Fig. 4.

Competition for cell-free shared resources. GFP (pdh-RiboJ-RBS-GFP-MGapt-Bba_B0015) and mCherry (pdh-RiboJ-RBS-mCherry-Bba_B0015) encoding plasmid DNA were simultaneously titrated into cell-free reactions at a range of concentrations from 0 to 40 nM. The light green points (with light green error bars indicating SEs) represent the experimentally measured GFP concentrations, while the dark green lines represent the simulated trajectories. The light red points (with light red error bars indicating SE) represent the experimentally measured mCherry concentrations, while the dark red lines represent the simulated trajectories. In reactions where no mCherry plasmid was present, the full mRNA time course signal was used in parameter inference. Where the mCherry plasmid was present, the mRNA MGapt data up to 90 min was used. The system was modeled using an ODE model with 29 species and 31 parameters (an SBML model is available in the GitHub software repository, see Methods). Model parameters were simultaneously inferred from all experimental data points (GFP mRNA time-course data are shown in SI Appendix, Fig. S30) using MCMC (SI Appendix, Fig. S29 and Table S10).