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Table 1 Functions of the markers used in TRAC analysis.

From: Monitoring of transcriptional regulation in Pichia pastoris under protein production conditions

  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  Ribosomes
RPL3 Protein component of the large (60S) ribosomal subunit
RPS23B Ribosomal protein 28 (rp28) of the small (40S) ribosomal subunit
  Heterologous protein
LC Fab light chain
HC Fab heavy chain
  1. Functions of the S. cerevisiae homologs of the P. pastoris gene markers (adapted from Saccharomyces Genome Database [20]) assigned in functional categories.