Table 10.
Energy metabolism.
| Gene | Function | Fold change | Fe content | Fur/RyhB regulation | Other regulation | ||
|---|---|---|---|---|---|---|---|
| 7 min | 25 min | 45 min | |||||
| asrA | Anaerobic sulfite reductase subunit A | 0.39 | 0.36 | 0.26 | Yes | ||
| asrC | Anaerobic sulfite reductase subunit C | 0.56 | 0.47 | 0.42 | Yes | ||
| cyoA | Cytochrome o ubiquinol oxidase subunit II | n.s. | 0.71 | 0.39 | No | [3, 5, 10, 16] | CpxAR [13] |
| cyoB | Cytochrome o ubiquinol oxidase subunit I | n.s. | n.s. | 0.41 | Yes | [3, 5, 10, 16] | FlhDC [4], CpxAR[13] |
| cyoC | Cytochrome o ubiquinol oxidase subunit III | 0.52 | 0.64 | 0.36 | No | [3, 5, 10, 16] | FlhDC [4], CpxAR[13] PspF [7] |
| cyoD | Cytochrome o ubiquinol oxidase subunit IV | 0.59 | 0.79 | 0.46 | No | [3, 5, 10, 16] | FlhDC [4], CpxAR[13] |
| dmsA | Anaerobic dimethyl sulfoxide reductase chain A precursor | 0.35 | 0.30 | 0.29 | Yes | [10] | FlhDC[1, 4, 15], PspF [7] |
| dmsB | Anaerobic dimethyl sulfoxide reductase chain B | 0.40 | 0.33 | 0.29 | Yes | [10] | FlhDC [1, 4], PspF [7] |
| dmsC | Anaerobic dimethyl sulfoxide reductase chain C | 0.43 | 0.42 | 0.39 | No | [3, 10] | FlhD [1] |
| fdhE | Formate dehydrogenase accessory protein | 0.38 | 0.42 | 0.43 | Yes | ||
| fdhF | Formate dehydrogenase H | 0.39 | 0.35 | 0.27 | Yes | ||
| fdoG | Formate dehydrogenase-O, major subunit | 0.15 | 0.23 | 0.16 | Yes | [5] | |
| fdoH | Formate dehydrogenase-O beta subunit | 0.16 | 0.23 | 0.20 | Yes | [5] | |
| fdoI | Formate dehydrogenase-O subunit gamma | 0.11 | 0.17 | 0.13 | Yes | [5] | PspF [7] |
| frdA | Fumarate reductase flavoprotein subunit | 0.58 | 0.44 | 0.38 | No | [3, 5, 10, 11, 12, 14] | FlhDC [4] |
| frdB | Fumarate reductase iron-sulfur subunit | 0.59 | 0.46 | 0.40 | Yes | [3, 5, 10] | FlhDC [4] |
| frdD | Fumarate reductase subunit D | n.s. | 0.50 | 0.48 | No | [3, 5, 10] | FlhDC [4] |
| glpA | Sn-glycerol-3-phosphate dehydrogenase subunit A | 0.50 | 0.33 | 0.25 | No | [3, 10] | FlhDC [1, 4], PspF [8], CpxAR [8] |
| glpB | Anaerobic glycerol-3-phosphate dehydrogenase subunit B | n.s. | 0.50 | 0.43 | No | [3, 10] | FlhDC [1, 4], PspF [8], CpxAR [8] |
| glpC | Sn-glycerol-3-phosphate dehydrogenase subunit C | 0.47 | 0.35 | 0.29 | Yes | [3, 10] | FlhDC [1], PspF [8], CpxAR [8] |
| hyaD | Hydrogenase 1 maturation protease | 0.55 | 0.49 | 0.47 | No | ||
| hybA | Hydrogenase 2 protein HybA | 0.30 | 0.31 | 0.30 | Yes | [5] | FlhDC [4] |
| hybD | Hydrogenase 2 maturation endopeptidase | 0.48 | 0.58 | 0.70 | No | [5] | FlhDC [4] |
| hybE | Hydrogenase 2-specific chaperone | 0.42 | n.s. | n.s. | [5] | ||
| hybF | Hydrogenase nickel incorporation protein HybF | 0.34 | 0.47 | 0.56 | No | [5] | FlhDC [4] |
| hycA | Formate hydrogenlyase regulatory protein HycA | n.s. | 0.40 | 0.36 | No | ||
| hycC | Formate hydrogenlyase subunit 3 | n.s. | 0.51 | 0.38 | No | ||
| hycD | Formate hydrogenlyase subunit 4 | n.s. | 0.42 | 0.27 | No | ||
| hycE | Formate hydrogenlyase subunit 5 | 0.47 | 0.33 | 0.29 | Yes | ||
| hycF | Formate hydrogenlyase complex iron-sulfur subunit | 0.40 | 0.28 | 0.20 | Yes | PspF [7] | |
| hycG | Formate hydrogenlyase subunit 7 | 0.54 | 0.44 | 0.45 | Yes | PspF [7] | |
| hycH | Formate hydrogenlyase maturation protein | 0.34 | 0.25 | 0.21 | No | ||
| hycI | Hydrogenase 3 maturation protease | 0.35 | 0.24 | 0.21 | No | PspF [7] | |
| hydN | Electron transport protein HydN | 0.21 | 0.22 | 0.18 | Yes | ||
| hypB | Hydrogenase nickel incorporation protein HypB | n.s. | 0.56 | 0.49 | No | ||
| hypC | Hydrogenase assembly chaperone | 0.60 | 0.50 | 0.47 | Yes | ||
| napA | Nitrate reductase catalytic subunit | n.s. | 0.38 | 0.35 | Yes | [3] | FlhDC [4] |
| napD | Assembly protein for periplasmic nitrate reductase | n.s. | 0.14 | 0.10 | No | [3] | FlhDC [4] |
| napF | Ferredoxin | 0.15 | 0.11 | 0.07 | Yes | [3] | FlhDC [4] |
| ndh | NADH dehydrogenase | 0.34 | 0.32 | 0.31 | No | ||
| nirB | Nitrite reductase large subunit | n.s. | 0.40 | 0.37 | Yes | [3, 14, 16] | PspF [7] |
| nirD | Nitrite reductase small subunit | n.s. | 0.46 | 0.48 | [3, 16] | ||
| nuoA | NADH dehydrogenase subunit A | 0.38 | 0.34 | 0.33 | No | [3, 5] | CpxAR [13] |
| nuoB | NADH dehydrogenase subunit B | 0.41 | 0.36 | 0.35 | Yes | [3, 5] | CpxAR [13] |
| nuoC | Bifunctional NADH:ubiquinone oxidoreductase subunit C/D | 0.30 | 0.35 | 0.33 | No | [3, 5] | CpxAR [13] |
| nuoE | NADH dehydrogenase subunit E | 0.34 | 0.40 | 0.37 | Yes | [3, 5] | CpxAR [13] |
| nuoF | NADH dehydrogenase I subunit F | 0.35 | 0.44 | 0.40 | Yes | [3, 5] | CpxAR [13] |
| nuoG | NADH dehydrogenase subunit G | 0.38 | 0.50 | 0.52 | Yes | [3, 5] | CpxAR [13] |
| nuoH | NADH dehydrogenase subunit H | 0.22 | 0.34 | 0.33 | No | [3, 5] | CpxAR [13] |
| nuoI | NADH dehydrogenase subunit I | 0.24 | 0.36 | 0.36 | Yes | [3, 5] | CpxAR [13] |
| nuoJ | NADH dehydrogenase subunit J | 0.27 | 0.39 | 0.39 | No | [3, 5] | CpxAR [13] |
| nuoK | NADH dehydrogenase subunit K | 0.27 | 0.42 | 0.41 | No | [3, 5] | CpxAR [13] |
| nuoL | NADH dehydrogenase subunit L | 0.31 | 0.56 | 0.56 | No | [3, 5] | CpxAR [13] |
| nuoM | NADH dehydrogenase subunit M | 0.39 | 0.61 | 0.64 | No | [3, 5] | CpxAR [13] |
| pflA | Pyruvate formate lyase-activating enzyme 1 | 0.65 | 0.56 | 0.44 | Yes | ||
| pflB | Formate acetyltransferase 1 | n.s. | 0.45 | 0.50 | No | ||
| pflE | Putative pyruvate formate-lyase 3 activating enzyme | 0.14 | 0.15 | 0.12 | No | ||
| pflF | Putative formate acetyltransferase 3 | 0.14 | 0.16 | 0.14 | No | [12] | |
| sdhA | Succinate dehydrogenase flavoprotein subunit | n.s. | 0.60 | 0.33 | No | [2, 5, 10, 14] | FlhDC [4], CpxAR[13] |
| sdhB | Succinate dehydrogenase iron-sulfur subunit | n.s. | n.s. | 0.45 | Yes | [2, 5, 6] | FlhDC [4], CpxAR[13] |
| sdhC | Succinate dehydrogenase cytochrome b556 large membrane subunit | 0.50 | 0.63 | 0.44 | Yes | [2, 5, 6, 9, 14] | FlhDC [4], CpxAR[13] |
| sdhD | Succinate dehydrogenase cytochrome b556 small membrane subunit | 0.41 | 0.60 | 0.35 | Yes | [2, 5, 6, 14] | FlhDC [4], CpxAR[13] |
| torT | TMAO reductase system periplasmic protein TorT | 0.45 | 0.45 | 0.35 | No | ||
| yfiD | Autonomous glycyl radical cofactor GrcA, stress-induced alternate pyruvate formate-lyase subunit | 0.13 | 0.05 | 0.05 | No | [9] | FlhDC [4] |
Highlighted fold changes correspond to up-regulated (dark gray) and down-regulated (light gray) genes. (n.s.), fold changes with p > 0.05.
Prüß et al., 2001 [1]; Massé and Gottesman, 2002 [2]; McHugh et al., 2003 [3]; Prüß et al., 2003 [4]; Massé et al., 2005 [5]; Zhang et al., 2005 [6]; Jovanovic et al., 2006 [7]; Bury-Moné et al., 2009 [8]; Kumar and Shimizu, 2011 [9]; Troxell et al., 2011 [10]; Kim and Kwon, 2013a [11]; Kim and Kwon, 2013b [12]; Raivio et al., 2013 [13]; Wright et al., 2013 [14]; Yang et al., 2013 [15]; Calderón et al., 2014 [16].