Extended Data Fig. 4: Predictions of the growth-optimized (naive) model for flux balance analysis of lysine harvesting.

We used a revised version of the S. cerevisiae genome-scale metabolic model (iMM904_NADcorrected²²). Six additional reactions related to cadaverine biosynthesis were added: two metabolic reactions for ornithine decarboxylase (H + lys_L → CO₂ + cadaverine) and spermine synthase (S-adenosyl 3-(methylthio)propylamine + cadaverine → S-methyl-5′-thioadenosine + aminopropyl-cadaverine), and four reactions for transporting and exchanging cadaverine and aminopropylcadaverine. In silico synthetic minimal media constraints were used according to the original model (iMM904⁴¹). For excess lysine uptake, the constraint of the l-lysine exchange reaction was fixed to a value of 1. Model simulation (FBA) was performed using the COBRA toolbox for maximum growth in both media conditions.