TABLE 6.
Transcript levels of putative key genes of the adapted Entner-Doudoroff pathway for galacturonate metabolism and the Wood-Ljungdahl pathway for acetogenesis in meta-transcriptome samples of the “Ca. G. soehngenii” chemostat enrichment cultures expressed as reads per kilobase million (RPKM, average ± average deviation) based on technical triplicates of duplicate enrichment cultures.
| Protein function | EC number | Gene ID | RPKM |
| Adapted entner-doudoroff pathway | |||
| Uronate isomerase | 5.3.1.12 | F7O84_RS17360 | 5852 ± 2398 |
| Tagaturonate reductase | 1.1.1.58 | F7O84_RS17370 | 3067 ± 1236 |
| Altronate dehydratase | 4.2.1.7 | F7O84_RS17375 | 8426 ± 3296 |
| 2-Dehydro-3-deoxygluconokinase | 2.7.1.45 | F7O84_RS17390 | 3863 ± 1343 |
| 2-Dehydro-3-deoxyphosphogluconate aldolase | 4.1.2.14 | F7O84_RS17395 | 1752 ± 245 |
| Acetate production | |||
| Pyruvate:ferredoxin oxidoreductase | 1.2.7.1 | F7O84_RS03200 | 4145 ± 278 |
| Pyruvate formate lyase | 6.2.1.3 | F7O84_RS03160 | 1893 ± 651 |
| Phosphate acetyltransferase | 2.3.1.8 | F7O84_RS05985 | 1500 ± 176 |
| Acetate kinase | 2.7.2.1 | F7O84_RS05980 | 1625 ± 200 |
| Wood-Ljungdahl pathway | |||
| Formate dehydrogenase | 1.17.1.9 | F7O84_RS07405 | 14 ± 3 |
| Formate–tetrahydrofolate ligase | 6.3.4.3 | F7O84_RS05385 | 256 ± 58 |
| Methenyl-tetrahydrofolate cyclohydrolase/methylene–tetrahydrofolate dehydrogenase | 3.5.4.9 and 1.5.1.5 | F7O84_RS05385 | 236 ± 9 |
| Methyl–tetrahydrofolate reductase | 1.5.1.20 | F7O84_RS08335 | 126 ± 13 |
| 5-methyl-tetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase | 2.1.1.258 | F7O84_RS02745 | 144 ± 19 |
| CO-methylating acetyl-CoA synthase | 2.3.1.169 | n.d. | |
| CO dehydrogenase | 1.2.7.4 | n.d. | |
| Prismane/CO dehydrogenase family | 1.7.99.1 | F7O84_RS02405 | 40 ± 8 |
| Prismane/CO dehydrogenase family | 1.7.99.1 | F7O84_RS11645 | 315 ± 51 |
| Energy-metabolism associated genes | |||
| Electron transport complex protein A | 7.2.1.2 | F7O84_RS03295 | 58 ± 5 |
| Electron transport complex protein B | 7.2.1.2 | F7O84_RS03300 | 261 ± 40 |
| Electron transport complex protein C | 7.2.1.2 | F7O84_RS03275 | 329 ± 22 |
| Electron transport complex protein DG | 7.2.1.2 | F7O84_RS03290 | 101 ± 13 |
| Electron transport complex protein E | 7.2.1.2 | F7O84_RS03285 | 143 ± 9 |
| Ferredoxin hydrogenase subunit A | 1.12.7.2 | F7O84_RS09545 | 196 ± 100 |
| Ferredoxin hydrogenase subunit B | 1.12.7.2 | F7O84_RS09550 | 356 ± 32 |
| Ferredoxin hydrogenase subunit C | 1.12.7.2 | F7O84_RS04820 | 124 ± 86 |
N.d., not detected.