Table 2.

List of 111 Candida albicans genes significantly (P ≤0.05) differentially expressed following co-incubation of C. albicans filamentation-induced cells with S. gordonii for 1 h at 37°C in YPT-Glc medium.

ORF	Gene name	Fold change (log2)1	Description2	Total abundance3 (log2)	P- value4
orf19.3537		5.47	Putative sulfiredoxin; biofilm-induced gene; regulated by Tsa1p, Tsa1Bp in minimal medium at 37°C	−3.310	<0.001
orf19.7469	ARG1	4.73	Argininosuccinate synthase; arginine biosynthesis; regulated by Gcn4p, Rim101p; induced by amino acid starvation (3-AT) and benomyl treatment; stationary phase enriched protein; repressed in alkalinizing medium; planktonic growth-induced	−2.256	0.002
orf19.3107		3.65	Ortholog of Candida dubliniensis CD36 : CD36_46490, Pichia stipitis Pignal : PICST_33598, Candida tropicalis MYA-3404 : CTRG_03758 and Candida albicans WO-1 : CAWG_03126	−3.325	<0.001
orf19.4630	CPA1	3.36	Putative carbamoyl-phosphate synthase subunit; alkaline down-regulated; transcription is up-regulated in both intermediate and mature biofilms	−2.646	0.022
orf19.2285		3.22	Increased transcription is observed upon benomyl treatment	−3.729	<0.001
orf19.3221	CPA2	3.17	Putative arginine-specific carbamoylphosphate synthetase; protein enriched in stationary phase yeast cultures; transcription is up-regulated in both intermediate and mature biofilms	−1.987	0.017
orf19.4789		3.13	Has domain(s) with predicted metal ion binding activity	−3.971	0.048
orf19.2165		3.08	Predicted ORF in Assemblies 19, 20 and 21; induced by nitric oxide	−2.750	<0.001
orf19.5610	ARG3	3.07	Putative ornithine carbamoyltransferase; Gcn4p-regulated; Hap43p-induced gene; repressed in alkalinizing medium	−3.019	0.003
orf19.6689	ARG4	3.03	Argininosuccinate lyase, catalyzes the final step in the arginine biosynthesis pathway; alkaline down- regulated; late-stage biofilm-induced	−2.027	0.042
orf19.2593	BIO2	2.95	Putative biotin synthase; transcriptionally up-regulated in high iron; transcription down-regulated by treatment with ciclopiroxolamine; up-regulated in clinical isolates from HIV+ patients with oral candidiasis; Hap43p-repressed	−3.257	<0.001
orf19.176	OPT4	2.76	Oligopeptide transporter; detected at germ tube plasma membrane; transcriptionally induced upon phagocytosis by macrophage; fungal-specific (no human or murine homolog); Hap43p-repressed; merged with orf19.2292 in Assembly 20	−3.061	<0.001
orf19.3770	ARG8	2.73	Putative acetylornithine aminotransferase; Gcn2p-, Gcn4p-regulated; transcription is up-regulated in both intermediate and mature biofilms	−2.480	0.028
orf19.6229	CAT1	2.71	Catalase; resistance to oxidative stress, neutrophils, peroxide; role in virulence; regulated by iron, ciclopirox, fluconazole, carbon source, pH, Rim101p, Ssn6p, Hog1p, Hap43p, Sfu1p, Sef1p, farnesol, core stress response	−1.845	0.010
orf19.6899		2.65	Putative oxidoreductase; mutation confers hypersensitivity to toxic ergosterol analog	−3.382	0.017
orf19.4788	ARG5,6	2.61	Arginine biosynthetic enzyme activities; in S. cerevisiae, processed into distinct polypeptides with acetylglutamate kinase (Arg6p) activity and acetylglutamate-phosphate reductase (Arg5p) activity; Gcn4p regulated; alkaline down-regulated	−2.088	0.003
orf19.3902		2.40	Predicted ORF in Assemblies 19, 20 and 21; decreased transcription is observed upon fluphenazine treatment or in an azole-resistant strain that over-expresses CDR1 and CDR2	−3.078	0.036
orf19.3395		2.36	Predicted membrane transporter, member of the drug:proton antiporter (12 spanner) (DHA1) family, major facilitator superfamily; induced by nitric oxide, oxidative stress, α-pheromone; fungal-specific; Hap43p-repressed	−3.151	0.001
orf19.5094	BUL1	2.31	Protein not essential for viability; macrophage/pseudohyphal-induced; similar to S. cerevisiae Bul1p, which may be involved in selection of substrates for ubiquitination	−2.361	0.001
orf19.4335	TNA1	2.29	Putative nicotinic acid transporter; fungal-specific (no human or murine homolog); detected at germ tube plasma membrane by mass spectrometry; transcriptionally induced upon phagocytosis by macrophage	−3.902	0.042
orf19.7042		2.25	Increased transcription is observed upon benomyl treatment or in an azole-resistant strain that over- expresses MDR1; induced by nitric oxide	−2.697	0.036
orf19.4773	AOX2	2.22	Alternative oxidase; induced by antimycin A, some oxidants; growth- and carbon-source-regulated; one of two isoforms (Aox1p and Aox2p); involved in cyanide-resistant respiratory pathway that is absent from S. cerevisiae; Hap43p-repressed	−2.949	0.014
orf19.4290	TRR1	2.19	Thioredoxin reductase; regulated by Tsa1p/Tsa1Bp, Hap43p; induced by nitric oxide, peroxide; oxidative stress-induced via Cap1p; up-regulated by human neutrophils; fungal-specific (no human/murine homolog); stationary phase enriched protein	−1.407	<0.001
orf19.125	EBP1	2.15	NADPH oxidoreductase; interacts with phenolic substrates such as 17β-estradiol; possible role in estrogen response; induced by oxidative, weak acid stress, nitric oxide, benomyl, GlcNAc; activated by Cap1p, Mnl1p; Sko1p; Hap43p-repressed	−2.803	0.021
orf19.6500	ECM42	2.10	Putative ornithine acetyltransferase; fungal-specific (no human or murine homolog); Gcn2p-, Gcn4p- regulated; clade-specific gene expression; possibly an essential gene, disruptants not obtained by UAU1 method	−2.809	0.009
orf19.113	CIP1	2.07	Possible oxidoreductase; transcription induced by cadmium but not by other heavy metals, heat shock, yeast-hyphal switch, oxidative stress (via Cap1p), or macrophage interaction; stationary phase enriched protein	−3.055	0.019
orf19.4689	PGA57	2.05	Putative GPI-anchored protein; Hap43p-induced gene	−3.348	<0.001
orf19.3131	OYE32	2.04	NAD(P)H oxidoreductase family protein; induced by nitric oxide, amphotericin B, oxidative stress (via Cap1p); increased transcription associated with MDR1 over-expression or benomyl treatment; macrophage-down-regulated protein abundance	−2.821	0.0003
orf19.5741	ALS1	2.01	Adhesin; ALS family of cell-surface glycoproteins; adhesion, virulence roles; immunoprotective; band at hyphal base; amyloid domain; biofilm-induced; Rfg1p, Ssk1p; strain background affects expression; N- term binds fucose-containing glycans	−0.998	<0.001
orf19.3981	MAL31	1.98	Putative high-affinity maltose transporter; transcription is up-regulated in clinical isolates from HIV+ patients with oral candidiasis; alkaline up-regulated	−2.581	0.005
orf19.5908	TEC1	1.97	TEA/ATTS transcription factor; involved in white cell pheromone response, regulates hypha-specific genes, biofilm formation; regulates BCR1; transcription regulated by Cph2 in some conditions; alkaline- and biofilm-induced	−2.348	0.050
orf19.2970	LYS2	1.96	Large subunit of heterodimeric α-aminoadipate reductase; enzyme of lysine biosynthesis; contains predicted binding sites for AMP and α-aminoadipate; feedback inhibited by lysine or thialysine; regulated by Gcn2p and Gcn4p	−1.794	0.030
orf19.4873		1.89	Biofilm-induced gene; expression is regulated upon white-opaque switching	−3.192	0.009
orf19.2724		1.88	Hap43p-repressed gene; late-stage biofilm induced	−2.217	0.007
orf19.4274	PUT1	1.83	Putative proline oxidase; alkaline up-regulated by Rim101p; biofilm-induced	−2.623	0.011
orf19.3803	MNN22	1.57	Putative Golgi α-1,2-mannosyltransferase; regulated by Tsa1p, Tsa1Bp in minimal media at 37°C; Hog1p-induced; induced by nitric oxide; down-regulated in core stress response; planktonic growth- induced gene	−2.198	0.002
orf19.2833	PGA34	1.55	Putative GPI-anchored protein; transcription is repressed in response to α-pheromone in Spider M medium; late-stage biofilm-induced gene; induced in oropharyngeal candidiasis	−3.811	0.035
CaalfMr16	RRNL	1.55	Mitochondrial ribosomal RNA of the large ribosomal subunit	0.022	0.002
orf19.4513		1.53	Protein not essential for viability	−2.036	0.013
orf19.701	CFL11	1.51	Protein similar to ferric reductase Fre10p; flucytosine repressed; possibly adherence-induced; possibly an essential gene, disruptants not obtained by UAU1 method	−3.182	0.008
orf19.2262		1.50	Protein similar to quinone oxidoreductases; increased transcription upon benomyl treatment; induced by nitric oxide; oxidative stress-induced via Cap1p; stationary-phase enriched protein	−2.494	0.002
orf19.276		1.48	Plasma membrane-associated protein; increased transcription is observed in an azole-resistant strain that over-expresses MDR1; Hap43p-repressed gene	−2.959	0.035
orf19.7637	YHB4	1.46	Protein related to flavohemoglobins; not required for wild-type nitric oxide resistance; has predicted globin, FAD-binding, and NAD(P)-binding domains but lacks some conserved residues of flavohemoglobins; Hap43p-repressed gene	−2.416	0.007
orf19.1651		1.44	Ortholog of Candida dubliniensis CD36 : CD36_81960, Candida tropicalis MYA-3404 : CTRG_02378 and Candida albicans WO-1 : CAWG_02525	−3.581	0.045
orf19.2020	HGT6	1.43	Putative high-affinity major facilitator superfamily glucose transporter; 20 family members; 12 probable membrane-spanning segments; core stress response, fluconazole-induced; biofilm-induced; induced in oropharyngeal candidiasis	−1.355	0.033
orf19.7417	TSA1	1.43	TSA/alkyl hydroperoxide peroxidase C (AhPC) family protein; similar to thiol-dependent peroxidases of oxidative stress signaling; antigenic; hyphal surface, nucleus; yeast-form nucleus, cytoplasm; biofilm, phagocytosis, peroxide induced	−1.232	0.034
orf19.7398		1.42	Hap43p-induced gene; decreased expression in response to prostaglandins	−1.227	0.031
orf19.4482	IFI3	1.42	Predicted ORF in Assemblies 19, 20 and 21; constitutive expression independent of MTL or white- opaque status	−2.289	0.003
orf19.85	GPX2	1.42	Similar to glutathione peroxidase; expression greater in high iron; alkaline up-regulated by Rim101p; transcriptionally induced by α-factor or interaction with macrophage; regulated by Efg1p; caspofungin repressed	−2.053	0.006
orf19.2809	CTN3	1.41	Predicted peroxisomal carnitine acetyl transferase; Ura+ deletion strain has no obvious metabolic, hyphal, or virulence defects; transcription induced by macrophage engulfment, hyphal growth, starvation, or non- fermentable carbon sources	−2.913	0.034
orf19.7244		1.40	Putative fumarylacetoacetate hydrolase; biofilm-induced gene; induced by nitric oxide independent of Yhb1p; regulated by Sef1p, Sfu1p, and Hap43p	−2.277	0.043
orf19.6501		1.40	Ortholog of Candida dubliniensis CD36 : CD36_71960, Spathaspora passalidarum NRRL Y-27907 : SPAPADRAFT_63786, Candida tropicalis MYA-3404 : CTRG_05049 and Candida albicans WO-1 : CAWG_05564	−3.862	0.043
orf19.5760	IHD1	1.39	Putative GPI-anchored protein; alkaline up-regulated; greater transcription in hyphal form than yeast form; regulated by Nrg1p, Rfg1p, Tup1p; regulated by Tsa1p, Tsa1Bp in minimal media at 37°C; induced in oropharyngeal candidiasis	−1.770	0.016
orf19.5140		1.38	Ortholog of Candida dubliniensis CD36 : CD36_72790 and Candida albicans WO-1 : CAWG_05648	−3.507	0.017
orf19.1037		1.37	Ortholog of Candida tenuis NRRL Y-1498 : CANTEDRAFT_114303, Candida dubliniensis CD36 : CD36_03460, Pichia stipitis Pignal : PICST_63037 and Spathaspora passalidarum NRRL Y-27907 : SPAPADRAFT_136773	−1.996	0.004
orf19.84	CAN3	1.36	Hap43p-repressed gene; expression is regulated upon white-opaque switching	−2.433	0.010
orf19.4370		1.35	Predicted ORF in Assemblies 19, 20 and 21; induced by nitric oxide; oxidative stress-induced via Cap1p; fungal-specific (no human or murine homolog)	−2.730	0.010
orf19.1363		1.34	Putative protein of unknown function; late-stage biofilm-induced gene; Plc1p-regulated; transcriptionally activated by Mnl1p under weak acid stress	−2.494	0.011
orf19.3142		1.34	Ortholog of C. parapsilosis CDC317 : CPAR2_501210, Candida tenuis NRRL Y-1498 : CANTEDRAFT_97195, Debaryomyces hansenii CBS767 : DEHA2E08800g and Candida dubliniensis CD36 : CD36_46140	−3.388	0.045
orf19.238	CCP1	1.30	Similar to cytochrome-c peroxidase N terminus; negatively regulated by Rim101p or alkaline pH; transcription induced by interaction with macrophage or low iron; oxygen-induced activity; regulated by Sef1p, Sfu1p, and Hap43p	−1.804	0.045
orf19.3122.2		1.29	Ortholog(s) have role in exocytosis, filamentous growth, mRNA export from nucleus, proteasomal ubiquitin-dependent protein catabolic process, proteasome assembly, regulation of cell cycle	−2.692	0.010
orf19.6994	BAT22	1.26	Putative branched chain amino acid aminotransferase; regulated by Gcn4p; induced by farnesol treatment, GlcNAc, amino acid starvation (3-aminotriazole treatment); present in exponential and stationary growth phase yeast cultures	−2.006	0.028
orf19.5762	PGA61	1.26	Putative GPI-anchored protein	−3.810	0.044
orf19.699		1.25	Biofilm-induced gene	−2.757	0.035
orf19.690	PLB2	1.25	Putative phospholipase B; conserved catalytic region; 6 putative N-glycosylation motifs; predicted secretion signal; no GPI anchor predicted; fungal-specific (no human or murine homolog)	−3.009	0.017
orf19.3443	OYE2	1.24	Putative NAPDH dehydrogenase; fungal-specific (no human or murine homolog); induced by nitric oxide	−2.530	0.011
orf19.4653		1.24	Transcriptionally regulated by iron; expression greater in low iron; similar to GPI-linked cell-wall proteins	−2.937	0.034
orf19.3528		1.21	Ortholog(s) have cytosol, nucleus localization	−3.001	0.023
orf19.847	YIM1	1.20	Protein similar to protease of mitochondrial inner membrane; increased transcription is observed upon benomyl treatment; macrophage-down-regulated gene	−2.193	0.019
orf19.1077	ATM1	1.15	Member of MDR subfamily of ABC family; similar to S. cerevisiae ABC transporter, Atm1p; transcriptionally regulated by iron; expression greater in low iron; induced by nitric oxide independent of Yhb1p	−2.405	0.030
CaalfMr17	RRNS	1.13	Mitochondrial ribosomal RNA of the small ribosomal subunit	0.567	0.014
orf19.1701	RKI1	1.11	Ortholog(s) have ribose-5-phosphate isomerase activity, role in pentose-phosphate shunt, pyridoxine biosynthetic process and cytoplasm, nucleus localization	−2.653	0.038
orf19.6947	GTT11	1.10	Glutathione S-transferase, localized to ER; induced in exponentially growing cells, under oxidative stress; induced by nitric oxide	−2.348	0.019
orf19.4147	GLR1	1.03	Glutathione reductase; up-regulated by human neutrophils; oxidative stress-induced regulation via Cap1p; over-expression correlates with multidrug resistance in a cap1 mutant, farnesol induced; stationary phase enriched protein	−1.585	0.029
orf19.7567		1.03	Predicted ORF in Assemblies 19, 20 and 21; transcription is induced in response to α-pheromone in Spider M medium	−2.655	0.043
orf19.2179.2	RPS10	−0.99	Ribosomal protein S10; down-regulated in the presence of human whole blood or polymorphonuclear (PMN) cells	−1.674	0.041
orf19.54	RHD1	−1.01	Putative β-mannosyltransferase, required for the addition of β-mannose to the acid-labile fraction of cell wall phosphopeptidomannan; member of a 9-gene family; transcriptionally regulated on yeast-hyphal and white-opaque switches	−1.871	0.034
orf19.1860.1		−1.03	Has domain(s) with predicted aminopeptidase activity and role in proteolysis	−1.689	0.041
orf19.5839	PDR17	−1.08	Fungal-specific protein (no human or murine homolog); role in sensitivity to fluconazole, specifically	−2.608	0.023
orf19.1264	CFL2	−1.08	Putative oxidoreductase, iron utilization; regulated by Sfu1p, Sef1p, Hap43p, Nrg1p, Tup1p, Rim101p; alkaline, low iron, fluphenazine, ciclopirox olamine, flucytosine, fluconazole, biofilm induced; caspofungin, amphotericin B repressed	−1.512	0.047
orf19.252		−1.09	Putative protein of unknown function; Hap43p-repressed gene; S. cerevisiae ortholog FMP37 localizes to mitochondria	−2.420	0.047
orf19.4151	SPO1	−1.25	Protein similar to phospholipase B; fungal-specific (no human or murine homolog)	−3.236	0.042
orf19.5673	OPT7	−1.25	Putative oligopeptide transporter; possibly transports GSH or related compounds; induced by biofilm formation; Hog1p-induced; expression of OPT6, -7, or -8 does not suppress defect of mutant lacking OPT1-3; fungal-specific; Hap43p-repressed	−2.516	0.049
orf19.1258		−1.30	Putative adhesin-like protein; regulated by Tsa1p, Tsa1Bp in minimal media at 37°C; transcription is induced in response to alpha pheromone in Spider M medium; clade-associated gene expression; Hap43p-induced gene	−2.537	0.030
orf19.5806	ALD5	−1.32	NAD-aldehyde dehydrogenase; decreased expression in fluconazole-resistant isolate, or in hyphae; biofilm induced; fluconazole-down-regulated; protein abundance is affected by URA3 expression in the CAI-4 strain; stationary phase enriched	−0.500	0.014
snR61		−1.40	C/D box small nucleolar RNA (snoRNA)	−3.152	0.045
orf19.5986	THI4	−1.48	Thiamine biosynthetic enzyme precursor; repressed during the mating process; fungal-specific (no human or murine homolog); stationary phase enriched protein; planktonic growth-induced gene	−3.220	0.046
orf19.2619	PHO113	−1.48	Putative constitutive acid phosphatase; transcription is negatively regulated by Rim101p; DTT- extractable; N-glycosylated; possibly an essential gene, disruptants not obtained by UAU1 method	−2.760	0.036
orf19.1608		−1.61	Ortholog(s) have cytosol, nucleus localization	−2.858	0.032
orf19.984	PHO8	−1.66	Putative repressible vacuolar alkaline phosphatase; transcription is positively regulated by Rim101p; regulated by Tsa1p, Tsa1Bp in minimal media at 37°C; possibly adherence-induced	−3.745	0.023
orf19.1263	CFL1	−1.78	Protein similar to ferric reductase Fre10p; possible functional homolog of S. cerevisiae Fre1p (reports differ); transcription is negatively regulated by Sfu1p, copper, amphotericin B, caspofungin; induced by ciclopirox olamine	−1.393	<0.001
orf19.6570	NUP	−1.82	Nucleoside permease; adenosine and guanosine are substrates, whereas cytidine, adenine, guanine, uridine, uracil are not; similar to a nucleoside permease of S. pombe; possibly processed by Kex2p	−2.942	0.006
orf19.3934	CAR1	−1.85	Arginase involved in arginine catabolism; transcription regulated by Nrg1p, Mig1p, and Tup1p; colony morphology-related regulation by Ssn6p; alkaline up-regulated; protein decreased in stationary phase; biofilm-induced; sumoylation target	−1.998	<0.001
tE(UUC)4	tE(UUC)4	−1.92	tRNA-Glu, predicted by tRNAscan-SE; UUC anticodon	−3.276	0.046
orf19.4211	FET3	−1.98	Multicopper oxidase; required for growth in low-iron; required for prostaglandin E2 production; functional homolog of S. cerevisiae Fet3p; ketoconazole, caspofungin, amphotericin B repressed; regulated by Sef1p, Sfu1p, and Hap43p	−0.909	<0.001
RDN18	RDN18	−2.01	18S ribosomal RNA; component of the small (40S) ribosomal subunit; encoded in about 55 copies of the rDNA repeat on Chromosome R	−0.717	0.003
tI(AAU)2	tI(AAU)2	−2.07	tRNA-Ile, predicted by tRNAscan-SE; AAU anticodon	−3.416	0.022
snR57b		−2.12	C/D box small nucleolar RNA (snoRNA)	−3.210	0.005
tE(UUC)6	tE(UUC)6	−2.12	tRNA-Glu, predicted by tRNAscan-SE; UUC anticodon	−3.135	0.050
orf19.3152	AMO2	−2.21	Protein similar to A. niger predicted peroxisomal copper amino oxidase; mutation confers hypersensitivity to toxic ergosterol analog; induced upon biofilm formation	−1.986	0.011
orf19.6520		−2.22	Putative allantoate permease; fungal-specific (no human or murine homolog)	−3.636	0.042
tE(UUC)3	tE(UUC)3	−2.24	tRNA-Glu, predicted by tRNAscan-SE; UUC anticodon	−3.269	0.028
snR69		−2.40	C/D box small nucleolar RNA (snoRNA)	−3.517	0.025
orf19.2652	TEF4	−2.46	Putative translation elongation factor; genes encoding ribosomal subunits, translation factors, and tRNA synthetases are down-regulated upon phagocytosis by murine macrophage	−3.230	0.003
orf19.7071	FGR2	−2.73	Protein similar to phosphate transporters; transposon mutation affects filamentous growth; expression is regulated upon white-opaque switching	−3.598	0.010
snR67		−2.78	C/D box small nucleolar RNA (snoRNA)	−3.508	0.009
orf19.2197		−2.95	Has domain(s) with predicted N,N-dimethylaniline monooxygenase activity, NADP binding, flavin adenine dinucleotide binding activity and role in oxidation-reduction process	−3.766	0.020
orf19.4599	PHO89	−3.70	Putative phosphate permease; expression is regulated upon white-opaque switching; alkaline up- regulated by Rim101p; induced upon biofilm formation; possibly adherence-induced	−2.523	0.001
orf19.1344		−4.12	Predicted ORF in Assemblies 19, 20 and 21; fluconazole-induced	−2.533	0.003
tL(UAA)3	tL(UAA)3	−4.66	tRNA-Leu, predicted by tRNAscan-SE; UAA anticodon	−3.785	0.003
xi-Rb		Inf	Long terminal repeat (LTR); about 387 bp long, 5 copies per genome	−4.329	0.029

¹Positive values, up-regulated; negative values, down-regulated (log₂ ≥1.0 equivalent to ≥ twofold linear change)

²Description details from the CGD (www.candidagenome.org)

³Abundance reads represent the fractional expression of all targets in the genome

⁴P-values were calculated from DESeq and adjusted P-values ≤ 0.050 were considered to be significant