Table 1 Functions of the markers used in TRAC analysis.
From: Monitoring of transcriptional regulation in Pichia pastoris under protein production conditions
| Â | Folding |
CPR5 | Cyclophilin type peptidyl-prolyl cis-trans isomerase (ER resident) |
ERO1 | Pdi oxidase, protein-thiol disulfide exchange; required for oxidative protein folding in the ER |
KAR2 | Binding protein BiP, ATPase involved in protein import into the ER, acts as a chaperone to mediate protein folding in the ER; regulates the unfolded protein response |
PDI1 | Protein disulfide isomerase, multifunctional protein resident in the ER lumen, essential for the formation of disulfide bonds in secretory and cell-surface proteins |
| Â | Glycosylation/ER quality control |
CNE1 | Calnexin; integral membrane ER chaperone involved in folding and quality control of glycoproteins |
DFM1 | ER localized derlin-like family member involved in ER stress and homeostasis; not involved in ERAD or substrate retrotranslocation |
PMT6 | Protein O-mannosyltransferase, transfers mannose from dolichyl phosphate-D-mannose to protein serine/threonine residues of secretory proteins |
ROT2 | Mannosyl-oligosaccharide glucosidase II, required for normal cell wall synthesis |
SEC53 | Phosphomannomutase, involved in synthesis of GDP-mannose and dolichol-phosphate-mannose; required for folding and glycosylation of secretory proteins in the ER lumen |
| Â | Secretion |
BMH2 | 14-3-3 protein, minor isoform; binds proteins and DNA, involved in regulation of many processes including exocytosis and vesicle transport |
SAR1 | GTPase, GTP-binding protein of the ARF family, component of COPII coat of vesicles; required for vesicle formation during ER to Golgi protein transport |
SEC18 | ATPase required for vacuole fusion and for ER to Golgi vesicle mediated transport |
SEC31 | Essential phosphoprotein component (p150) of the COPII coat of secretory pathway vesicles, in complex with Sec13p; required for ER-derived transport vesicle formation |
SEC61 | Essential subunit of Sec61 complex, forms a channel for SRP-dependent protein import and retrograde transport of misfolded proteins out of the ER |
SNC1 | Vesicle membrane receptor protein (v-SNARE) involved in the fusion between Golgi-derived secretory vesicles with the plasma membrane |
SSO2 | Plasma membrane t-SNARE involved in fusion of secretory vesicles at the plasma membrane |
| Â | ERAD (ER-associated protein degradation) |
HRD1 | Ubiquitin-protein ligase (EC 6.3.2.19) required for ERAD of misfolded proteins |
UBC1 | Ubiquitin-conjugating enzyme E2 (EC 6.3.2.19) that mediates selective degradation of short-lived and abnormal proteins; plays a role in vesicle biogenesis and ERAD |
| Â | DNA repair |
RAD16 | Subunit of Nucleotide Excision Repair Factor 4 |
RAD2 | Single-stranded DNA endonuclease, cleaves ssDNA during nucleotide excision repair to excise damaged DNA; subunit of Nucleotide Excision Repair Factor 3 (NEF3) |
RAD54 | DNA-dependent ATPase, stimulates strand exchange by modifying the topology of double-stranded DNA; involved in the recombinational repair of ds breaks in DNA |
| Â | Travers UPR |
ARL3 | GTPase of the Ras superfamily, required to recruit Arl1p to the Golgi |
RIB1 | GTP cyclohydrolase 2 |
VPS17 | Subunit of the membrane-associated retromer complex essential for endosome-to-Golgi retrograde protein transport |
| Â | Core metabolism |
ACS1 | Acetyl-coA synthetase isoform which catalyzes the formation of acetyl-CoA from acetate and CoA |
CIT1 | Citrate synthase, catalyzes the condensation of acetyl coenzyme A and oxaloacetate to form citrate; the rate-limiting enzyme of the TCA cycle |
PFK1 | Phosphofructokinase alpha subunit |
TAL1 | Transaldolase, enzyme in the non-oxidative pentose phosphate pathway; converts sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate to erythrose 4-phosphate and fructose 6-phosphate |
TKL1 | Transketolase, catalyzes conversion of xylulose-5-phosphate and ribose-5-phosphate to sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate in the pentose phosphate pathway; needed for synthesis of aromatic amino acids |
| Â | General stress response |
BFR2 | Essential protein possibly involved in secretion; multicopy suppressor of sensitivity to Brefeldin A, homolog of LTV1 (low temperature viability protein) |
CUP5 | Vacuolar ATP synthase proteolipid subunit (EC 3.6.3.14) required for vacuolar acidification and important for copper and iron metal ion homeostasis |
GCN4 | Transcriptional activator of amino acid biosynthetic genes in response to amino acid starvation |
HEM12 | Uroporphyrinogen decarboxylase, catalyzes the fifth step in the heme biosynthetic pathway |
HOG1 | Mitogen-activated and osmosensing protein kinase, involved in osmoregulation |
IMH1 | Protein involved in vesicular transport, mediates transport between an endosomal compartment and the Golgi, contains a GRIP domain that interacts with activated Arl1p-GTP to localize Imh1p to the Golgi |
KIN2 | Serine/threonine protein kinase involved in regulation of exocytosis; localizes to the cytoplasmic face of the plasma membrane |
MSN2 | Transcriptional activator; activated in stress conditions; binds DNA at stress response elements; response to aging, freezing, osmotic, oxidative stress and glucose starvation |
SNZ2/3 | Member of a stationary phase-induced gene family, involved in pyridoxine and thiamin biosynthesis |
| Â | Thioredoxin |
TRR1 | Cytoplasmic thioredoxin reductase, key regulatory enzyme that determines the redox state of the thioredoxin system, which acts as a disulfide reductase system and protects cells against both oxidative and reductive stress |
TSA1 | Thioredoxin peroxidase, reduces reactive oxygen, nitrogen and sulfur species using thioredoxin as hydrogen donor |
| Â | Amino acid synthesis |
ARG1 | Arginosuccinate synthetase, catalyzes the formation of L-argininosuccinate from citrulline and L-aspartate in the arginine biosynthesis pathway |
ARO4 | 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase, catalyzes the first step in aromatic amino acid biosynthesis |
GLT1 | NAD(+)-dependent glutamate synthase, synthesizes glutamate from glutamine and alpha-ketoglutarate |
| Â | Glutathione |
GLR1 | Glutathione oxidoreductase, converts oxidized glutathione to reduced glutathione |
GSH2 | Glutathione synthetase, catalyzes the ATP-dependent synthesis of glutathione (GSH) from gamma-glutamylcysteine and glycine; induced by oxidative stress and heat shock |
| Â | Cytosolic hsps |
HSP12 | Plasma membrane localized protein that protects membranes from desiccation; induced by heat shock, oxidative stress, osmostress, stationary phase entry, glucose depletion, regulated by the HOG and Ras-Pka pathways |
HSP90/82 | Cytoplasmic chaperone (Hsp90 family), required for the activation of many key cellular regulatory and signaling proteins, like kinases and transcription factors |
SSA4 | Cytoplasmic member of the HSP70 family; highly induced upon stress; plays a role in SRP-dependent cotranslational protein-membrane targeting and translocation |
SSE1/2 | ATPase that is a component of the Hsp90 chaperone complex; binds unfolded proteins; member of the HSP70 family; localized to the cytoplasm |
| Â | Ribosomes |
RPL3 | Protein component of the large (60S) ribosomal subunit |
RPS23B | Ribosomal protein 28 (rp28) of the small (40S) ribosomal subunit |
| Â | Heterologous protein |
LC | Fab light chain |
HC | Fab heavy chain |