Qualitative Modeling and Simulation of the Carbon Starvation Response in E. coli Exercises Delphine Ropers and Hidde de Jong

The common intestinal bacterium Escherichia coli is without any doubt the best-studied organism in the world. Apart from the fact that pathogenic strains of this bacterium cause, among other things, urinary infections in humans, it is important as a model organism for other bacteria and higher organisms. This has led the editors of a reference work on E. coli to remark that “all cell biologists have two cells of interest: the one they are studying and Escherichia coli ” ([23], p. 4). Upon depletion of an essential nutrient, like a carbon source, an exponentially-growing E. coli population may enter a non-growth state, thus making a transition from exponential to stationary phase (figure 1). During this growth-phase transition, individual bacteria develop a resistance to multiple stresses that allow them to survive the adverse environmental conditions. In this set of exercises, we will build mathematical models of the key part of the genetic regulatory network controlling the carbon starvation response of E. coli cells. The models will be used to simulate the transition from exponential to stationary phase by means of the program Genetic Network Analyzer (GNA). After a brief introduction to the biology of the carbon starvation response in section 1