TABLE 3.
Selected genes that are up- or downregulated when expression levels of genes of wild-type D. vulgaris cells grown under two different conditions are compared
| Gene designation | Annotation | Gene expression ratio for cells grown under the following conditions:
|
|||||
|---|---|---|---|---|---|---|---|
| 5% H2 vs lactate
|
50% H2 vs lactate
|
5% H2 vs 50% H2
|
|||||
| Log2RC | q value (%) | Log2RC | q value (%) | Log2RC | q value (%) | ||
| DVU1917 | [NiFeSe] hydrogenase, small subunit (hysB) | 4.62 | 0.00 | 0.95 | 0.00 | 3.67 | 0.00 |
| DVU1918 | [NiFeSe] hydrogenase, large subunit (hysA) | 4.5 | 0.00 | 1.10 | 0.00 | 3.31 | 0.00 |
| DVU1769 | Periplasmic [Fe] hydrogenase, large subunit (hydA) | −4.35 | 0.00 | −2.98 | 0.00 | −1.68 | 0.00 |
| DVU1770 | Periplasmic [Fe] hydrogenase, small subunit (hydB) | −2.95 | 0.00 | −2.52 | 0.00 | −1.00 | 0.11 |
| DVU2286 | Coo hydrogenase CooM | 0.40 | 22.8 | −0.62 | 0.19 | 1.24 | 0.93 |
| DVU2287 | Coo hydrogenase CooK | −0.21 | 21.88 | −0.44 | 0.19 | 0.336 | 3.03 |
| DVU2288 | Coo hydrogenase CooL | −0.96 | 0.17 | −1.55 | 0.00 | 0.75 | 0.93 |
| DVU2289 | Coo hydrogenase CooX | 0.83 | 0.50 | −0.81 | 0.00 | 1.86 | 0.00 |
| DVU2290 | Coo hydrogenase CooU | −1.38 | 0.00 | −1.65 | 0.00 | 0.25 | 3.03 |
| DVU2291 | Coo hydrogenase CooH | 0.10 | 22.80 | −0.70 | 0.04 | 0.54 | 1.80 |
| DVU0429 | Ech hydrogenase EchF | 0.21 | 21.88 | 0.13 | 0.14 | 0.08 | 5.19 |
| DVU0430 | Ech hydrogenase EchE | 3.28 | 0.00 | 0.18 | 0.14 | 3.16 | 0.15 |
| DVU0431 | Ech hydrogenase EchD | 0.77 | 0.50 | 0.90 | 0.00 | −0.14 | 4.88 |
| DVU0432 | Ech hydrogenase EchC | 1.35 | 0.00 | 1.24 | 0.00 | 0.14 | 5.19 |
| DVU0433 | Ech hydrogenase EchB | 0.85 | 0.50 | 1.07 | 0.00 | −0.21 | 4.88 |
| DVU0434 | Ech hydrogenase EchA | 1.44 | 0.00 | 1.64 | 0.00 | −0.10 | 4.88 |
| DVU0531 | HmcF | −0.12 | 23.54 | −1.04 | 0.00 | 0.81 | 0.67 |
| DVU0532 | HmcE | −0.58 | 2.07 | −0.85 | 0.04 | 0.94 | 1.28 |
| DVU0533 | HmcD | −0.46 | 4.51 | −0.99 | 0.04 | 0.72 | 1.28 |
| DVU0534 | HmcC | −0.58 | 0.99 | −1.36 | 0.00 | 0.82 | 2.74 |
| DVU0535 | HmcB | 0.66 | 3.59 | −0.18 | 0.19 | 1.22 | 0.21 |
| DVU0536 | HmcA | 0.09 | 29.47 | −0.52 | 0.04 | 0.97 | 0.47 |
| DVU2791 | Cytochrome c family protein | 1.13 | 0.06 | −0.37 | 0.19 | 1.50 | 0.00 |
| DVU2792 | Electron transport complex protein RnfC | 0.80 | 0.33 | −0.25 | 0.19 | 1.00 | 0.21 |
| DVU2793 | Electron transport complex protein RnfD | 1.63 | 0.00 | 0.93 | 0.00 | 0.71 | 1.28 |
| DVU2794 | Electron transport complex protein RnfG | 1.05 | 0.06 | 0.17 | 0.14 | 0.83 | 0.47 |
| DVU2795 | Electron transport complex protein RnfE | 1.94 | 0.00 | 1.38 | 0.00 | 0.55 | 2.40 |
| DVU2796 | Electron transport complex protein RnfA | 1.77 | 0.00 | 0.93 | 0.00 | 0.82 | 0.93 |
| DVU0846 | Adenylyl-sulfate reductase | −1.90 | 0.00 | −1.10 | 0.00 | −0.75 | 1.28 |
| DVU0847 | Adenylyl-sulfate reductase | −1.97 | 0.00 | −0.88 | 0.04 | −1.03 | 0.11 |
| DVU0848 | QmoA | −2.16 | 0.00 | −1.43 | 0.00 | −0.71 | 1.66 |
| DVU0849 | QmoB | −2.50 | 0.00 | −1.62 | 0.00 | −0.86 | 0.67 |
| DVU0850 | QmoC | −2.90 | 0.00 | −1.73 | 0.00 | −1.26 | 0.00 |
| DVU1286 | DsrP | −1.58 | 0.00 | −1.89 | 0.00 | 0.35 | 2.74 |
| DVU1287 | DsrO | −1.53 | 0.00 | −1.60 | 0.00 | 0.10 | 5.19 |
| DVU1288 | DsrJ | −1.87 | 0.00 | −2.25 | 0.00 | 0.45 | 2.56 |
| DVU1289 | DsrK | −1.80 | 0.00 | −1.83 | 0.00 | 0.06 | 5.19 |
| DVU1290 | DsrM | −0.80 | 3.59 | −1.01 | 0.04 | 0.27 | 5.19 |
| DVU0774 | ATP synthase (atpC) | −2.05 | 0.00 | −0.18 | 0.19 | −1.86 | 0.00 |
| DVU0775 | ATP synthase (atpD) | −1.81 | 0.00 | 0.11 | 0.14 | −1.90 | 0.00 |
| DVU0776 | ATP synthase (atpG) | −1.98 | 0.00 | −0.20 | 0.19 | −1.75 | 0.00 |
| DVU0777 | ATP synthase (atpA) | −1.93 | 0.00 | −0.14 | 0.19 | −1.68 | 0.00 |
| DVU0778 | ATP synthase (atpH) | −1.56 | 0.00 | 0.49 | 0.04 | −1.97 | 0.00 |
| DVU0779 | ATP synthase F0, B | −1.14 | 0.00 | 0.96 | 0.00 | −2.08 | 0.00 |
| DVU0780 | ATP synthase F0, B′ | −1.00 | 0.10 | 0.85 | 0.00 | −1.79 | 0.00 |
| DVU1056 | NikO | −0.21 | 24.17 | 0.53 | 0.14 | −0.54 | 4.88 |
| DVU1057 | NikQ | 1.13 | 0.17 | 1.24 | 0.00 | 0.07 | 5.19 |
| DVU1058 | NikM | 0.80 | 0.33 | 1.09 | 0.00 | −0.27 | 4.88 |
| DVU2769 | NikK | −0.02 | 28.70 | 0.69 | 0.04 | −0.68 | 1.66 |
| DVU0647 | Iron compound ABC transporter | 1.62 | 0.00 | 0.24 | 0.14 | 1.42 | 0.15 |
| DVU0648 | Iron compound ABC transporter | 1.69 | 0.00 | 0.81 | 0.04 | 1.13 | 0.21 |
| DVU0649 | Iron compound ABC transporter | 0.55 | 5.87 | 0.11 | 0.14 | 0.42 | 3.03 |
| DVU2292 | Hydrogenase nickel insertion protein | −1.38 | 0.00 | −1.10 | 0.00 | −0.31 | 4.88 |
| DVU2402 | Heterodisulfide reductase, A subunit (HdrA) | 1.10 | 0.00 | 0.09 | 0.14 | 1.07 | 0.36 |
| DVU2403 | Heterodisulfide reductase, B subunit (HdrB) | 1.81 | 0.00 | 0.92 | 0.00 | 0.92 | 0.41 |
| DVU2404 | Heterodisulfide reductase, C subunit (HdrC) | 1.59 | 0.00 | 0.57 | 0.04 | 1.09 | 0.93 |
| DVU0587 | Formate dehydrogenase, alpha | 2.95 | 0.00 | 1.61 | 0.00 | 1.45 | 0.00 |
| DVU0588 | Formate dehydrogenase, beta | 2.81 | 0.00 | 1.89 | 0.00 | 2.22 | 0.00 |
| DVU2797 | Cytochrome c553 | 1.23 | 0.00 | 0.69 | 0.00 | 0.56 | 1.80 |
| DVU3171 | Cytochrome c3 (TpI-c3) | −0.65 | 3.59 | −2.45 | 0.00 | 1.86 | 0.00 |
| DVU2201 | Alcohol dehydrogenase | −2.81 | 0.00 | −1.67 | 0.00 | −1.07 | 0.00 |
| DVU2396 | Alcohol dehydrogenase | 1.25 | 0.00 | 0.49 | 0.04 | 0.78 | 1.66 |
| DVU2405 | Alcohol dehydrogenase | −1.30 | 0.06 | 0.06 | 0.19 | −1.43 | 1.66 |
| DVU2545 | Alcohol dehydrogenase | 0.43 | 7.10 | 1.01 | 0.00 | −0.68 | 1.66 |
| DVU2885 | Alcohol dehydrogenase | 0.92 | 0.33 | 1.04 | 0.00 | 0.18 | 5.19 |
| DVU0353 | Alcohol dehydrogenase | −0.49 | 8.60 | 0.63 | 0.11 | −1.13 | 0.36 |