Table 1.
Changes in the gene expression of C. neoformans H99 cells exposed to FLC
| BROAD ID (CNAG_*****) | C. n. gene name | S. c. gene name | Description | Fold change |
|---|---|---|---|---|
| Ergosterol biosynthesis | ||||
| 04804 | SRE1 | Sterol regulatory element-binding protein 1 | + 4.04 | |
| 01737 | ERG25 | C-4 methyl sterol oxidase | + 3.95 | |
| 00854 | ERG2 | C-8 sterol isomerase | + 3.47 | |
| 02896 | ERG13 | Hydroxymethylglutaryl-CoA synthase | + 3.03 | |
| 06644 | ERG5 | C-22 sterol desaturase | + 2.50 | |
| 00040 | ERG11 | ERG11 | Lanosterol 14 alpha-demethylase | + 2.47 |
| 06829 | ERG1 | Squalene monooxygenase | + 2.37 | |
| 00519 | ERG3 | C-5 sterol desaturase | + 2.21 | |
| 01129 | ERG7 | Lanosterol synthase | + 2.09 | |
| Transport | ||||
| 04632 | FUR4 | Uracil permease | + 5.87 | |
| 07448 | DUR3 | Urea transporter | + 4.78 | |
| 04758 | MEP2/AMP2 | Ammonium transporter | + 3.78 | |
| 06652 | DAL5 | Allantoate permease | + 2.83 | |
| 01742 | AQY1 | Water channel | + 2.73 | |
| 07902 | CAN1 | Amino acid transporter | + 2.52 | |
| 01960 | YMR279C | Efflux protein EncT | + 2.47 | |
| 06338 | PDR15 | ABC transporter PMR5 | + 2.37 | |
| 04898 | ATR1 | MFS transporter | + 2.37 | |
| 00284 | YOR378W | Efflux protein EncT | + 2.36 | |
| 00097 | ITR1 | ITR1 | + 2.26 | |
| 00895 | ZRT1 | Low-affinity zinc ion transporter | + 2.20 | |
| 04210 | MPH2 | Sugar transporter | + 2.15 | |
| 04617 | OPT2 | Small oligopeptide transporter | + 2.11 | |
| 05592 | PMR1 | Calcium-transporting ATPase | + 2.06 | |
| 01059 | YBR241C | Vacuolar membrane protein | + 2.02 | |
| 00904 | AZR1 | Aflatoxin efflux pump AFLT | - 2.10 | |
| 01769 | AGC1 | Mitochondrial inner membrane protein | - 2.16 | |
| 04142 | FEN2 | Tartrate transporter | - 2.17 | |
| 04567 | TPO2 | Drug transporter | - 2.22 | |
| 05387 | HXT5 | Galactose transporter | - 2.28 | |
| 02355 | YEA4 | UDP-N-acetylglucosamine transporter | - 2.30 | |
| 05994 | FLR1 | Multidrug transporter | - 2.35 | |
| 02733 | STL1 | Hexose transport-related protein | - 2.46 | |
| 03794 | YBR287W | Endoplasmic reticulum protein | - 2.58 | |
| 00815 | SIT1 | Siderochrome-iron (Ferrioxamine) uptake transporter | - 2.92 | |
| 01354 | TNA1 | Transporter | - 3.39 | |
| 02104 | SFH5 | SFH5 | Phosphatidylinositol transfer protein SFH5 | - 4.54 |
| 07695 | UGA4 | Gamma-aminobutyric acid transporter | - 5.16 | |
| 00749 | YIL166C | Transporter | - 5.65 | |
| 02083 | ARN2 | Siderochrome-iron transporter | - 9.48 | |
| Cell wall maintenance | ||||
| 02217 | CHS7 | Chitin synthase 7 | + 3.62 | |
| 06336 | BGL2 | Glucan 1,3 beta-glucosidase protein | + 2.61 | |
| 03326 | CHS2 | Chitin synthase 2, CHS2 | + 2.20 | |
| 01239 | CDA3 | CDA2 | Chitin deacetylase | - 4.35 |
| Capsule biosynthesis | ||||
| 03644 | CAS3 | CAS3p | + 12.16 | |
| 01489 | CAS9 | YJL218W | Putative O-acetyl transferase | - 3.84 |
| Lipid and fatty acid metabolism | ||||
| 06085 | PLB1 | PLB1 | Phospholipase B | + 2.18 |
| 06623 | MIOX | Myo-inositol oxygenase | + 2.12 | |
| 03128 | ECM38 | Lincomycin-condensing protein lmbA | - 2.01 | |
| 00424 | PCT1 | Choline-phosphate cytidylyltransferase | - 2.02 | |
| 05042 | CAT2 | Carnitine acetyltransferase | - 2.10 | |
| 02000 | FOX2 | Short-chain dehydrogenase | - 2.95 | |
| 00834 | PSD2 | Phosphatidylserine decarboxylase | - 3.10 | |
| 02968 | PLC2 | Phospholipase C-2 | - 4.11 | |
| Cell stress | ||||
| 03400 | GRE2 | Oxidoreductase | + 3.54 | |
| 05256 | CTA1 | Catalase 2 | + 2.81 | |
| 02440 | HSC82 | Cation-transporting ATPase | + 2.54 | |
| 01750 | HSP70 | SSA1 | Heat shock protein 70 | + 2.48 |
| 06917 | TSA3 | PRX1 | Thiol-specific antioxidant protein 3 | + 2.09 |
| 03185 | LOT6 | Low temperature-responsive protein | + 2.05 | |
| 04622 | SNG1 | Response to drug-related protein | - 2.17 | |
| 00575 | CTT1 | Catalase | - 2.21 | |
| 01464 | FHB1 | YHB1 | Flavo-haemoglobin | - 2.32 |
| Amino acid metabolism | ||||
| 02284 | PDA1 | Branched-chain alpha-keto acid dehydrogenase E1-alpha subunit | + 2.42 | |
| 04862 | GLT1 | Glutamate synthase (NADH) | + 2.39 | |
| 04017 | MXR2 | Protein-methionine-R-oxide reductase | + 2.32 | |
| 01231 | CAR1 | Arginase | + 2.27 | |
| 03828 | ARO8 | Aromatic amino acid aminotransferase I | + 2.26 | |
| 06540 | ILV3 | Dihydroxy-acid dehydratase | + 2.18 | |
| 00247 | LYS9 | Saccharopine dehydrogenase (NADP+, L-glutamate-forming) | + 2.02 | |
| 02270 | MET2 | Homoserine O-acetyltransferase | - 2.11 | |
| 01076 | UGA1 | 4-aminobutyrate transaminase | - 2.18 | |
| 00237 | LEU1 | 3-isopropylmalate dehydratase | - 2.27 | |
| 01264 | LYS12 | Isocitrate dehydrogenase | - 2.31 | |
| 00879 | GDH2 | Glutamate dehydrogenase | - 2.33 | |
| 04467 | UGA2 | Succinate-semialdehyde dehydrogenase (NAD(P)+) | - 2.83 | |
| 02851 | GLY1 | Threonine aldolase | - 3.04 | |
| 02049 | PUT1 | Proline dehydrogenase | - 5.74 | |
| 05602 | PUT2 | 1-pyrroline-5-carboxylate dehydrogenase | - 6.65 | |
| Carbohydrate metabolism | ||||
| 06374 | MAE1 | Malic enzyme | + 6.04 | |
| 02225 | CELC | EXG1 | Cellulase | + 3.99 |
| 02552 | TKL1 | Transketolase | + 3.28 | |
| 04025 | TAL1 | Transaldolase | + 3.00 | |
| 00696 | AMS1 | Alpha-mannosidase | + 2.52 | |
| 05913 | MAL12 | Alpha-glucosidase | + 2.34 | |
| 05113 | ALD4 | Aldehyde dehydrogenase (ALDDH) | + 2.11 | |
| 05264 | YJL216C | Alpha-amylase AmyA | + 2.08 | |
| 03946 | GAL1 | Galactokinase | - 2.16 | |
| 07752 | GLF | UDP-galactopyranose mutase | - 2.23 | |
| 04659 | PDC1 | Pyruvate decarboxylase | - 2.33 | |
| 06924 | SUC2 | Beta-fructofuranosidase | - 2.57 | |
| 00269 | SOR1 | Sorbitol dehydrogenase | - 2.62 | |
| 00393 | GLC3 | GLC3 | 1,4-alpha-glucan-branching enzyme | - 2.93 |
| 07745 | MPD1 | ADH3 | Mannitol-1-phosphate dehydrogenase | - 3.54 |
| 04217 | PCK1 | Phosphoenolpyruvate carboxykinase | - 8.67 | |
| 04621 | GSY1 | Glycogen (Starch) synthase | - 11.00 | |
| 04523 | TDH3 | Glyceraldehyde-3-phosphate dehydrogenase | - 11.45 | |
| Protein biosynthesis, modification, transport, and degradation | ||||
| 02389 | YPK1 | AGC-group protein kinase | + 3.04 | |
| 02531 | FUS3 | Mitogen-activated protein kinase CPK1 | + 2.91 | |
| 03176 | ERO1 | Endoplasmic oxidoreductin 1 | + 2.36 | |
| 05932 | CPR6 | CPR6 | Peptidyl-prolyl cis-trans isomerase D | + 2.35 |
| 01861 | NAS6 | Proteolysis and peptidolysis-related protein | + 2.35 | |
| 04635 | PEP4 | Endopeptidase | + 2.31 | |
| 06872 | YKL215C | 5-oxoprolinase | + 2.27 | |
| 05005 | ATG1 | ATG1 | Serine/threonine-protein kinase ATG1 | + 2.20 |
| 00919 | KEX1 | Carboxypeptidase D | + 2.13 | |
| 04625 | PRB1 | Serine-type endopeptidase | - 2.01 | |
| 00130 | RCK2 | Serine/threonine-protein kinase | - 2.12 | |
| 04108 | PKP1 | Kinase | - 2.17 | |
| 02327 | YFR006W | Prolidase | - 2.28 | |
| 02418 | DED81 | Asparagine-tRNA ligase | - 2.40 | |
| 03563 | DPS1 | Aspartate-tRNA ligase | - 2.50 | |
| 04275 | OMA1 | Metalloendopeptidase | - 2.50 | |
| 02006 | NTA1 | Protein N-terminal asparagine amidohydrolase | - 2.75 | |
| 03949 | PHO13 | 4-nitrophenylphosphatase | - 3.32 | |
| TCA cycle | ||||
| 03596 | KGD2 | 2-oxoglutarate metabolism-related protein | - 2.02 | |
| 03920 | IDP1 | Isocitrate dehydrogenase (NADP+) | - 2.06 | |
| 03674 | KGD1 | Oxoglutarate dehydrogenase (Succinyl-transferring) | - 2.52 | |
| 00747 | LSC2 | Succinate-CoA ligase (ADP-forming) | - 2.70 | |
| 07363 | IDH2 | Isocitrate dehydrogenase | - 2.80 | |
| 01137 | ACO1 | Aconitase | - 2.99 | |
| 07851 | IDH1 | Isocitrate dehydrogenase (NAD+), putative | - 3.80 | |
| Glycerol metabolism | ||||
| 06132 | RHR2 | Glycerol-1-phosphatase | + 2.31 | |
| 02815 | GUT2 | Glycerol-3-phosphate dehydrogenase | - 2.00 | |
| Nucleotide metabolism | ||||
| 05545 | HNT2 | Nucleoside-triphosphatase | + 2.25 | |
| 03078 | NPP1 | Type I phosphodiesterase/nucleotide pyrophosphatase family protein | + 2.08 | |
| 06489 | ADO1 | Adenosine kinase | - 2.08 | |
| 00613 | FCY1 | Cytosine deaminase | - 2.69 | |
| Thiamin metabolism | ||||
| 03592 | THI20 | Phosphomethylpyrimidine kinase | - 2.51 | |
| Alcohol metabolism | ||||
| 05258 | SMG1 | Glucose-methanol-choline (GMC) oxidoreductase | + 6.67 | |
| 05024 | SPS19 | L-xylulose reductase | + 2.53 | |
| 06168 | GNO1 | SFA1 | GSNO reductase | - 2.02 |
| Carbon utilization | ||||
| 05144 | CAN2 | NCE103 | Carbonic anhydrase 2 | - 3.18 |
| Cell cycle control | ||||
| 03385 | PCL1 | G1/s-specific cyclin pcl1 (Cyclin hcs26) | + 2.37 | |
| 02604 | HOP1 | Putative uncharacterized protein | + 2.19 | |
| 00995 | MSC1 | Meiotic recombination-related protein | - 3.63 | |
| Chromatin and chromosome structures | ||||
| 02115 | NHP6B | Nonhistone protein 6 | - 2.47 | |
| Transcription | ||||
| 01841 | GLN3 | Predicted protein | + 5.72 | |
| 02990 | YOR052C | Nucleus protein | + 2.16 | |
| 04594 | UGA3 | PRO1 protein | - 2.01 | |
| 05290 | SPT3 | Transcription cofactor | - 2.01 | |
| 06495 | RNH70 | Ribonuclease H | - 2.06 | |
| 05333 | PUT3 | Putative uncharacterized protein | - 2.14 | |
| 02338 | GIS2 | DNA-binding protein hexbp | - 2.47 | |
| 05479 | ASG1 | Putative uncharacterized protein | - 3.57 | |
| Signal transduction | ||||
| 03316 | RDI1 | Rho GDP-dissociation inhibitor 1 | + 2.07 | |
| 00363 | HHK5 | SLN1 | CnHHK5 protein | - 2.44 |
| 01262 | GPB1 | STE4 | G-protein beta subunit GPB1 | - 2.55 |
| Oxidoreduction | ||||
| 04652 | YLR460C | Enoyl reductase | + 2.63 | |
| 06035 | ADH1 | Alcohol dehydrogenase | + 2.41 | |
| 00605 | ZTA1 | Cytoplasm protein | + 2.20 | |
| 00038 | SOR2 | Alcohol dehydrogenase | + 2.13 | |
| 01954 | YPR127W | Aldo/keto reductase | + 2.09 | |
| 02958 | FET5 | Ferroxidase | + 2.06 | |
| 02935 | YMR226C | Oxidoreductase | - 2.01 | |
| 01558 | XYL2 | Zinc-binding dehydrogenase | - 2.28 | |
| 00876 | FRE7 | Ferric-chelate reductase | - 2.49 | |
| 03168 | MET10 | Sulfite reductase (NADPH) | - 2.55 | |
| 07862 | YEL047C | Fumarate reductase (NADH) | - 2.58 | |
| 03498 | FRE2 | Metalloreductase | - 2.85 | |
| 03874 | AIF1 | Oxidoreductase | - 2.89 | |
| Other | ||||
| 00331 | YMR210W | Anon-23da protein | + 3.43 | |
| 04934 | TAR1 | Temperature associated repressor | + 2.37 | |
| 05678 | ADY2 | Membrane protein | + 2.28 | |
| 00818 | AGE2 | AGD15 | + 2.23 | |
| 04867 | YJR054W | Vacuole protein | + 2.22 | |
| 06574 | APP1 | Antiphagocytic protein 1 | + 2.21 | |
| 06482 | AMD2 | Amidase | + 2.20 | |
| 01252 | TUM1 | Thiosulfate sulfurtransferase | - 2.05 | |
| 03452 | AFG1 | AFG1 family mitochondrial ATPase | - 2.16 | |
| 05831 | MMF1 | Brt1 | - 2.19 | |
| 03991 | YGR149W | Integral to membrane protein | - 2.39 | |
| 02039 | YPL264C | Integral membrane protein | - 2.46 | |
| 02943 | SLM1 | Cytoplasm protein | - 2.49 | |
| 06668 | AIM38 | Mitochondrion protein | - 2.61 | |
| 00638 | LSG1 | GTPase | - 2.89 | |
| 01653 | CIG | Cytokine inducing-glycoprotein | - 3.26 | |
| 04314 | YEF1 | NAD+ kinase | - 3.74 | |
| 04690 | FMP41 | Mitochondrion protein | - 5.52 | |
Genes that were found to be differentially expressed were ordered by expression level and categorized, if available, into functional groups as described in Materials and Methods. Results are presented as the mean fold-increase (symbol +) or -decrease (symbol -) of biological triplicates. Abbreviations: C. n., C. neoformans; S. c., S. cerevisiae.