Table 2 Transcripts derepressed by both Fe-repletion and a php4Δ deletion
Gene IDGene NameGeneDB AnnotationFold ChangesPutative CCAAT Boxes
WT (+Fe vs. −Fe)php4Δ vs. WT (−Fe)
Meiotically upregulated genes
 SPAC869.06chry1+HHE domain cation binding protein (predicted)6.8264.734386, 250a
 SPBC359.06mug14+Adducin5.1272.229649
 SPCC1235.12cmug146+Schizosaccharomyces specific protein Mug463.7154.370854a, 804a, 753, 414a
 SPBC6B1.03cPal1 family protein2.6802.636709a, 539a
 SPCC1281.04Pyridoxal reductase (predicted)2.6583.033102
 SPAC3F10.05cmug113+T5orf172 family protein2.5052.309792a, 597, 340, 251, 153
 SPAPB1A10.08Schizosaccharomyces specific protein2.5012.682874a, 365a, 47a
 SPBC21.07cppk24+Serine/threonine protein kinase Ppk242.4843.687741a, 655a, 294
 SPAC3F10.07cerf4+Palmitoyltransferase complex subunit Erf42.2752.914None
 SPAC25A8.03cDUF185 protein, mitochondrial2.2662.487None
 SPAC5D6.09cmug86+Acetate transmembrane transporter (predicted)2.2242.736848a, 70, 32
 SPCC320.07cmde7+RNA-binding protein Mde72.1932.727951, 818a, 264, 107
 SPBP8B7.27mug30+HECT-type ubiquitin-protein ligase E3 (predicted)2.1662.433226a, 134, 57
 SPAC4F10.08mug126+Schizosaccharomyces pombe specific protein2.1572.617158, 85
 SPBC28E12.02RNA-binding protein2.1292.936970a, 754a, 271, 50
 SPAC22F8.02cpvg5+PvGal biosynthesis protein Pvg52.0942.205665a, 267a, 9
 SPCC1259.14cmeu27+UPF0300 family protein 52.0542.557465a, 426a
 SPBC19F8.06cmeu22+Amino acid transmembrane transporter, predicted Meu222.0042.641826a, 724, 118
Noncoding RNAs
 SPNCRNA.325Noncoding RNA (predicted)36.51028.320541
 SPNCRNA.31prl31Noncoding RNA, poly(A)-bearing (predicted)5.1924.596965, 764, 448a, 274a
 SPNCRNA.867Intergenic RNA (predicted)4.8604.306None
 SPNCRNA.1314Intergenic RNA (predicted), possible alternative UTR3.9937.783719a
 SPNCRNA.1457Antisense RNA (predicted)3.6265.226None
 SPSNORNA.31snoR39aSmall nucleolar RNA snR393.4482.009975a
 SPNCRNA.242Noncoding RNA (predicted)3.4292.017738a
 SPNCRNA.1063Intergenic RNA (predicted), possible alternative UTR3.3092.821542, 130a
 SPNCRNA.495Noncoding RNA (predicted)3.1846.122937, 892a, 399a, 349a
 SPNCRNA.1205Intergenic RNA (predicted), possible alternative UTR2.9123.260612, 567a, 74a, 24a
 SPNCRNA.727Intergenic RNA (predicted)2.8602.013None
 SPNCRNA.861Intergenic RNA (predicted)2.6512.458771, 504, 40
 SPNCRNA.1325Intergenic RNA (predicted), possible alternative UTR2.4563.597634a
 SPNCRNA.1157Intergenic RNA (predicted)2.4252.310922a
 SPNCRNA.32prl32Noncoding RNA, poly(A)-bearing (predicted)2.4192.740895a, 872a, 821a, 725, 675a, 273
 SPSNORNA.16snoR56Small nucleolar RNA snR56 (predicted)2.3432.225922a
 SPNCRNA.30Noncoding RNA (predicted)2.3133.648546a, 387, 219, 179a
 SPNCRNA.1087Antisense RNA (predicted)2.2233.662770a, 670, 590, 531a
 SPNCRNA.940Intergenic RNA (predicted)2.1732.142515, 303, 76a
 SPNCRNA.1617Antisense RNA (predicted)2.1612.088433a, 338, 265
 SPNCRNA.1604Intergenic RNA (predicted)2.1152.139908, 901a
 SPNCRNA.276Noncoding RNA (predicted)2.0092.873628a, 203
 SPNCRNA.1343Intergenic RNA (predicted)2.0052.108384a
Electron transport chain/mitochondrial respiration
 SPCC191.07cyc1+Cytochrome c6.9535.821907, 612, 525, 438, 380, 216a, 211a, 178
 SPBC16H5.06rip1+Ubiquinol-cytochrome-c reductase complex subunit 53.4803.197906, 769a, 759, 657, 584, 453a, 313a
 SPCC737.02cqcr7+Ubiquinol-cytochrome-c reductase complex subunit 6 (predicted)2.6222.715729a, 611, 591, 462, 119a, 90
 SPCC338.10ccox5+Cytochrome c oxidase subunit V (predicted)2.5112.422947a, 696a, 562a, 112, 90
 SPBC29A3.18cyt1+Cytochrome c1 Cyt1 (predicted)2.5092.195813, 457, 435a, 145, 65
 SPAC15A10.17coa2+Cytochrome C oxidase assembly factor Coa2 (predicted)2.5012.102838, 146a, 139a, 132a
 SPBC947.15cnde1+Mitochondrial NADH dehydrogenase (ubiquinone) Nde1 (predicted)2.4962.357624, 489, 272a
 SPBC16C6.08cqcr6+Ubiquinol-cytochrome-c reductase complex subunit 8, hinge protein (predicted)2.3722.100158
 SPAC20G8.04ccir2+Mitochondrial electron transfer flavoprotein-ubiquinone oxidoreductase Cir2 (predicted)2.1582.420520a, 479a, 437a
Carbohydrates metabolic process
 SPBC32H8.13Cmok12+α-1,3-glucan synthase Mok123.0963.371None
 SPBC11C11.05KRE9 family cell wall 1,6-β-glucan biosynthesis protein (predicted)2.8383.237836
 SPAC5H10.11gmh1+α-1,2-galactosyltransferase Gmh1 (predicted)2.7513.462495
 SPAC23H3.11CGlucosidase (predicted)2.4492.194902a, 654a, 642a
 SPAC13F5.03cgld1+Mitochondrial glycerol dehydrogenase Gld12.2524.537None
 SPAC1039.11Cgto1+α-glucosidase (predicted)2.2492.387706, 666a, 498a, 339
 SPCC970.02Mannan endo-1,6-α-mannosidase (predicted)2.2182.865879a
 SPBC19C7.12comh1+α-1,2-mannosyltransferase Omh12.1822.102175a, 167a
Amino acid biosynthesis
 SPAC9E9.03leu2+3-isopropylmalate dehydratase Leu2 (predicted)5.0125.971815a, 750a, 293
 SPAPB1E7.07glt1+Glutamate synthase Glt1 (predicted)2.9823.254913a, 881a, 266a, 199
 SPAC17G8.06cDihydroxy-acid dehydratase (predicted)2.7813.534327, 284a
 SPBC21H7.07chis5+Imidazoleglycerol-phosphate dehydratase His52.6362.623994, 269, 165a
 SPAC13G7.06met16+Phosphoadenosine phosphosulfate reductase2.4632.461820a, 636a, 186, 63a
 SPCC622.12cgdh1+NADP-specific glutamate dehydrogenase Gdh1 (predicted)2.2322.610917a, 650, 528, 487a
 SPCC1442.09trp3+Anthranilate synthase component I (predicted)2.1492.136686, 138a
RNA-related proteins
 SPBC1718.03ker1+DNA-directed RNA polymerase I complex subunit Ker12.9843.601None
 SPBC17D1.01Transcriptional regulatory protein Spp41 (predicted)2.8702.079None
 SPAC3F10.06crit1+Initiator methionine tRNA 2’-O-ribosyl phosphate transferase (predicted)2.4802.776390a, 328a, 244a, 112
 SPAC4G8.07ctRNA (m5U54) methyltransferase Trm2 (predicted)2.4723.223924a, 10a
 SPCC757.09crnc1+RNA-binding protein that suppresses calcineurin deletion Rnc12.3762.13023
 SPCC11E10.06celp4+Elongator complex subunit Elp4 (predicted)2.0912.046614, 41, 19
 SPCC320.11Cnip7+RNA-binding protein involved in ribosome biogenesis Nip7 (predicted)2.0342.228839, 608a
TCA cycle
 SPBP23A10.16sdh4+TIM22 inner membrane protein import complex anchor subunit Tim1823.70030.990897a, 532, 77, 53
 SPAC140.01sdh2+Succinate dehydrogenase (ubiquinone) iron-sulfur protein subunit (predicted)20.16018.790100, 28
 SPAC1556.02csdh1+Succinate dehydrogenase Sdh1 (predicted)6.4716.920178, 43
 SPAC24C9.06caco1+Aconitate hydratase Aco1 (predicted)5.9976.175440, 135
 SPCC330.12csdh3+Succinate dehydrogenase (ubiquinone) cytochrome b subunit (predicted)5.9236.510868a, 822a, 708a, 375, 253a, 175, 144, 11
 SPBC3H7.03c2-oxoglutarate dehydrogenase (lipoamide) (e1 component of oxoglutarate Dehydrogenase complex) (predicted)2.6742.764None
Fe-S cluster biogenesis/Fe-S cluster-containing proteins
 SPAC26F1.14caif1+Apoptosis-inducing factor homolog Aif1 (predicted)11.38012.590951a, 355, 161
 SPCC645.03cisa1+Mitochondrial iron-sulfur protein Isa111.35012.330762, 207
 SPCC1235.02bio2+Biotin synthase5.3425.227259
 SPBC14F5.06rli1+Iron-sulfur ATPase involved in ribosome biogenesis and translation Rli1 (predicted)3.5374.235980a, 393a, 255, 200a, 46a
mRNA metabolic process
 SPBC609.01Ribonuclease II (RNB) family, involved in nuclear-transcribed mRNA Catabolic process (predicted)2.8993.048646a, 424a, 386
 SPAP8A3.05ski7+Ski complex interacting GTPase Ski72.4812.641586, 198, 126
 SPBC16H5.10cprp43+ATP-dependent RNA helicase Prp432.1292.144678, 671a, 616
 SPBC2F12.08cceg1+mRNA guanylyltransferase Ceg12.0082.186None
Mitochondrial membrane-related
 SPBC3B9.19mge1+Mitochondrial GrpE domain chaperone protein (predicted)3.0762.745971, 684, 415
 SPCC1235.11mpc1+Mitochondrial pyruvate transmembrane transporter subunit Mpc1 (predicted)2.9383.139434a, 273, 141
 SPBC27B12.14Mitochondrial membrane protein complex assembly protein (predicted)2.1223.004810a
Oxidative stress response
 SPCC757.07cctt1+Catalase9.3846.620575a, 480
 SPAC1486.01Manganese superoxide dismutase2.0732.746None
Sterol and fatty acid biosynthesis
 SPCC16A11.10coca8+Cytochrome b5 (predicted)3.3573.327None
 SPAC1687.16cerg31+C-5 sterol desaturase Erg313.2383.671941a
Nitrogen assimilation
 SPCPB1C11.01amt1+Ammonium transmembrane transporter Amt14.2565.213964, 941, 301
 SPAC23H4.06gln1+Glutamate-ammonia ligase Gln12.5553.026742, 690a, 680, 640
Heme biosynthesis
 SPAC24B11.13hem3+Hydroxymethylbilane synthase Hem3 (predicted)2.9883.212None
 SPAP14E8.05cUPF0136 family mitochondrial protein, implicated in heme biosynthesis2.5713.208977a, 501a
Other functions
 SPBPB21E7.02cPhosphoglycerate mutase family3.7112.355349, 153
 SPAC869.08pcm2+Protein-L-isoaspartate O-methyltransferase Pcm2 (predicted)3.6332.488447a, 108a
 SPAC186.02cHydroxyacid dehydrogenase (predicted)3.6263.690465
 SPCC663.13Cnaa50+NatA N-acetyltransferase subunit Naa50 (predicted)3.4713.694948a, 726a
 SPCC663.14ctrp663+TRP-like ion channel (predicted)3.4493.690782a
 SPAC17G8.08cHuman TMEM165 homolog, implicated in calcium transport3.4433.283441a, 435a
 SPAC1486.11fmc1+Mitochondrial matrix protein, F1F0 ATP synthase assembly factor Fmc1 (predicted)2.9593.052312a, 174
 SPBC1711.12Serine-type peptidase activity2.9433.055316
 SPBC725.03Pyridoxamine 5′-phosphate oxidase (predicted)2.9233.438270
 SPBC1652.02APC amino acid transmembrane transporter (predicted)2.8142.296929a, 671a, 323a, 128
 SPBC1711.11Autophagy associated protein (predicted)2.6572.450536, 212, 39a, 26
 SPCC1020.01cpma2+P-type proton ATPase, P3-type Pma22.6543.201119, 74, 42
 SPAC869.02cNitric oxide dioxygenase (predicted)2.6122.938315, 301a, 115a
 SPAC1556.03azr1+Serine/threonine protein phosphatase Azr12.5603.738755a, 620a
 SPBC1703.06pof10+F-box protein Pof102.5202.113814
 SPBC1703.12ubp9+Ubiquitin C-terminal hydrolase Ubp92.5202.093612
 SPCC830.08cyop1+ER membrane protein DP1/Yop12.3982.355None
 SPBC19C7.09cuve1+Endonuclease Uve12.3142.4231000, 789, 242
 SPBC1711.05Nucleocytoplasmic transport chaperone Srp40 (predicted)2.2872.328479, 356a, 68
 SPAC8C9.03cgs1+cAMP-dependent protein kinase regulatory subunit Cgs12.2342.154667
 SPBC26H8.02csec9+SNAP-25 homolog, t-SNARE component Sec92.0662.010582, 461
 SPBC1683.10cpcl1+Ferrous iron/manganese transmembrane transporter Pcl12.0342.967205
 SPBC21D10.10bdc1+Bromodomain containing protein 1, Bdc12.0052.317None
Unknown functions
 SPAC750.05cSchizosaccharomyces pombe specific 5Tm protein family5.5703.266810a, 453, 444, 23a
 SPBP19A11.02cSchizosaccharomyces pombe specific protein, predicted GPI anchored4.0884.34682a
 SPBPB2B2.19cSchizosaccharomyces pombe specific 5Tm protein family3.9102.918809a, 453, 444, 23a
 SPBC685.03Schizosaccharomyces specific protein3.8393.018590, 246a, 200a
 SPBC18E5.07DUF3210 family protein2.9974.136850a, 228a
 SPAC11D3.13hsp3104+ThiJ domain protein2.7152.307658a
 SPAC6C3.02cMitochondrial CHCH domain protein (predicted)2.6922.250728, 256
 SPCC191.06Schizosaccharomyces pombe specific protein2.6704.362671, 498a, 311, 16
 SPCC736.05wtf7+Wtf element Wtf72.5813.383None
 SPCC4G3.03WD40/YVTN repeat-like protein2.5052.426458, 441
 SPBC1A4.04Schizosaccharomyces specific protein2.4922.929920a, 412, 358, 203a
 SPAC15A10.07Schizosaccharomyces specific protein2.4743.266973, 694a, 383, 29
 SPBC31A8.02Pseudogene2.4322.690None
 SPCC1322.10Cell wall protein Pwp12.2082.411934a, 461a
 SPCC417.15Dubious2.1902.763987a, 964a, 913a, 817, 767a, 365
 SPAPB1E7.11CSchizosaccharomyces specific protein2.0172.349811a, 325a
 SPAC694.04cConserved eukaryotic protein2.0102.336301
  • ID, identified; DB, database; WT, wild type; Fe, iron; S, sulfur; PvGal, pyruvic acid 4,6-ketal-linked galactose; UTR, untranslated region; NADH, nicotinamide adenine dinucleotide hydride; NADP, nicotinamide adenine dinucleotide phosphate; tRNA, transfer RNA; ATPase, adenosine triphosphatase; mRNA, messenger RNA; GTPase, guanosine triphosphatase; ATP, a denosine triphosphate; APC, amino acid-polyamine-organocation; ER, endoplasmic reticulum; cAMP, cyclic adenosine monophosphate; SNAP-25, synaptosome-associated protein 25 kDa; t-SNARE, target membrane soluble N-ethylmaleimide-sensitive attachment protein receptor.

  • a CCAAT boxe(s) in reverse orientation relative to the initiator codon of the indicated gene.