Table 1 Impact of the growth substrate on global gene expression in S. lividans ΔYA8-DG2. The data represent the 40 most strongly upregulated genes during growth on protocatechuate compared to mannitol (p < 0.05, log2fold change > 2.0). The encoded enzymes of the TCA cycle (
), the EMP pathway, gluconeogenesis (
), aromatic catabolism (
), and the ethylmalonyl-CoA pathway (
). Further genes encode other enzymes (M) and regulators (R), as well as proteins of unknown function (U). The samples were taken from 10 mM cultures after 12 h of incubation (Fig. 2). n = 3
), the EMP pathway, gluconeogenesis (
), aromatic catabolism (
), and the ethylmalonyl-CoA pathway (
). Further genes encode other enzymes (M) and regulators (R), as well as proteins of unknown function (U). The samples were taken from 10 mM cultures after 12 h of incubation (Fig. Function | Annotation | Gene | PCA | 4HB |
|---|---|---|---|---|
R | Two component histidine kinase | SLYA8N_18305 | 10.2 | 6.3 |
| Cytochrome B subunit | SLYA8N_33310 | 8.7 | 8.5 |
M | Glycosyl transferase | SLYA8N_18300 | 8.1 | 3.4 |
M | ABC transporter, ATP-binding protein | SLYA8N_13690 | 8.0 | 1.1* |
| Succinate dehydrogenase/fumarate reductase iron-sulfur subunit | SLYA8N_33320 | 7.6 | 8.5 |
| Hypothetical protein | SLYA8N_33325 | 7.4 | 8.3 |
M | Protease | SLYA8N_17590 | 7.3 | 0.2* |
| Succinate dehydrogenase flavoprotein subunit | SLYA8N_33315 | 7.1 | 7.6 |
| Benzaldehyde dehydrogenase | SLYA8N_02130 | 6.7 | 8.4 |
R | Transcriptional regulatory protein | SLYA8N_18310 | 6.4 | 2.8 |
| 4-Carboxymuconolactone decarboxylase | SLYA8N_05020 | 6.4 | 6.2 |
| Crotonyl-CoA reductase | SLYA8N_06060 | 6.3 | 3.6 |
| β-Ketoadipyl-CoA thiolase | SLYA8N_05000 | 6.1 | 6.2 |
U | Integral membrane protein | SLYA8N_13695 | 6.0 | 0.3* |
| Succinyl-CoA:3-ketoacid coenzyme A transferase subunit A | SLYA8N_04990 | 6.0 | 6.3 |
U | Hypothetical protein | SLYA8N_18295 | 6.0 | 0.5* |
| 3-Carboxy-cis, cis-muconate cycloisomerase | SLYA8N_05015 | 5.9 | 5.8 |
| Succinyl-CoA:3-ketoacid coenzyme A transferase subunit B | SLYA8N_04995 | 5.9 | 6.2 |
| Protocatechuate 3,4-dioxygenase subunit B | SLYA8N_05005 | 5.8 | 5.0 |
| Pyruvate phosphate dikinase | SLYA8N_25215 | 5.7 | 6.1 |
| Transmembrane transporter | SLYA8N_02135 | 5.7 | 7.3 |
| Protocatechuate 3,4-dioxygenase subunit A | SLYA8N_05010 | 5.7 | 5.3 |
R | Response regulator | SLYA8N_17595 | 5.5 | − 0.1* |
| Benzoylformate decarboxylase | SLYA8N_02125 | 5.4 | 6.6 |
M | Transport integral membrane protein | SLYA8N_13895 | 4.8 | 1.5 |
| β-Ketoadipyl-CoA thiolase | SLYA8N_04415 | 4.5 | 3.8 |
M | Alcohol dehydrogenase | SLYA8N_29215 | 4.3 | 3.8 |
| Transcriptional regulator | SLYA8N_04985 | 4.3 | 4.3 |
| Protein MeaA | SLYA8N_06065 | 4.3 | 3.4 |
M | Long-chain-fatty-acid-CoA ligase | SLYA8N_04410 | 4.2 | 3.6 |
M | Aldehyde dehydrogenase | SLYA8N_29210 | 4.0 | 3.5 |
M | Exopolysaccharide phosphotransferase | SLYA8N_08030 | 3.9 | 2.0 |
| Oxidoreductase | SLYA8N_06050 | 3.9 | 3.3 |
U | Hypothetical protein | SLYA8N_34285 | 3.8 | 3.7 |
M | Acyl-CoA dehydrogenase | SLYA8N_29235 | 3.7 | 3.5 |
M | Hypothetical protein | SLYA8N_32305 | 3.6 | 6.1 |
M | Iron-sulfur oxidoreductase subunit beta | SLYA8N_05120 | 3.5 | 1.9 |
M | Membrane protein | SLYA8N_03150 | 3.4 | 2.4 |
| Phosphoenolpyruvate carboxykinase | SLYA8N_13500 | 3.3 | 3.3 |
| p-Hydroxybenzoate hydroxylase | SLYA8N_22275 | 3.2 | 9.0 |
