Figure 3.

A sketch of the chemical reaction network of the presented model. The RNA polymerase is assumed to be available in a fixed amount and recruited to the gene (green) promoter region (red) at a rate determined by the TFs bound to the URR (blue). The RNA transcription rate depends on the concentration of activated RNA building blocks (X_A) and consumes nX_A per RNA. The RNAs decay to inactivated components (X_I), which are reactivated via consumption of activated, energy-rich metabolites (E_A). The gene products are categorized into structural (SR) and gene regulatory (TF) RNAs. The SRs catalyse the activation of metabolites (E_I) and the incorporation of membrane building blocks $(M_{\text{I}}^{\text{int}})$ into the membrane (M). The internal pool of $M_{\text{I}}^{\text{int}}$ is coupled with the exterior pool $(M_{\text{I}}^{\text{ext}})$ via diffusion through the membrane. All the parameters for transcription factor binding to regulatory regions and the catalytic efficiencies of structural proteins are obtained by a mapping process (see text for details), and are therefore targets of evolution.