Figure 1

Schematic of the two versions of the model system. Our simulations compare two versions of a bacterial gene expression model. (A) In the first version, the genome is represented as an "average" open generating generic transcripts, rather than as the full set of individual genes. Bulk experimental measurements are used to generate the correct average number of transcripts from this generic operon in the genome. In this version of the model, the promoter residing on a plasmid of interest (plas) competes with the genomic operons for access to RNA polymerase (Rpoly) enzymes. (B) In this version, all references to the host cell genome are excluded from the model, leaving only the plasmid-borne promoter (plas) to be transcribed by RNA polymerase (Rpoly). Full lists of the reactions that constitute the models are given in Tables 1 and 2, with a list of species names given in Table 3.