Table S2.
Results of global transcriptome analyses of C. glutamicum Δpup mutant vs. ATCC 13032 WT grown in CGXII minimal medium with 4% (wt/vol) glucose supplemented with 1 µM FeSO4
| Locus tag | Gene name | Annotation | mRNA ratio, Δpup/WT | DtxR target | RipA target |
| cg0012 | ssuR | Sulphonate sulfur utilization transcriptional regulator | 2.15 | — | — |
| cg0018 | — | Putative conserved membrane protein | 2.08 | — | — |
| cg0159 | — | Hypothetical protein | 2.28 | R | — |
| cg0160 | — | Hypothetical protein | 15.60 | R | — |
| cg0177 | — | Hypothetical protein | 3.14 | — | — |
| cg0310 | katA | Catalase | 0.16 | — | R |
| cg0405 | — | Putative ABC-type iron(III) dicitrate transporter, secreted siderophore-binding lipoprotein | 3.01 | R | — |
| cg0445 | sdhC | Succinate:menachinone oxidoreductase, cytochrome b | 0.39 | A | R |
| cg0446 | sdhA | Succinate:menachinone oxidoreductase, flavoprotein subunit | 0.32 | A | R |
| cg0447 | sdhB | Succinate:menachinone oxidoreductase, iron sulfur protein | 0.39 | A | R |
| cg0465 | — | Putative membrane protein, conserved | 5.27 | R | — |
| cg0466 | htaA | Secreted heme transport-associated protein | 4.74 | R | — |
| cg0467 | hmuT | Hemin-binding periplasmic protein precursor | 5.08 | R | — |
| cg0468 | hmuU | Hemin transport system, permease protein | 2.85 | R | — |
| cg0470 | htaB | Secreted heme transport-associated protein | 15.19 | R | — |
| cg0471 | htaC | Secreted heme transport-associated protein | 10.17 | R | — |
| cg0506 | — | Putative spermidine/putrescine/iron(III) transporter, ATPase subunit | 0.42 | — | — |
| cg0507 | — | Putative spermidine/putrescine/iron(III) transporter, permease subunit | 0.39 | — | — |
| cg0508 | — | Putative spermidine/putrescine/iron(III) transporter, substrate-binding lipoprotein | 0.39 | — | — |
| cg0543 | — | Hypothetical protein | 0.50 | — | — |
| cg0589 | — | Putative siderophore ABC transporter, ATP-binding protein | 4.96 | R | — |
| cg0590 | — | Putative siderophore ABC transporter, permease protein | 8.02 | R | — |
| cg0591 | — | Putative siderophore ABC transporter, permease protein | 4.17 | R | — |
| cg0701 | — | Putative drug/metabolite transporter, DMT superfamily | 2.08 | — | — |
| cg0737 | — | Putative high affinity ABC-type methionine transporter, substrate-binding lipoprotein | 2.25 | — | — |
| cg0755 | metY | O-Acetylhomoserine sulfhydrylase | 2.22 | — | — |
| cg0759 | prpD2 | 2-Methylcitrate dehydratase, involved in propionate catabolism | 0.33 | — | — |
| cg0760 | prpB2 | 2-Methylisocitrate lyase, involved in propionate catabolism | 0.30 | — | — |
| cg0762 | prpC2 | 2-Methylcitrate synthase, involved in propionate catabolism | 0.28 | — | — |
| cg0767 | — | Putative cytoplasmic siderophore-interacting protein | 2.23 | — | — |
| cg0768 | — | Putative iron-siderophore ABC transporter, ATP-binding protein | 4.06 | R | — |
| cg0769 | — | Putative iron-siderophore ABC transporter, permease subunit | 6.49 | R | — |
| cg0770 | — | Putative iron-siderophore ABC transporter, permease subunit | 2.67 | R | — |
| cg0771 | irp1 | Putative iron-siderophore ABC transporter, secreted siderophore-binding lipoprotein | 5.50 | R | — |
| cg0812 | dtsR1 | Acetyl-/propionyl-CoA carboxylase, β-subunit | 2.15* | — | — |
| cg0921 | — | Putative cytoplasmic siderophore-interacting protein | 2.26 | R | — |
| cg0922 | — | Putative secreted siderophore-binding lipoprotein | 5.81 | R | — |
| cg0924 | — | Putative ABC-type iron-siderophore transporter, substrate-binding lipoprotein | 5.23 | R | — |
| cg0926 | — | Putative iron-siderophore transporter, permease subunit | 3.55 | R | — |
| cg0927 | — | Putative iron-siderophore ABC transporter, permease subunit | 3.46 | R | — |
| cg0961 | — | Putative homoserine O-acetyltransferase | 0.45 | — | |
| cg1120 | ripA | Transcriptional regulator of iron proteins and repressor of aconitase, AraC family | 6.91 | R | — |
| cg1129 | aroF | 3-Deoxy-7-phosphoheptulonate synthase | 2.38 | — | — |
| cg1169 | metP | Na+:methionine symporter, SNF-family | 0.39 | — | — |
| cg1227 | ykoE | Thiamine-regulated ECF transporter for hydroxymethylpyrimidine, substrate-specific component | 6.87 | — | — |
| cg1228 | ykoD | Thiamine-regulated ECF transporter for hydroxymethylpyrimidine, duplicated ATPase component | 2.37* | — | — |
| cg1229 | ykoC | Thiamine-regulated ECF transporter for hydroxymethylpyrimidine, transmembrane component | 7.38 | — | — |
| cg1230 | — | Hypothetical protein | 2.02* | — | — |
| cg1291 | — | Putative membrane protein | 2.47 | — | — |
| cg1299 | cydD | ABC transporter, subunit II, essential for cytochrome bd oxidase assembly | 0.31 | — | — |
| cg1300 | cydB | Cytochrome bd oxidase, subunit II | 0.42 | — | — |
| cg1341 | narI | Nitrate reductase, γ-subunit, cytochrome b | 0.33 | — | R |
| cg1342 | narJ | Nitrate reductase, δ-subunit, assembly factor | 0.32 | — | R |
| cg1343 | narH | Nitrate reductase, β-subunit, iron sulfur protein | 0.39 | — | R |
| cg1344 | narG | Nitrate reductase, α-subunit | 0.37 | — | R |
| cg1345 | narK | Nitrate/nitrite antiporter | 0.48* | — | R |
| cg1418 | — | Putative secreted siderophore-binding lipoprotein | 2.16 | R | — |
| cg1419 | — | Putative Na+-dependent transporter, BASS family | 3.57 | — | — |
| cg1432 | ilvD | Dihydroxy-acid dehydratase | 0.41* | — | — |
| cg1435 | ilvB | Acetolactate synthase I, large subunit | 0.42* | — | — |
| cg1436 | ilvN | Acetolactate synthase, small subunit | 0.41 | — | — |
| cg1475 | — | Hypothetical protein | 3.25 | — | — |
| cg1476 | thiC | Thiamine biosynthesis protein ThiC | 10.08 | — | — |
| cg1487 | leuC | Isopropylmalate isomerase, large subunit | 0.43 | — | R |
| cg1488 | leuD | Isopropylmalate isomerase, small subunit | 0.51† | — | R |
| cg1514 | — | Putative secreted protein, CGP1 Region | 2.00 | — | — |
| cg1580 | argC | N-acetyl-γ-glutamyl-phosphate reductase | 2.45 | — | — |
| cg1581 | argJ | Monofunctional NAGS N-acetyl glutamate synthase | 3.43 | — | — |
| cg1582 | argB | Acetylglutamate kinase | 3.79 | — | — |
| cg1583 | argD | Acetylornithine aminotransferase | 5.09 | — | — |
| cg1584 | argF | Ornithine carbamoyltransferase | 3.29 | — | — |
| cg1585 | argR | Transcriptional repressor of arginine biosynthesis, ArgR family | 2.88 | — | — |
| cg1612 | — | Putative acetyltransferase | 0.27 | — | — |
| cg1626 | — | Hypothetical protein | 2.67 | — | — |
| cg1654 | thiD1 | Thiamine-phosphate pyrophosphorylase | 2.47 | — | — |
| cg1655 | thiM | Hydroxyethylthiazole kinase | 2.02 | — | — |
| cg1694 | recB | Exonuclease, RecB family | 0.49 | — | — |
| cg1695 | — | Putative plasmid maintenance system antidote protein | 0.40 | — | — |
| cg1701 | metH | Homocysteine methyltransferase, methionine synthase | 2.25 | — | — |
| cg1724 | meaB | Accessory protein of methylmalonyl-CoA mutase | 0.46 | — | — |
| cg1725 | mutA | Methylmalonyl-CoA mutase, α-subunit | 0.46 | — | — |
| cg1736 | — | Putative membrane protein | 0.49 | — | — |
| cg1737 | acn | Aconitase | 0.16 | — | R |
| cg1930 | — | Putative secreted hydrolase, CGP3 region | 6.88 | R | — |
| cg1931 | — | Putative secreted protein, CGP3 region | 5.17 | R | — |
| cg2181 | oppA | ABC-type peptide transport system, secreted component | 0.30 | — | — |
| cg2182 | oppB | ABC-type peptide transport system, permease component | 0.38 | — | — |
| cg2183 | oppC | ABC-type peptide transport system, permease component | 5.35 | — | — |
| cg2184 | oppD | ABC-type peptide transport system, ATPase component | 2.86 | — | — |
| cg2234 | — | Putative ABC-type iron(III) dicitrate transporter, substrate-binding lipoprotein | 3.31 | R | — |
| cg2236 | thiE | Thiamine-phosphate pyrophosphorylase | 2.14 | — | — |
| cg2237 | thiO | Putative d-amino acid oxidase flavoprotein, oxidoreductase | 2.86 | — | — |
| cg2238 | thiS | Sulfur transfer protein, involved in thiamine biosynthesis | 3.16 | — | — |
| cg2239 | thiG | Thiazole synthase, involved in thiamine biosynthesis | 3.63 | — | — |
| cg2240 | thiF | Molybdopterin biosynthesis protein MoeB, involved in thiamine biosynthesis | 3.33 | — | — |
| cg2252 | — | Hypothetical protein | 2.20 | — | — |
| cg2283 | — | Hypothetical protein | 2.82 | — | — |
| cg2348 | — | Putative secreted protein | 0.48 | — | — |
| cg2438 | — | Hypothetical protein | 0.50 | — | — |
| cg2445 | hmuO | Heme oxygenase | 2.16 | R | — |
| cg2556 | — | Putative iron-regulated membrane protein | 0.45 | — | — |
| cg2610 | — | Putative ABC-type dipeptide/oligopeptide/nickel transport system, secreted component | 0.37 | — | — |
| cg2636 | catA1 | Catechol 1,2-dioxygenase | 0.35* | — | R |
| cg2675 | — | Putative ATPase component of ABC-type transport system, contains duplicated ATPase domains | 2.28 | — | — |
| cg2676 | — | Putative ABC-type dipeptide/oligopeptide/nickel transport system, permease component | 2.96 | — | — |
| cg2677 | — | Putative ABC-type dipeptide/oligopeptide/nickel transport system, permease component | 2.58 | — | — |
| cg2782 | ftn | Ferritin | 0.43* | A | — |
| cg2837 | sucC | Succinyl-CoA synthetase, β-subunit | 0.43 | — | — |
| cg3047 | ackA | Acetate kinase | 0.40* | — | R |
| cg3048 | pta | Phosphotransacetylase, phosphate acetyltransferase | 0.34* | — | R |
| cg3107 | adhA | Zn-dependent alcohol dehydrogenase | 0.32 | — | — |
| cg3156 | htaD | Secreted heme transport-associated protein | 10.37 | R | — |
| cg3195 | — | Putative flavin-containing monooxygenase FMO | 0.24 | — | — |
| cg3216 | gntP | Gluconate permease, Gluconate:H+ symporter, GntP family | 0.45 | — | — |
| cg3266 | tnp5c | Transposase | 2.46 | — | — |
| cg3267 | — | Putative membrane protein, putative pseudogene, C-terminal fragment | 2.68 | — | — |
| cg3372 | — | Hypothetical protein | 4.52 | — | — |
| cg3373 | cyeR | Redox-sensing transcriptional regulator, ArsR family | 2.28 | — | — |
| cg3374 | cye1 | Putative NADH-dependent flavin oxidoreductase | 2.53 | — | — |
| cg3404 | — | Putative ABC-type iron(III) dicitrate transporter, substrate-binding lipoprotein | 3.77 | R | — |
| cg3431 | rnpA | Ribonuclease P | 0.48 | — | — |
Cells for RNA isolation were harvested at an OD600 of 3. The precultivation was performed under the same conditions as the main cultures. The mRNA levels of all listed genes were at least twofold up- or down-regulated (P ≤ 0.1) in three independent biological replicates including one color-swap. Differentially expressed genes were determined by quality filter using the criteria flags ≥0 and signal/noise ratio of Cy5 (F635Median/B635Median) or Cy3 (F532Median/B532Median) ≥3 (GenePix Pro-7). Genes with P values ≤0.05 were regarded as statistically significant. Gene locus tags displayed in bold indicate genes coding for pupylated proteins (23). A, activation; R, repression.
*
Ratios of genes with P values 0.05 < P ≤ 0.1.
†
In two of the three replicates, cg1488 (leuD) showed a fold change >2.