Table 3 Impact of the carbon source on the expression of genes encoding substrate uptake and degradation pathways in S. lividans ΔYA8-DG2. The strain was grown on minimal medium with 10 mM mannitol, protocatechuate (PCA), or 4-hydroxybenzoate (4HB) as the sole carbon source. Samples were taken from the cultures after 12 h (Fig. 3). The expression levels are normalized to the mannitol-based culture and are given as log2-fold change. The significance level (Benjamini‒Hochberg, FDR) was set to < 0.05, n = 3
Gene | Annotation | PCA | 4HB |
|---|---|---|---|
Mannitol uptake | |||
 SLYA8N_09400 | Phosphocarrier protein HPr | − 1.48 | − 0.87 |
 SLYA8N_17190 | Trehalose import ATP-binding protein SugC | − 1.43 | − 1.13 |
 SLYA8N_21700 | DeoR family transcriptional regulator | − 3.40 | − 2.42 |
 SLYA8N_21705 | 1-Phosphofructokinase | − 3.07 | − 2.75 |
 SLYA8N_21710 | Fructose-specific permease | − 3.47 | − 2.43 |
 SLYA8N_28205 | Hypothetical protein | − 4.56 | − 5.01 |
 SLYA8N_28210 | Zinc-binding dehydrogenase | − 4.28 | − 3.31 |
 SLYA8N_28215 | Integral membrane sugar transporter | − 4.35 | − 4.28 |
 SLYA8N_28220 | Integral membrane sugar transport protein | − 4.57 | − 5.71 |
 SLYA8N_28225 | Substrate binding protein | − 4.61 | − 5.28 |
 SLYA8N_28230 | Transcriptional regulator deoR-type | − 4.54 | − 4.20 |
Aromatic uptake and degradation | |||
 SLYA8N_02125 | Benzoylformate decarboxylase | 5.35 | 6.61 |
 SLYA8N_02130 | Benzaldehyde dehydrogenase [NAD( +)] | 6.69 | 8.36 |
 SLYA8N_02135 | Transmembrane transporter, Aromatic acid:H+ symporter | 5.66 | 7.30 |
 SLYA8N_04990 | Succinyl-CoA:3-ketoacid coenzyme A transferase subunit A | 6.02 | 6.29 |
 SLYA8N_04995 | Succinyl-CoA:3-ketoacid coenzyme A transferase subunit B | 5.89 | 6.22 |
 SLYA8N_05000 | β-Ketoadipyl-CoA thiolase | 6.13 | 6.17 |
 SLYA8N_05005 | Protocatechuate 3,4-dioxygenase beta chain | 5.78 | 5.04 |
 SLYA8N_05010 | Protocatechuate 3,4-dioxygenase alpha subunit | 5.65 | 5.28 |
 SLYA8N_05015 | 3-Carboxy-cis, cis-muconate cycloisomerase | 5.94 | 5.81 |
 SLYA8N_05020 | 4-Carboxymuconolactone decarboxylase | 6.42 | 6.19 |
 SLYA8N_22275 | p-Hydroxybenzoate hydroxylase | 3.23 | 9.01 |