Shared resources by the numbers

Without accounting for the limited availability of shared cellular resources, the standard model of gene expression fails to reliably predict experimental data obtained both in vivo and in vitro. To overcome this limitation, we developed a dynamical model of gene expression explicitly modeling competition for scarce resources. In addition to accurately describing the experimental data, this model only depends on a handful of easily identifiable parameters with clear physical interpretation. Based on this model, we characterized the combinations of protein concentrations that are simultaneously realizable with shared resources, matching experimental data both in vitro and in vivo. Application examples of these results include the design of optimal experiments for parts characterization, the characterization of parts whose expression is not accessible through direct measurements, and the standardization of cell-free extracts. Finally, some ongoing efforts will be discussed within the context of biological controller design to address some of the issues caused by the scarcity of shared resources.