Figure 2

Four types of transcriptional modifications during the optimization process that affect the gene expression of the ith gene. (A) a gene moves to other operon, (B and C) addition or deletion of tandem promoters, and (D) replace a tandem promoter (see Methods section named “Automatic genome design: rules for mutation and selection”). All genetic perturbations are represented by the regulatory scheme with their corresponding ODE before (left) and after (right) the genome modification. Color boxes represent mathematical terms added or removed from the ODEs to simulate gene expression of the ith gene after the genetic modification.