Table 4.

Expression levels of genes involved in gluconeogenesis, the phosphoenolpyruvate-pyruvate-oxaloacetate node and the ethylmalonyl-CoA pathway (log₂ fold change). 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
Gluconeogenesis
SLYA8N_13150	Fructose-1,6-bisphosphatase	2.06	2.98
SLYA8N_13500	Phosphoenolpyruvate carboxykinase [GTP]	3.34	3.28
SLYA8N_35210	Pyruvate carboxylase	1.12	0.46
Phosphoenolpyruvate-pyruvate-oxaloacetate node
SLYA8N_11390	Pyruvate kinase	− 1.28	− 1.05
SLYA8N_12060	Putative NAD-dependent malic enzyme	1.14	2.06
SLYA8N_22045	Phosphoenolpyruvate carboxylase	− 0.90	− 3.63
SLYA8N_22940	NAD-dependent malic enzyme	0.16*	0.82
SLYA8N_25215	Pyruvate phosphate dikinase	5.70	6.14
SLYA8N_27640	Pyruvate kinase	− 1.03	− 1.57
Ethylmalonyl-CoA pathway
SLYA8N_04575	Fatty oxidation protein	0.21*	− 0.31*
SLYA8N_04850	Fatty acid oxidative multifunctional enzyme	− 0.52	− 1.04
SLYA8N_04855	Putative acyltransferase	− 0.33*	− 1.27
SLYA8N_06050	Oxidoreductase	3.87	3.31
SLYA8N_06055	Transcriptional regulator	0.41*	− 0.41*
SLYA8N_06060	Crotonyl-CoA reductase	6.28	3.55
SLYA8N_06065	Protein MeaA	4.29	3.42
SLYA8N_06070	Citrate lyase	2.89	2.24
SLYA8N_06075	Hypothetical protein	2.98	2.68
SLYA8N_06080	Acyl-CoA dehydrogenase	1.58	1.15
SLYA8N_06790	Acetyl-/propionyl-coenzyme A carboxylase alpha chain	0.74	− 0.61
SLYA8N_11430	Isobutyryl-CoA mutase A	0.30*	1.42
SLYA8N_11500	Putative acetyl-CoA acetyltransferase	0.65	1.47
SLYA8N_11505	Hypothetical protein	1.03	0.57
SLYA8N_11570	3-Hydroxybutyryl-CoA dehydrogenase	0.58	1.29
SLYA8N_13745	Propionyl-CoA carboxylase beta chain	0.80	− 0.56
SLYA8N_13770	Acetyl-/propionyl-coenzyme A carboxylase alpha chain	0.58	− 0.60
SLYA8N_14030	Methylmalonyl-CoA mutase	0.51	1.30
SLYA8N_14360	Isobutyryl-CoA mutase small subunit	0.42	0.34
SLYA8N_23780	Putative acyl-CoA dehydrogenase	1.24	1.57
SLYA8N_23785	Hydroxymethylglutaryl-CoA lyase	1.09	1.61
SLYA8N_23790	Acetyl-/propionyl-coenzyme A carboxylase alpha chain	0.99	1.26
SLYA8N_23795	Methylcrotonoyl-CoA carboxylase beta chain	1.35	1.51

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