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