TABLE 3

Overrepresented KEGG pathways, Pfam domains, and secondary-metabolism-related annotation terms among the down- and upregulated genes of the ΔrpnR strain compared to the wild typea

Gene regulationLocationOverrepresented term in ΔrpnR strain
DownregulatedKEGG pathwaysKEGG third level: ribosome
KEGG second level: translation
KEGG first level: genetic information processing
KEGG second level: nucleotide metabolism
KEGG third level: RNA transport
Secondary-metabolism clustersPart of secondary-metabolism cluster 49
UpregulatedKEGG pathwaysKEGG first level: metabolism
KEGG second level: overview
KEGG third level: valine, leucine and isoleucine degradation
KEGG second level: xenobiotics biodegradation and metabolism
KEGG third level: fatty acid metabolism
KEGG second level: amino acid metabolism
KEGG third level: fatty acid biosynthesis
KEGG fourth level: K00059:fabG; 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
KEGG EC: acyl-carrier protein
KEGG third level: biosynthesis of unsaturated fatty acids
KEGG second level: lipid metabolism
KEGG second level: carbohydrate metabolism
KEGG third level: biotin metabolism
KEGG third level: propanoate metabolism
KEGG third level: chlorocyclohexane and chlorobenzene degradation
KEGG third level: benzoate degradation
KEGG third level: toluene degradation
KEGG EC: EC 1.1.1.65
KEGG fourth level: K05275:E1.1.1.65; pyridoxine 4-dehydrogenase (EC 1.1.1.65)
KEGG fourth level: K01714:dapA; 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)
KEGG EC: EC 4.3.3.7
KEGG second level: metabolism of cofactors and vitamins
KEGG third level: metabolism of xenobiotics by cytochrome P450
KEGG third level: aminobenzoate degradation
KEGG third level: caprolactam degradation
KEGG third level: fatty acid degradation
KEGG third level: carbon metabolism
KEGG third level: vitamin B6 metabolism
KEGG third level: PPAR signaling pathway
KEGG third level: butanoate metabolism
KEGG third level: chemical carcinogenesis
Pfam domainsPF13561.1 enoyl-(acyl carrier protein) reductase
PF08659.5 KR domain
PF00106.20 short-chain dehydrogenase
PF00107.21 zinc-binding dehydrogenase
PF00701.17 dihydrodipicolinate synthetase family
Secondary-metabolism clustersPart of secondary-metabolism cluster 75
Part of secondary-metabolism cluster: decorating
Other termsTransmembrane domain
  • a All the strains were grown in TM-G for 16 h, followed by 4 h in MM-X.