Table 1.

Differentially expressed genes associated with the plasma membrane and cell wall cellular compartments and functions^a

Process (GO term, no. of genes,b P value)	Upregulated genes			Downregulated genes
	Gene	Protein description	Fold changec	Gene	Protein description	Fold 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 membranes	1.65	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 mitochondria	1.90
	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 acids	2.84
	HTD2	Mitochondrial 3-hydroxyacyl-thioester dehydratase involved in fatty acid biosynthesis; required for respiratory growth and for normal mitochondrial morphology	0.98
	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 membrane	0.92
	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 activities	1.06
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 element	4.10
	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-58	1.89
	CHO1	Phosphatidylserine synthase; functions in phospholipid biosynthesis; catalyzes the reaction CDP-diacylglycerol + l-serine = CMP + l-1-phosphatidylserine; transcriptionally repressed by myo-inositol and choline	1.15
	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 pathway	1.28
	CHO2	PEMT, catalyzes the first step in the conversion of phosphatidylethanolamine to phosphatidylcholine during the methylation pathway of phosphatidylcholine biosynthesis	1.13
	OPI3	Phospholipid methyltransferase (methylene-fatty-acyl-phospholipid synthase); catalyzes the last two steps in phosphatidylcholine biosynthesis	0.95
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 growth	2.00	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 CFTR	1.65
	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 element	3.19
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 transposition	5.09
	MUP1	High-affinity methionine permease; integral membrane protein with 13 putative membrane-spanning regions; also involved in cysteine uptake	4.63
	MUP3	Low-affinity methionine permease similar to Mup1p	1.87
	MMP1	High-affinity S-methylmethionine permease; required for utilization of S-methylmethionine as a sulfur source; has similarity to S-adenosylmethionine permease Sam3p	2.28
	SAM3	High-affinity S-adenosylmethionine permease; required for utilization of S-adenosylmethionine as a sulfur source; has similarity to S-methylmethionine permease Mmp1p	2.23
	ALP1	Arginine transporter; expression is normally very low, and it is unclear what conditions would induce significant expression	1.22
	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 gene	4.33
	SUL2	High-affinity sulfate permease; sulfate uptake is mediated by specific sulfate transporters Sul1p and Sul2p, which control the concn of endogenous activated sulfate intermediates	1.47
	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 intermediates	1.80
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 Sps100p	4.03	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 pathway	4.99	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 wall	2.01	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 constitutively	2.63	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 proteins	2.06	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 Sed1p	4.74	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 FKS1	1.88	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 wall	1.73	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 limitation	0.97	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 resistance	1.07
	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 Pbi2p	1.30
	DIA3	Protein of unknown function involved in invasive and pseudohyphal growth	1.35
	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 wall	1.15

^aAbbreviations: CoA, coenzyme A; PEMT, phosphatidylethanolamine methyltransferase; ABC, ATP binding cassette; CFTR, cystic fibrosis transmembrane receptor; GFP, green fluorescent protein; GPI, glycosylphosphatidylinositol; cAMP, cyclic AMP.

^bNumber of genes associated with the reported Gene Ontology accession number. The total number of differentially expressed genes was 453.

^cLog₂ ratio of expression in treated cells to that in control cells.