Among multiple interconnected pathways for L-Lysine catabolism in pseudomonads, it has been reported that Pseudomonas aeruginosa PAO1 employs the decarboxylase and the transaminase pathways. However, knowledge of several genes involved in operation and regulation of these pathways was still missing. Transcriptome analyses coupled with promoter activity measurements and growth phenotype analyses led us to identify new members in L-Lys and D-Lys catabolism and regulation, including gcdR-gcdHG for glutarate utilization, dpkA, amaR-amaAB and PA2035 for D-Lys catabolism, lysR-lysXE for putative L-Lys efflux and lysP for putative L-Lys uptake. The amaAB operon is induced by L-Lys, D-Lys and pipecolate supporting the convergence of Lys catabolic pathways to pipecolate. Growth on pipecolate was retarded in the gcdG and gcdH mutants, suggesting the importance of glutarate in pipecolate and 2-aminoadipate utilization. Furthermore, this study indicated links in control of interconnected networks of lysine and arginine catabolism in P. aeruginosa.

Effect of D-amino acids and the genes involved in their metabolism are of great interest in both bacteria and mammals. D-Arg utilization in PAO1 requires the coupled dehydrogenases DauB and DauA. In this study, DauB was found to use only L-Arg as its substrate unlike its partner dehydrogenase DauA with wide substrate specificity. However, evidence from this study and previous studies suggest that the coupled enzymes DauB and DauA are unique for D-Arg catabolism.

The three D-amino acid dehydrogenases DguA, DadA and DauA were found to have somewhat limited in vivo substrate specificity compared to that found in vitro tested using purified enzymes. Many studies showed that D-amino acids are toxic to bacteria. The ΔdguA, ΔdadA and ΔdauA triple mutant had two-fold lower minimum inhibition concentration of carbenicillin and tetracycline compared to wild-type PAO1. Both in the wild-type PAO1 and the triple mutant, synergy was observed between gentamicin or tetracycline (at concentrations below the MIC) and D-amino acids resulting in growth inhibition or reduction, respectively. However, no special synergistic or antagonistic effects were observed specifically in the ΔdguA, ΔdadA and ΔdauA triple mutant as compared to the wild-type PAO1 when D-amino acids were given in combination with antibiotics.