Table 1. Expression profiles of major genes of the central metabolism of M. caenitepidi Gela4 cells grown on methanol in pure culture and in co-culture with M. marinum S8; log2FC refers to log-fold changes in expression, and FDR refers to false discovery rate.
| Predicted gene product | Gene | RPKM (pure culture) |
RPKM (co-culture) |
log2FC (co-culture/pure culture) | FDR | |
|---|---|---|---|---|---|---|
| Methanol oxidation | ||||||
| GL4_0421 | Methanol dehydrogenase large subunit | mxaF | 42779 | 40524 | -0.08 | 0.308 |
| GL4_0422 | Methanol dehydrogenase small subunit | mxaJ | 8017 | 8518 | 0.09 | 0.330 |
| GL4_0423 | Cytochrome c-L | mxaG | 7201 | 6546 | -0.14 | 0.074 |
| GL4_0424 | Methanol dehydrogenase, small subunit | mxaI | 18826 | 21130 | 0.17 | 0.041 |
| GL4_0437 | Methanol dehydrogenase | xoxF1 | 1117 | 1368 | 0.29 | 0.001 |
| GL4_1130 | Methanol dehydrogenase | xoxF2 | 80 | 98 | 0.29 | 0.001 |
| GL4_1360 | Methanol dehydrogenase | xoxF3 | 1123 | 547 | -1.04 | 0.000 |
| GL4_1361 | Methanol dehydrogenase | xoxF4 | 1918 | 1115 | -0.78 | 0.000 |
| Serine cycle | ||||||
| GL4_1969 | Serine hydroxymethyltransferase | glyA | 523 | 571 | 0.13 | 0.097 |
| GL4_3378 | Serine-glyoxylate aminotransferase | sga | 320 | 162 | -0.98 | 0.000 |
| GL4_2615 | Serine-glyoxylate aminotransferase | sga2 | 1023 | 467 | -1.13 | 0.000 |
| GL4_3377 | Hydroxypyruvate reductase | hpr | 568 | 235 | -1.27 | 0.000 |
| GL4_3381 | D-glycerate 2-kinase | gckA | 78 | 89 | 0.18 | 0.021 |
| GL4_2130 | Enolase | eno | 176 | 201 | 0.20 | 0.021 |
| GL4_3372 | Phosphoenolpyruvate carboxylase | ppc | 248 | 153 | -0.69 | 0.000 |
| GL4_0105 | Malate dehydrogenase | mdh | 272 | 417 | 0.61 | 0.000 |
| GL4_3373 | Malate-CoA ligase alpha chain | mtkB | 705 | 405 | -0.80 | 0.000 |
| GL4_3374 | Malate-CoA ligase beta chain | mtkA | 684 | 435 | -0.65 | 0.000 |
| GL4_3371 | Malyl-CoA lyase | mcl1 | 971 | 638 | -0.61 | 0.000 |
| Acetyl-CoA synthetase and EMC pathway | ||||||
| GL4_0367 | Acetyl-coenzyme A synthetase | acsA | 98 | 1181 | 3.57 | 0.000 |
| GL4_0014 | Acetyl-CoA acetyltransferase | atoB | 749 | 812 | 0.11 | 0.200 |
| GL4_0015 | Acetoacetyl-CoA reductase | phaB | 331 | 418 | 0.34 | 0.001 |
| GL4_3328 | 3-hydroxybutyryl-CoA dehydrogenase | hbdA | 371 | 517 | 0.48 | 0.000 |
| GL4_3337 | Crotonyl-CoA carboxylase/reductase | ccr | 869 | 1097 | 0.34 | 0.000 |
| GL4_3336 | Methylsuccinyl-CoA dehydrogenase | mcd | 283 | 293 | 0.05 | 0.593 |
| GL4_2084 | Methylmalonyl-CoA epimerase | Mcee | 173 | 165 | -0.06 | 0.430 |
| GL4_3338 | Ethylmalonyl-CoA mutase | ecm | 161 | 218 | 0.43 | 0.000 |
| GL4_0095 | Mesaconyl-CoA hydratase | mch | 188 | 181 | -0.05 | 0.367 |
| GL4_3371 | malyl-CoA lyase | mcl1 | 971 | 638 | -0.61 | 0.000 |
| GL4_0468 | L-malyl-CoA/beta-methylmalyl-CoA lyase | mcl2 | 50 | 237 | 2.22 | 0.000 |
| TCA cycle | ||||||
| GL4_2103 | Citrate synthase | citA | 250 | 403 | 0.69 | 0.000 |
| GL4_0055 | Aconitate hydratase | acnA | 294 | 153 | -0.94 | 0.000 |
| GL4_1694 | Isocitrate dehydrogenase | icd | 346 | 185 | -0.90 | 0.000 |
| GL4_0108 | 2-oxoglutarate dehydrogenase E1 component | sucA | 386 | 652 | 0.75 | 0.000 |
| GL4_0109 | 2-oxoglutarate dehydrogenase E2 component | sucB | 265 | 585 | 1.14 | 0.000 |
| GL4_0107 | Succinyl-CoA ligase alpha chain | sucD | 132 | 700 | 2.40 | 0.000 |
| GL4_0106 | Succinyl-CoA ligase beta chain | sucC | 217 | 673 | 1.63 | 0.000 |
| GL4_0100 | Succinate dehydrogenase flavoprotein subunit | sdhA | 252 | 217 | -0.22 | 0.004 |
| GL4_0101 | Succinate dehydrogenase iron-sulfur protein | sdhB | 296 | 274 | -0.11 | 0.091 |
| GL4_0098 | Succinate dehydrogenase cytochrome b-556 subunit | sdhC | 677 | 779 | 0.20 | 0.009 |
| GL4_0099 | Succinate dehydrogenase hydrophobic membrane anchor protein | sdhD | 140 | 136 | -0.05 | 0.585 |
| GL4_1597 | Fumarate hydratase | fum | 131 | 104 | -0.33 | 0.000 |
| GL4_0105 | Malate dehydrogenase | mdh | 272 | 417 | 0.61 | 0.000 |
| Ethanol oxidation | ||||||
| GL4_0818 | Alcohol dehydrogenase | adhA | 78 | 56 | -0.49 | 0.000 |
| GL4_0813 | Aldehyde dehydrogenase | aldA | 222 | 6354 | 4.83 | 0.000 |