Table 1

Differentially expressed genes associated with the plasma membrane and cell wall cellular compartments and functionsa

Process (GO term, no. of genes,bP value)Upregulated genesDownregulated genes
GeneProtein descriptionFold changecGeneProtein descriptionFold change
Fatty acid metabolic process (0006631, 7, 3.58E−02) CAT2 Carnitine acetyl-CoA transferase present in both mitochondria and peroxisomes; transfers activated acetyl groups to carnitine to form acetylcarnitine, which can be shuttled across membranes1.65 ELO1 Elongase I, medium-chain acyl elongase, catalyzes carboxy-terminal elongation of unsaturated C12–C16 fatty acyl-CoAs to C16–C18 fatty acids−2.21
OLE1 Delta(9) fatty acid desaturase, required for monounsaturated fatty acid synthesis and for normal distribution of mitochondria1.90
POT1 3-Ketoacyl-CoA thiolase with broad chain-length specificity; cleaves 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA during beta-oxidation of fatty acids2.84
HTD2 Mitochondrial 3-hydroxyacyl-thioester dehydratase involved in fatty acid biosynthesis; required for respiratory growth and for normal mitochondrial morphology0.98
EHT1 Acyl-coenzyme A:ethanol O-acyltransferase that plays a minor role in medium-chain fatty acid ethyl ester biosynthesis; possesses short-chain esterase activity; localizes to lipid particles and the mitochondrial outer membrane0.92
FAS2 Alpha subunit of fatty acid synthetase, which catalyzes the synthesis of long-chain saturated fatty acids; contains the acyl-carrier protein domain and beta-ketoacyl reductase, beta-ketoacyl synthase and self-pantetheinylation activities1.06
Glycerophospholipid metabolism (0564 [KEGG], 6, 1.42E−02 INO1 Inositol 1-phosphate synthase, involved in synthesis of inositol phosphates and inositol-containing phospholipids; transcription is coregulated with other phospholipid biosynthetic genes by Ino2p and Ino4p, which bind the UASINO DNA element4.10
CLD1 Mitochondrial cardiolipin-specific phospholipase; functions upstream of Taz1p to generate monolyso-cardiolipin; transcription increases upon genotoxic stress; involved in restricting Ty1 transposition; has homology to mammalian CGI-581.89
CHO1 Phosphatidylserine synthase; functions in phospholipid biosynthesis; catalyzes the reaction CDP-diacylglycerol + l-serine = CMP + l-1-phosphatidylserine; transcriptionally repressed by myo-inositol and choline1.15
CKI1 Choline kinase, catalyzing the first step in phosphatidylcholine synthesis via the CDP-choline (Kennedy pathway); exhibits some ethanolamine kinase activity contributing to phosphatidylethanolamine synthesis via the CDP-ethanolamine pathway1.28
CHO2 PEMT, catalyzes the first step in the conversion of phosphatidylethanolamine to phosphatidylcholine during the methylation pathway of phosphatidylcholine biosynthesis1.13
OPI3 Phospholipid methyltransferase (methylene-fatty-acyl-phospholipid synthase); catalyzes the last two steps in phosphatidylcholine biosynthesis0.95
Xenobiotic transporter activity (0042910, 3, 2.18E−02) PDR5 Plasma membrane ABC transporter; multidrug transporter actively regulated by Pdr1p; also involved in steroid transport, cation resistance, and cellular detoxification during exponential growth2.00 PDR12 Plasma membrane ABC transporter; weak-acid-inducible multidrug transporter required for weak organic acid resistance; induced by sorbate and benzoate and regulated by War1p; mutants exhibit sorbate hypersensitivity−1.54
YOR1 Plasma membrane ABC transporter; multidrug transporter mediates export of many different organic anions, including oligomycin; similar to human CFTR1.65
PDR15 Plasma membrane ABC transporter, multidrug transporter, and general stress response factor implicated in cellular detoxification; regulated by Pdr1p, Pdr3p, and Pdr8p; promoter contains a PDR-responsive element3.19
Amino acid and sulfur transmembrane transport (0003333 and 0072348, 9, 0.00136–0.01) AGP3 Low-affinity amino acid permease; may act to supply the cell with amino acids as nitrogen source under nitrogen-poor conditions; transcription is induced under conditions of sulfur limitation; plays a role in regulating Ty1 transposition5.09
MUP1 High-affinity methionine permease; integral membrane protein with 13 putative membrane-spanning regions; also involved in cysteine uptake4.63
MUP3 Low-affinity methionine permease similar to Mup1p1.87
MMP1 High-affinity S-methylmethionine permease; required for utilization of S-methylmethionine as a sulfur source; has similarity to S-adenosylmethionine permease Sam3p2.28
SAM3 High-affinity S-adenosylmethionine permease; required for utilization of S-adenosylmethionine as a sulfur source; has similarity to S-methylmethionine permease Mmp1p2.23
ALP1 Arginine transporter; expression is normally very low, and it is unclear what conditions would induce significant expression1.22
YCT1 High-affinity cysteine-specific transporter with similarity to the Dal5p family of transporters; GFP fusion protein localizes to the endoplasmic reticulum; YCT1 is not an essential gene4.33
SUL2 High-affinity sulfate permease; sulfate uptake is mediated by specific sulfate transporters Sul1p and Sul2p, which control the concn of endogenous activated sulfate intermediates1.47
SUL1 High-affinity sulfate permease of the SulP anion transporter family; sulfate uptake is mediated by specific sulfate transporters Sul1p and Sul2p, which control the concn of endogenous activated sulfate intermediates1.80
Cell wall organization (0005576, 22, 7.86E−02) YGP1 Cell wall-related secretory glycoprotein; induced by nutrient deprivation-associated growth arrest and upon entry into stationary phase; may be involved in adaptation prior to stationary-phase entry; has similarity to Sps100p4.03 HPF1 Haze-protective mannoprotein that reduces the particle size of aggregated proteins in white wines−2.52
PIR3 O-glycosylated covalently bound cell wall protein required for cell wall stability; expression is cell cycle regulated, peaking in M/G1, and also subject to regulation by the cell integrity pathway4.99 GAS3 Low-abundance, possibly inactive member of the GAS family of GPI-containing proteins; putative 1,3-beta-glucanosyltransferase with similarity to other GAS family members; localizes to the cell wall; mRNA induced during sporulation−2.27
FIT2 Mannoprotein that is incorporated into the cell wall via a GPI anchor; involved in the retention of siderophore iron in the cell wall2.01 UTR2 Chitin transglycosylase that functions in the transfer of chitin to beta(1-6) and beta(1-3) glucans in the cell wall; similar to and functionally redundant with Crh1; GPI-anchored protein localized to bud neck−2.56
SUC2 Invertase, sucrose-hydrolyzing enzyme; a secreted, glycosylated form is regulated by glucose repression, and an intracellular, nonglycosylated enzyme is produced constitutively2.63 SUN4 Cell wall protein related to glucanases; possibly involved in cell wall septation; member of the SUN family−2.21
TIP1 Major cell wall mannoprotein with possible lipase activity; transcription is induced by heat and cold shock; member of the Srp1p/Tip1p family of serine-alanine-rich proteins2.06 DSE4 Daughter cell-specific secreted protein with similarity to glucanases; degrades cell wall from the daughter side, causing daughter to separate from mother−1.89
SPI1 GPI-anchored cell wall protein involved in weak acid resistance; basal expression requires Msn2p/Msn4p; expression is induced under conditions of stress and during the diauxic shift; similar to Sed1p4.74 SCW11 Cell wall protein with similarity to glucanases; may play a role in conjugation during mating based on its regulation by Ste12p−2.99
PST1 Cell wall protein that contains a putative GPI attachment site; secreted by regenerating protoplasts; upregulated by activation of the cell integrity pathway, as mediated by Rlm1p; upregulated by cell wall damage via disruption of FKS11.88 DSE2 Daughter cell-specific secreted protein with similarity to glucanases; degrades cell wall from the daughter side, causing daughter to separate from mother; expression is repressed by cAMP−3.16
FIT3 Mannoprotein that is incorporated into the cell wall via a GPI anchor; involved in the retention of siderophore iron in the cell wall1.73 CTS1 Endochitinase; required for cell separation after mitosis; transcriptional activation during the G1 phase of the cell cycle is mediated by transcription factor Ace2p−2.36
HSP150 O-mannosylated heat shock protein that is secreted and covalently attached to the cell wall via beta-1,3-glucan and disulfide bridges; required for cell wall stability; induced by heat shock, oxidative stress, and nitrogen limitation0.97 EGT2 GPI-anchored cell wall endoglucanase required for proper cell separation after cytokinesis; expression is activated by Swi5p and tightly regulated in a cell cycle-dependent manner−2.09
CWP1 Cell wall mannoprotein that localizes specifically to birth scars of daughter cells, linked to a beta-1,3- and beta-1,6-glucan heteropolymer through a phosphodiester bond; required for propionic acid resistance1.07
PRB1 Vacuolar proteinase B (yscB), a serine protease of the subtilisin family; involved in protein degradation in the vacuole and required for full protein degradation during sporulation; activity inhibited by Pbi2p1.30
DIA3 Protein of unknown function involved in invasive and pseudohyphal growth1.35
TDH1 Glyceraldehyde-3-phosphate dehydrogenase, isozyme 1, involved in glycolysis and gluconeogenesis; tetramer that catalyzes the reaction of glyceraldehyde-3-phosphate to 1,3-bis-phosphoglycerate; detected in the cytoplasm and cell wall1.15
  • a Abbreviations: CoA, coenzyme A; PEMT, phosphatidylethanolamine methyltransferase; ABC, ATP binding cassette; CFTR, cystic fibrosis transmembrane receptor; GFP, green fluorescent protein; GPI, glycosylphosphatidylinositol; cAMP, cyclic AMP.

  • b Number of genes associated with the reported Gene Ontology accession number. The total number of differentially expressed genes was 453.

  • c Log2 ratio of expression in treated cells to that in control cells.