Lisa Davis: Modeling Ribosome Regulation Mechanisms in Prokaryotes

We construct a model of the feedback mechanisms that regulate the abundance of ribosomes in E.coli, a prototypical prokaryotic organism. The translation process contains an important feedback loop: ribosomes are made up of proteins, which need to be translated by ribosomes. The model accounts for the main feedback loops that control abundance of ribosomes in response to external conditions. It includes the concentrations of free ribosomes, ribosomal RNA (rRNA), and ribosomal proteins. We include direct negative feedback loops where ribosomal proteins, when in excess, slow down their own translation. The effect of the signaling molecule ppGpp is also included as a negative feedback mechanism, along with the effect of the abundance of building blocks for mRNA and rRNA synthesis. The model consists of a system of six differential equations parameterized by 23 parameters. An equlibrium analysis shows that for all values of parameters, the model system has either one equilibrium S, or two equilibria S and P in the biologically feasible region of parameters.