Extended Data Fig. 8: TSEN model is compatible with reversible enzyme kinetics and predicts nutrient perturbation responses.

a) Predictions of the minimal TSEN (3 total reactions, single intermediate) with a reversible intermediate reaction for a temperature upshift from 27 °C to 37 °C (Supplementary Text). Simulations are shown for various values of the Michaelis-Menten constants for the reversible reaction. The standard bottleneck is defined as \({K}_{M}=20\) mM, which has an activation energy of \({E}_{a}=22.5\) kcal/mol. Standard reactions have \({K}_{M}=1\) mM and \({E}_{a}=15\) kcal/mol. Simulations were conducted with saturating external nutrients (\({c}_{0}=100\) mM). Other parameters of the minimal TSEN can be found in Fig. 4a, b. Green: with a forward bottleneck only, described by a very large reverse \({K}_{M}=1000\) mM. Red: with bottlenecks in both the forward and reverse reactions. Blue: with a forward bottleneck and standard reverse reaction. Purple: with forward and reverse reactions both possessing standard \({K}_{M}\) values. b) The TSEN model responds to a nutrient pulse from a steady state with low nutrient concentration through increased metabolite production. The full TSEN (5 intermediate reactions) with a single bottleneck (standard kinetic values in black, bottleneck values in red on left) was simulated under sub-saturating, low-nutrient conditions (\({c}_{0}=\,\)0.1 mM) until steady state was reached, and then an instantaneous nutrient pulse of 28 mM was added at \(t=\) 0 min, with no nutrients subsequently provided. Simulations were performed in a 1 L container. Left: growth rate dynamics predicted by the bottlenecked TSEN after the nutrient pulse. Standard (black) and bottleneck (red) parameter values are shown. Middle: predicted intracellular metabolite concentrations, colored by location in network during the nutrient pulse and subsequent depletion. Dynamics depend on network position. Right: External nutrient concentration throughout the simulation. c) The TSEN model responds to starvation exit through slow metabolite production. The full TSEN (5 intermediate reactions) with a single bottleneck (standard kinetic values in black, bottleneck values in red on left) was simulated under starvation-like conditions (\({c}_{0}=\,\)0.01 mM) until steady state was reached, and then the nutrient concentration was shifted to a saturating condition (\({c}_{0}=\)100 mM) at \(t=\) 0 min. Left: growth rate dynamics after the nutrient shift predicted by the bottlenecked TSEN. Standard (black) and bottleneck (red) parameter values are shown. Right: intracellular metabolite concentrations, colored by position in network, during the shift.