Table 2 Impact of the growth substrate on global gene expression in S. lividans ΔYA8-DG2. The data represent the 40 most strongly unregulated genes during growth on protocatechuate compared to mannitol (p < 0.05, log2fold change > 2.0). The encoded enzymes of the EMP pathway are linked to glycolysis and gluconeogenesis (
), mannitol catabolism (
), and pigment biosynthesis (
). 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. 3). n = 3
), mannitol catabolism (
), and pigment biosynthesis (
). 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 |
|---|---|---|---|---|
M | Monooxygenase | SLYA8N_19810 | − 5.7 | − 0.9* |
M | Heavy metal reductase | SLYA8N_19790 | − 5.5 | − 0.7 |
M | Arsenite resistance protein ArsB | SLYA8N_19800 | − 5.2 | − 2.0 |
R | Transcriptional regulator | SLYA8N_19795 | − 5.0 | − 2.4 |
| Substrate binding protein, smoE | SLYA8N_28225 | − 4.6 | − 5.3 |
| Integral membrane sugar transport protein, smoF | SLYA8N_28220 | − 4.6 | − 5.7 |
| Hypothetical protein | SLYA8N_28205 | − 4.6 | − 5.0 |
| Transcriptional regulator, smoR | SLYA8N_28230 | − 4.5 | − 4.2 |
| DNA-binding protein | SLYA8N_19785 | − 4.4 | − 0.6 |
| Integral membrane sugar transporter, smoG | SLYA8N_28215 | − 4.4 | − 4.3 |
| Zinc-binding dehydrogenase, smoD | SLYA8N_28210 | − 4.3 | − 3.3 |
U | Hypothetical protein | SLYA8N_36995 | − 4.2 | − 5.2 |
U | Hypothetical protein | SLYA8N_36990 | − 4.1 | − 5.3 |
U | Hypothetical protein | SLYA8N_36975 | − 4.1 | − 5.3 |
M | Oxidoreductase | SLYA8N_36985 | − 4.0 | − 5.0 |
M | Methyltransferase | SLYA8N_36945 | − 4.0 | − 5.6 |
M | Endoglucanase | SLYA8N_01130 | − 3.9 | − 3.0 |
M | Methylesterase | SLYA8N_36955 | − 3.9 | − 5.5 |
| Enolase 2 | SLYA8N_01125 | − 3.8 | − 3.4 |
| Deoxyribodipyrimidine photo-lyase | SLYA8N_36980 | − 3.7 | − 5.3 |
| Phytoene dehydrogenase | SLYA8N_36965 | − 3.7 | − 4.9 |
| Geranylgeranyl pyrophosphate synthase | SLYA8N_36970 | − 3.7 | − 4.2 |
| Lycopene cyclase | SLYA8N_36940 | − 3.7 | − 4.7 |
| Lipoprotein | SLYA8N_36920 | − 3.5 | − 3.7 |
| Fructose-specific permease | SLYA8N_21710 | − 3.5 | − 2.4 |
M | Secreted protein | SLYA8N_01030 | − 3.4 | − 0.4* |
| DeoR family transcriptional regulator | SLYA8N_21700 | − 3.4 | − 2.4 |
| Phytoene synthase | SLYA8N_36960 | − 3.3 | − 5.2 |
M | Sigma factor | SLYA8N_36925 | − 3.2 | − 1.4 |
| Glyceraldehyde-3-phosphate dehydrogenase | SLYA8N_01755 | − 3.2 | − 2.6 |
M | Dehydrogenase | SLYA8N_36950 | − 3.2 | − 4.8 |
M | Integral membrane lysyl-tRNA synthetase | SLYA8N_20785 | − 3.2 | − 1.5 |
| 1-Phosphofructokinase | SLYA8N_21705 | − 3.1 | − 2.8 |
U | Hypothetical protein | SLYA8N_36915 | − 2.8 | − 3.8 |
M | Secreted protein | SLYA8N_19820 | − 2.6 | 0.1 |
| Fructokinase | SLYA8N_27935 | − 2.6 | − 1.8 |
U | Hypothetical protein | SLYA8N_20790 | − 2.5 | − 0.9 |
M | Neutral zinc metalloprotease | SLYA8N_11275 | − 2.5 | 0.3* |
M | Lipoprotein | SLYA8N_17715 | − 2.4 | − 2.9 |
R | MarR family regulatory protein | SLYA8N_01120 | − 2.4 | − 2.6 |
