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

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

^* Genes not significant (Benjamini‒Hochberg FDR > 0.05) but included for completeness