TABLE 2.

Genes derepressed by both Fe repletion and a php4Δ deletion

Function and gene identifierGene nameGeneDB annotationFold changecPosition(s) of putative CCAAT boxesb
WT (+Fe vs −Fe)php4Δ vs WT (−Fe)d
TCA cycle
    SPBP23A10.16sdh4+Mitochondrial inner membrane import complex anchor subunit13.58.91037, 816, 451
    SPAC140.01sdh2+Succinate dehydrogenase (ubiquinone) Fe-S protein subunit12.414.11130, 169, 97
    SPCC330.12csdh3+Succinate dehydrogenase (ubiquinone) cytochrome b subunit7.37.4868, 822, 708, 375, 253, 175, 144, 11
    SPAC1556.02csdh1+Succinate dehydrogenase5.64.51062, 178, 43
    SPAC24C9.06cAconitate hydratase3.63.91102, 797, 186
    SPBP4H10.15Aconitate hydratase2.62.6*1047, 725, 680, 592, 290
    SPBC776.15cDihydrolipoamide S-succinyltransferase2.41.8*1010, 941
Electron transport chain/mitochondrial respiration
    SPCC191.07cyc1+Cytochrome c (putative)15.98.31094, 907, 612, 525, 438, 380, 216, 211, 178
    SPAC20G8.04cElectron transfer flavoprotein-ubiquinone oxidoreductase8.06.6520, 479, 437
    SPBC16H5.06rip1+Ubiquinol-cytochrome c reductase complex subunit 55.12.0903, 769, 759, 657, 584, 453,313
    SPBC29A3.18cyt1+Cytochrome c13.82.1*1174, 813, 457, 435, 145, 65
    SPCC338.10ccox5+Cytochrome c oxidase subunit V3.71.8983, 732, 598, 148, 126
    SPCC737.02cqcr7+Ubiquinol-cytochrome c reductase complex subunit 63.61.5729, 611, 591, 462, 119, 86
    SPAC1782.07qcr8+Ubiquinol-cytochrome c reductase complex subunit 73.41.6660, 348, 335, 81
    SPAC24C9.02cCytochrome c1 heme lyase2.31.81137, 1050, 927, 22
Heme biosynthesis
    SPAC24B11.13hem3+Hydroxymethylbilane synthase3.23.6
    SPAC31G5.08ups1+Uroporphyrinogen III synthase1.71.4
Amino acid biosynthesis
    SPAPB1E7.07glt1+Glutamate synthase (predicted)4.44.2*913, 881, 266, 199
    SPAC9E9.03leu2+3-Isopropylmalate dehydratase (predicted)2.94.6*1082, 1069, 815, 750, 293
    SPAC17G8.06cDihydroxy-acid dehydratase2.73.1*327, 284
    SPAC343.16lys2+Homoaconitate hydratase2.31.91093, 1008, 797, 665, 492
    SPBC21H7.07chis5+Imidazoleglycerol phosphate dehydratase2.22.1994, 269, 165
    SPAC1782.11met14+Adenylyl-sulfate kinase (predicted)2.12.1724, 599, 458, 22
    SPBC27.08csua1+Sulfate adenylyltransferase1.81.4683
Oxidative stress response
    SPCC757.07cctt1+Catalase7.111.4575, 480
    SPAPB2B4.02grx5+Monothiol glutaredoxin2.53.1*
    SPAC1D4.11clkh1+Dual-specificity protein kinase2.22.2693, 388, 304
    SPBC12D12.07ctrx2+Mitochondrial thioredoxin1.91.5296, 228
    SPAC664.09ggt1+γ-Glutamyltranspeptidase1.81.91062, 936, 566, 525, 394
Sterol and fatty acid biosynthesis
    SPAC13A11.02cerg11+Sterol 14-demethylase2.92.51018, 832, 728, 716, 653, 375
    SPCC16A11.10coca8+Cytochrome b5 (predicted)2.22.5
    SPAC19A8.04erg5+C-22 sterol desaturase (predicted)1.61.61105, 836, 806, 466, 335, 64
    SPAC17H9.12cNADH-cytochrome reductase1.51.4559, 306, 81
Purine/pyrimidine biosynthesis
    SPBC2G2.08ade9+C-1-tetrahydrofolate synthase1.91.51037, 793, 89
    SPAC22G7.06cura1+Carbamoyl-phosphate synthase1.71.81176
Fe-S cluster biogenesis and Fe-S cluster-containing proteins
    SPCC645.03cisa1+Iron-sulfur protein3.24.81098, 1003, 762, 207
    SPCC1235.02bio2+Biotin synthase2.94.61195, 1174, 259
    SPBC14F5.06Iron-sulfur protein2.62.8980, 393, 255, 200, 46
    SPBC8D2.15Mitochondrial lipoic acid synthetase (predicted)2.21.544
    SPBC1709.19cNifU-like protein1.71.81070, 516, 387, 236
Fe related
    SPBC1683.10cpcl1+Ferrous iron transporter16.821.9205
    SPAC23E2.01fep1+Iron-sensing transcription factor3.53.1816, 322, 188
Nitrogen assimilation
    SPCPB1C11.01amt1+Ammonium transporter (predicted)4.03.8*1120, 1016, 964, 941, 301
    SPAC23H4.06gln1+Glutamate-ammonia ligase3.02.5742, 690, 680, 640
    SPAC10F6.01cSulfite reductase beta subunit (predicted)2.72.5677
Iron-containing proteins (no specific prosthetic group)
    SPAC13F5.03cMitochondrial iron-containing alcohol dehydrogenase family1.51.5*
    SPBC25D12.04suc22+Ribonucleotide reductase small subunit1.41.41026, 155
Mitochondrial membrane related
    SPBC27B12.14Mitochondrial membrane protein complex assembly protein3.23.31192, 810
    SPAC17C9.09ctim13+TIM22 inner membrane protein import complex subunit2.21.9427, 143
    SPBC17A3.01ctim50+TIM23 translocase complex subunit (predicted)2.11.6289
    SPBC27B12.09cFlavin adenine dinucleotide transporter1.72.01124, 348, 254
RNA related
    SPAPB1E7.03rcp82+RNA polymerase III complex subunit (predicted)3.93.8823, 91, 15
    SPNCRNA.03prl3+Noncoding RNA (predicted)2.72.1NA
    SPNCRNA.32prl32+Noncoding RNA (predicted)2.13.8NA
    SPAC57A10.10csla1+La protein homolog2.31.6
    SPNCRNA.131tos2+Noncoding RNA2.02.5NA
    SPAC6G9.10csen1+ATP-dependent 5′ to 3′ DNA/RNA helicase1.91.51154, 1091, 726, 523
    SPBC2D10.15cPeptidyl-tRNA hydrolase Pth1 (predicted)1.81.7426, 179
    SPAC4G8.07ctRNA (m5U54) methyltransferase Trm2 (predicted)1.82.1924, 10
    SPAC4G8.06ctrm12+tRNA methyltransferase (predicted)1.71.61053, 1006, 775, 630, 412, 225
    SPAC8C9.07rRNA processing protein Fyv7 (predicted)1.61.51132, 934, 64
    SPBC9B6.11cCCR4/nocturin family endoribonuclease1.51.5769, 553, 426, 155
    SPAC19A8.07cU3 snoRNP-associated protein Imp4 (predicted)1.51.51028, 1021, 751
Other functions
    SPBC29A3.21Sequence orphan14.215.91069, 1045, 810, 716, 580, 550, 373, 129
    SPAP14E8.05cUPF0136 family protein10.510.6977, 501
    SPAC17G8.08cHuman TMEM165 homolog7.66.7323, 284
    SPAC26F1.14caif1+Apoptosis-inducing factor homolog7.9a6.31144, 1059, 463, 269
    SPAC694.04cConserved eukaryotic protein4.94.2301
    SPAC1039.01Amino acid permease, unknown 53.11.6*793
    SPBC947.15cNADH dehydrogenase2.92.4*624, 489, 272
    SPAC1782.02cConserved fungal protein2.52.5984, 924, 894, 848, 733, 160
    SPBC887.17Uracil permease (predicted)2.31.91101, 729, 656, 561
    SPAC1039.02Phosphoprotein phosphatase (predicted)2.31.5*183, 61
    SPAC1556.03azr1+Serine/threonine protein phosphatase2.21.5755, 620
    SPBC12C2.12cglo1+Glyoxalase I1.72.61054, 736, 492, 238
    SPAC6C3.02cCHCH domain protein1.72.2727,256
    SPAC1142.05ctr5+Copper transporter complex subunit1.71.9822
    SPAC22E12.18Conserved fungal protein1.71.51025, 16
    SPBC18E5.07Sequence orphan1.72.0850, 228
    SPAC683.02czf-CCHC-type zinc finger protein1.61.6*1154, 1111, 1059, 836, 572, 18
    SPAC15A10.04czpr1+EF-1 alpha binding zinc finger protein (predicted)1.61.51171, 640, 120, 70
    SPAC20H4.08Phosphatase activator (predicted)1.61.61006, 992, 893, 787, 643, 123, 68
    SPBP16F5.08cFlavin dependent mono-oxygenase (predicted)1.51.41166, 580, 220, 95
    SPAC11D3.04cSnoaL1.51.71016, 230
    SPBC12D12.06srb11+Cyclin CycC1.51.6452, 344, 316
    SPAP14E8.04oma1+Metallopeptidase (predicted)1.51.6940, 400, 224, 161, 33
  • a Determined by RNase protection assays.

  • b NA, not applicable. Underlining, CCAAT boxes in reverse orientation (position relative to the 5′ C).

  • c +Fe, iron replete; −Fe, iron depleted. Boldface, value below the threshold but associated with enzymes that need or potentially need iron for their activity.

  • d *, value originates from only one biological repeat (second value not available or aberrant).