protein with internal repeats | 27.5/4.2 | Y | extr: 22, cyto: 3.5 | |
| Pir2 | core | F2QZM1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Cell wall protein with internal repeats | 31.7/4.4 | Y | extr: 27 | |
| PP7435_Chr2‐752 | core | F2QSQ9 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Hypothetical protein not conserved (domain: syndecan) | 23.7/6.0 | Y | Highly probable | extr: 25, mito: 1 |
| PP7435_Chr3‐1213 | core | F2QXM5 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Hypothetical protein not conserved (domain: Bacterial adhesins) | 6.9/4.3 | Y | Highly probable | extr: 18, E.R.: 3 |
| PP7435_Chr3‐1225 | F2QXN7 | 1 | 1 | 1 | 1 | Hypothetical protein conserved (domain: PASTA, Colicin E3 immunity protein) | 23.2/4.1 | Y | extr: 26 | ||||||
| PP7435_Chr4‐69 | F2QZL9 | 1 | Protein with similarity to YMR244W (Putative protein of unknown function) | 36.6/4.9 | Y | Highly probable | extr: 24, mito: 1 | ||||||||
| Pry2 | core | F2QNB4 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Putative sterol binding protein involved in the export of acetylated sterols | 29.3/4.1 | Y | Highly probable | extr: 22, mito: 2 |
| Pst1 | F2QR22 | 1 | Cell wall protein that contains a putative GPI‐attachment site, secreted by regenerating protoplasts | 41.5/3.8 | Y | Highly probable | extr: 26 | ||||||||
| Rce3 | core | F2QYL8 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Endo‐glucanase similar to R. oryzae RCE3 with 3 fungal cellulose binding domains | 62.0/4.0 | Y | extr: 26 | |
| Rpl4A | F2QSW4 | 1 | Ubiquitin‐ribosomal 6S subunit protein L4A fusion protein | 14.6/9.9 | N | nucl: 18, cyto_nucl: 16 | |||||||||
| Rps17B | F2QS1 | 1 | 1 | 1 | Ribosomal protein 51 (rp51) of the small (4s) subunit | 15.7/1.3 | N | mito: 16, nucl: 5 | |||||||
| Scw1 | core | F2QNG1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Cell wall protein with similarity to glucanases | 34.0/4.9 | Y | Highly probable | extr: 24, cyto: 2 |
| Scw11 | core | F2QU52 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Cell wall protein with similarity to glucanases | 46.7/4.4 | Y | extr: 22, cyto: 2.5 | |
| Sod1 | F2QY66 | 1 | 1 | 1 | 1 | 1 | 1 | Cytosolic copper‐zinc superoxide dismutase | 15.7/5.9 | N | cyto: 23.5, cyto_nucl: 14 | ||||
| Ssp12 | F2RE9 | 1 | 1 | 1 | 1 | 1 | Protein of unknown function | 25.7/4.8 | Y | extr: 11, E.R.: 4 | |||||
| Sun4 | core | F2QQT7 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Cell wall protein related to glucanases, possibly involved in cell wall septation, member of the SUN family | 43.2/4.3 | Y | extr: 26 | |
| Tdh3 | F2QT12 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Glyceraldehyde‐3‐phosphate dehydrogenase | 35.6/6.2 | N | pero: 16, cyto: 8 | |||
| Tef2 | F2QQG8 | 1 | 1 | 1 | 1 | Translational elongation factor EF‐1 alpha | 5.1/9.1 | N | cyto: 26.5, cyto_nucl: 14 | ||||||
| Tos1 | core | F2QQJ | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Covalently‐bound cell wall protein of unknown function | 43.1/5.0 | Y | extr: 26 | |
| Ubp11 | F2QNR5 | 1 | 1 | 1 | Ubiquitin‐specific protease | 18.8/8.0 | N | nucl: 2, cyto: 5 | |||||||
| Uth1 | core | F2RE1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Cell wall biogenesis involved protein | 34.0/4.8 | Y | extr: 26 | |
| Utr2 | F2QP19 | 1 | 1 | 1 | 1 | 1 | Chitin transglycosylase that functions in the transfer of chitin to beta(1‐6) and beta(1‐3) glucans in the cell wall | 48.8/3.9 | Y | Highly probable | extr: 23, golg: 2 | ||||
| Vps72 | F2QX78 | 1 | 1 | 1 | 1 | 1 | 1 | Htz1p‐binding component of the SWR1 complex, required for vacuolar protein sorting | 84.0/4.9 | N | nucl: 21, cyto: 5 | ||||
| Ynk1 | F2QQT | 1 | 1 | Nucleoside diphosphate kinase | 17.0/6.1 | N | cyto: 19.5, cyto_nucl: 13.3 | ||||||||
| Yps1‐1 | core | F2QYS7 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | Aspartic protease, member of the yapsin family of proteases | 6.5/4.4 | Y | extr: 24, mito: 1 | |
a
Molecular weight/isoelectric point predicted by ExPASy ProtParam.
b
Predicted by Signal P4.1 – Y, signal peptide predicted, N, not predicted
c
Predicted by PredGPI.
d
Predicted by WolF PSORT.