Table 2. RNAseq analysis of genes involved in genes predicted to have a potential role in fermentation metabolism (see Table 3).
| Conditions | Slow growth O2-limited vs. fast growth O2-limited | Slow growth O2-limited vs. fast growth CH4-limited | Fast growth O2-limited vs. fast growth CH4-limited | Cytochrome oxidase aa3 vs. WT (both slow growth O2-limited) | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Gene | Enzyme | Locus tag | Fold change | Adjusted p values | Fold change | Adjusted p values | Fold change | Adjusted p values | Fold change | Adjusted p values |
| xfp1 | phospho-ketolase | METBUDRAFT_1551 | 2.1 | 0.031 | 1.6 | 0.258 | 0.7 | 0.013 | 1.7 | 0.219 |
| xfp2 | phospho-ketolase | METBUDRAFT_0185 | 1.3 | 0.404 | 1.3 | 0.478 | 1 | 0.904 | 1.1 | 0.997 |
| ack | acetate kinase | METBUDRAFT_1552 | 0.9 | 0.674 | 0.8 | 0.65 | 1 | 0.839 | 1.2 | 0.948 |
| acs | acetylCoA synthase | METBUDRAFT_1565 | 1.6 | 0.141 | 1.3 | 0.516 | 0.8 | 0.227 | 1.2 | 0.902 |
| pta | phosphotrans-acetylase | METBUDRAFT_1957 | 1.1 | 0.819 | 1.1 | 0.802 | 1 | 0.837 | 1 | 1 |
| ldh | lactate dehydrogenase | METBUDRAFT_3726 | 1 | 0.95 | 0.8 | 0.665 | 0.9 | 0.33 | 1 | 1 |
| mdh | malate dehydrogenase | METBUDRAFT_2208 | 1 | 0.934 | 0.9 | 0.862 | 1 | 0.825 | 1.1 | 0.997 |
| Malic enzyme | malic enzyme | METBUDRAFT_2185 | 1 | 0.916 | 1 | 0.918 | 0.9 | 0.584 | 1.1 | 0.997 |
| hox | hydrogenase | METBUDRAFT_1387 | 2.6 | 1.0 E−04 | 1.5 | 0.181 | 0.6 | 2.5 E−05 | 1.5 | 0.422 |
| METBUDRAFT_1388 | 2 | 0.01 | 1.4 | 0.364 | 0.7 | 0.004 | 1.5 | 0.51 | ||
| METBUDRAFT_1389 | 1.9 | 0.021 | 1.5 | 0.258 | 0.8 | 0.07 | 1.3 | 0.858 | ||
| METBUDRAFT_1390 | 1.5 | 0.206 | 1.5 | 0.255 | 1 | 0.866 | 1.2 | 0.901 | ||
| ndh1 | NADH dehydrogenase | METBUDRAFT_1319 | 1.2 | 0.534 | 1.3 | 0.556 | 1 | 0.871 | 1.1 | 0.997 |
| ndh2a | NADH dehydrogenase | METBUDRAFT_2827 | 0.5 | 0.03 | 0.6 | 0.091 | 1.2 | 0.45 | 1.2 | 0.907 |
| ndh2b | METBUDRAFT_2828 | 0.6 | 0.175 | 0.9 | 0.785 | 1.4 | 0.139 | 1.2 | 0.898 | |
| petA | bc1 complex | METBUDRAFT_2502 | 1.4 | 0.33 | 1.2 | 0.755 | 0.8 | 0.385 | 1.3 | 0.794 |
| petB | METBUDRAFT_2503 | 1.7 | 0.147 | 1.4 | 0.401 | 0.8 | 0.358 | 1.4 | 0.678 | |
| petC | METBUDRAFT_2504 | 1.6 | 0.138 | 1.3 | 0.555 | 0.8 | 0.128 | 1.2 | 0.919 | |
| ctaC | cytochrome oxidase (aa3-type) | METBUDRAFT_0311 | 1.9 | 0.044 | 2.1 | 0.011 | 1.1 | 0.501 | (deleted) | |
| ctaD | METBUDRAFT_0312 | 1.5 | 0.317 | 1.8 | 0.1 | 1.2 | 0.207 | (deleted) | ||
| ctaG | METBUDRAFT_0313 | 1.4 | 0.129 | 1.4 | 0.201 | 1 | 0.978 | (very low expression) | 3.57 E−09 | |
| ctaE | METBUDRAFT_0314 | 1.1 | 0.786 | 1.1 | 0.92 | 0.9 | 0.791 | (very low expression) | 1.57 E−07 | |
| cbaA | cytochrome oxidase (ba3-type) | METBUDRAFT_1311 | 1.4 | 0.24 | 2.1 | 0.005 | 1.5 | 0.001 | 1.3 | 0.856 |
| cbaB | METBUDRAFT_1312 | 1.4 | 0.302 | 2.1 | 0.011 | 1.5 | 0.002 | 1.3 | 0.858 | |
| cbaD | METBUDRAFT_1313 | 1.3 | 0.358 | 2.1 | 0.005 | 1.5 | 0.001 | 1.1 | 0.997 | |
| gnd1 | 6-phosphogluconate dehydrogenase (NADP) | METBUDRAFT_3313 | 1.6 | 0.04 | 1.5 | 0.118 | 0.9 | 0.693 | 1.5 | 0.431 |
| gnd2 | 6-phosphogluconate dehydrogenase (NAD) | METBUDRAFT_3982 | 0.9 | 0.674 | 1.1 | 0.847 | 1.3 | 0.089 | 0.9 | 0.997 |
| mtd1 | methylene H4MPT dehydrogenase | METBUDRAFT_1893 | 1.3 | 0.306 | 1.3 | 0.496 | 1 | 0.811 | 1.2 | 0.997 |
| mtd2 | methylene H4MPT dehydrogenase | METBUDRAFT_1894 | 1.1 | 0.821 | 1.1 | 0.855 | 1 | 0.95 | 1.1 | 0.997 |
| fdh1a | formate dehydrogenase (tungsten) | METBUDRAFT_0831 | 0.7 | 0.22 | 0.6 | 0.103 | 0.9 | 0.67 | 1.2 | 0.997 |
| fdh1b | METBUDRAFT_0832 | 0.6 | 0.224 | 0.6 | 0.163 | 1 | 0.977 | 1.3 | 0.728 | |
| fdh2a | formate dehydrogenase (molybdenum) | METBUDRAFT_2829 | 0.9 | 0.912 | 0.9 | 0.868 | 1 | 0.874 | 1.1 | 0.997 |
| fdh2b | METBUDRAFT_2830 | 0.8 | 0.315 | 0.7 | 0.17 | 0.9 | 0.485 | 1.1 | 0.997 | |
| fdh2c | METBUDRAFT_2831 | 1.5 | 0.115 | 0.8 | 0.4 | 0.5 | 1.64 E−06 | 1.2 | 0.989 | |
| bhr | Bacterio-hemerythrin | METBUDRAFT_0310 | 9.9 | 1.39 E−11 | 391.4 | 1.96 E−198 | 2.2 | 0.001 | 1.2 | 0.883 |