An Integrated Modeling and Experimental Approach to Study the Influence of Environmental Nutrients on Biofilm Formation of Pseudomonas aeruginosa

Table 1

Top ten biofilm-associated reactions with large flux increase upon addition of amino acids into the medium (adapted from [9]).

Reactions	Biological subsystems
Rxn 1: 2 H^+ + H2O + urea → CO2 + 2 ammonium	Arginine metabolism
Rxn 2: acetate + ATP + coenzyme A → acetyl-CoA + AMP + diphosphate	Pyruvate metabolism
Rxn 3: L-threonine → 2-oxobutanoate + ammonium	Ammonia production
Rxn 4: 2 ATP + L-glutamine + H2O + bicarbonate → 2 ADP + carbamoyl phosphate + L-glutamate + 2 H^+ + phosphate	Arginine metabolism
Rxn 5: nicotinamide adenine dinucleotide + O-phospho-4-hydroxy-L-threonine → 2-amino-3-oxo-4-phosphonooxybutyrate + H^+ + nicotinamide adenine dinucleotide – reduced	Pyridoxine metabolism
Rxn 6: 4-aminobutanoate + 2-oxoglutarate → L-glutamate + succinic semialdehyde	Glutamate production
Rxn 7: L-aspartate + ATP + L-citrulline → AMP + N(omega)-(L-arginino)succinate + H^+ + diphosphate	Arginine metabolism
Rxn 8: reduced glutathione + methylglyoxal → (R)-S-lactoylglutathione	Pyruvate metabolism
Rxn 9: S-adenosyl-L-methionine + butyryl-[acyl-carrier protein] → 5-methylthioadenosine + acyl carrier protein + H^+ + N-butyryl-L-homoserine lactone	Quorum sensing
Rxn 10: alpha-oxobenzeneacetic acid ↔ benzaldehyde + CO2	CO2 production