TABLE 2.
Selected genes differentially expressed upon overexpression of σBa
| Gene group or locus tagb | Gene name | log2FC | Adjusted P value | Predicted function |
|---|---|---|---|---|
| Genes upregulated by aerobic stress and positively regulated by σB | ||||
| CD630DERM_00530 | mrnC | 1.9 | 3.29E-05 | Ribonuclease III domain |
| CD630DERM_01750 | 8.2 | 1.11E-06 | Oxidoreductase, Fe-S subunit | |
| CD630DERM_01760 | 8.0 | 1.52E-06 | Oxidoreductase, NAD/flavin adenine dinucleotide (FAD) binding subunit | |
| CD630DERM_01920 | cls | 2.6 | 2.35E-04 | Cardiolipin synthetase 1 |
| CD630DERM_03500 | 1.9 | 4.63E-05 | Putative hydrolase, HAD superfamily | |
| CD630DERM_03510 | 1.8 | 5.66E-05 | Conserved hypothetical protein | |
| CD630DERM_05600 | nfo | 4.0 | 3.5E-05 | Endonuclease IV |
| CD630DERM_05610 | 2.0 | 2.39E-05 | Putative aldo-/ketoreductase; putative ferredoxin | |
| CD630DERM_05650 | nth | 3.7 | 5.66E-06 | Endonuclease III |
| CD630DERM_05660 | 2.5 | 6.62E-06 | Putative tRNA/rRNA methyltransferase | |
| CD630DERM_05800 | gapN | 6.2 | 1.38E-06 | Glyceraldehyde-3-phosphate dehydrogenase (NADP+) (GAPDH) |
| CD630DERM_11250 | 5.5 | 1.15E-05 | Nitroreductase family protein | |
| CD630DERM_11570 | norV | 4.0 | 5.16E-06 | Anaerobic nitric oxide reductase flavorubredoxin (FlRd) (FlavoRb) |
| CD630DERM_13410 | exoA | 1.8 | 6.76E-05 | Exodeoxyribonuclease |
| CD630DERM_14630 | 1.8 | 1.77E-04 | Conserved hypothetical protein | |
| CD630DERM_15240 | 4.8 | 1.88E-05 | Putative rubrerythrin | |
| CD630DERM_15260 | pyrC | 1.6 | 1.98E-04 | Dihydroorotase |
| CD630DERM_15760 | 1.6 | 2.71E-02 | Putative arylesterase | |
| CD630DERM_16220 | 2.7 | 1.03E-04 | Putative lipoprotein | |
| CD630DERM_16230 | 6.5 | 4.21E-06 | NADH-oxygen oxidoreductase | |
| CD630DERM_16240 | vanR | 1.6 | 8.84E-05 | Two-component response regulator |
| CD630DERM_16900 | trxA | 5.3 | 1.31E-06 | Thioredoxin reductase |
| CD630DERM_16910 | trxB | 5.3 | 1.62E-06 | Putative thioredoxin disulfide reductase |
| CD630DERM_17780 | 2.6 | 1.19E-05 | Conserved hypothetical protein | |
| CD630DERM_17790 | 2.4 | 1.46E-05 | Conserved hypothetical protein | |
| CD630DERM_18180 | ispH | 1.8 | 5.35E-05 | 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase |
| CD630DERM_18220 | bcp | 6.1 | 2.70E-05 | Putative thiol peroxidase |
| CD630DERM_18970 | 1.8 | 3.20E-05 | Conserved hypothetical protein | |
| CD630DERM_19430 | 3.3 | 3.62E-06 | Conserved hypothetical protein | |
| CD630DERM_20460 | 5.5 | 5.60E-06 | Conserved hypothetical protein | |
| CD630DERM_21170 | trxB2 | 5.0 | 1.86E-05 | Thioredoxin reductase |
| CD630DERM_21650 | 2.2 | 1.04E-04 | Transcriptional regulator, helix-turn-helix (HTH)-type | |
| CD630DERM_24760 | 4.6 | 5.84E-06 | Conserved hypothetical protein | |
| CD630DERM_27960 | cwp10 | 5.1 | 2.47E-05 | Cell surface protein |
| CD630DERM_27970 | 5.1 | 1.75E-05 | Putative calcium binding adhesion protein | |
| CD630DERM_29930 | 3.8 | 3.07E-05 | Conserved hypothetical protein | |
| CD630DERM_30380 | 3.9 | 2.21E-05 | Conserved hypothetical protein | |
| CD630DERM_30390 | 4.1 | 1.07E-05 | Putative ATPase | |
| CD630DERM_30400 | 2.1 | 8.46E-05 | Conserved hypothetical protein | |
| CD630DERM_30420 | 2.6 | 2.47E-05 | Putative membrane protein | |
| CD630DERM_33070 | 3.8 | 1.51E-06 | Putative phosphoesterase | |
| CD630DERM_33100 | 3.1 | 6.31E-06 | Putative d-isomer specific 2-hydroxyacid dehydrogenase | |
| CD630DERM_33110 | 2.9 | 1.19E-05 | Conserved hypothetical protein | |
| CD630DERM_34080 | 2.3 | 3.38E-05 | Putative DNA mismatch repair ATPase MutS | |
| CD630DERM_34090 | scoC (hprK) | 2.4 | 1.74E-05 | Phosphotransferase (PTS) system, HPr kinase/phosphorylase |
| CD630DERM_34100 | uvrC | 2.7 | 1.19E-05 | Excinuclease subunit C |
| CD630DERM_34730 | atpC2 | 1.6 | 2.90E-04 | ATP synthase C chain |
| CD630DERM_34760 | atpZ | 1.6 | 2.42E-04 | Putative ATP synthase protein |
| CD630DERM_36100 | 4.6 | 2.38E-05 | Conserved hypothetical protein | |
| CD630DERM_36140 | 2.5 | 1.07E-05 | Conserved hypothetical protein, DUF1130 family | |
| Other genes involved in oxidative/nitrosative stress positively regulated by σB | ||||
| CD630DERM_01740 | cooS | 8.3 | 1.20E-06 | Carbon monoxide dehydrogenase |
| CD630DERM_12790 | iscS2 | 2.8 | 2.00E-03 | Cysteine desulfurase |
| CD630DERM_12800 | 3.0 | 1.56E-03 | Putative NifU-like protein | |
| CD630DERM_14740 | 5.0 | 1.28E-05 | Putative rubrerythrin (Rr) | |
| CD630DERM_15940 | cysK | 3.4 | 4.44E-03 | O-acetyl-serine thiol-lyase A (O-acetyl-sulfhydrylase) (OAS-TL) |
| CD630DERM_18230 | 6.8 | 5.93E-06 | Conserved hypothetical protein, UPF0246 family | |
| CD630DERM_21660 | msrAB | 4.7 | 1.24E-05 | Peptide methionine sulfoxide reductase MsrA/MsrB |
a
Genes positively regulated by σB and aerobic stress and other genes involved in oxidative/nitrosative stress (7, 19) are highlighted here.
b
CD numbers corresponding to the published annotation of strain CD630 (52) can be derived by removing “630DERM” and removing the last digit (in case of a 0) or replacing it with an A (in the case of a 1).