Fig. 5: Different theoretical frameworks lead to different predictions for the relaxation dynamics.
A–C Compare simulations of three different models for nutrient shift dynamics: this work (red solid line), the FCR model (ref. 13 - brown dashed line), and the Flux-Parity Model (FPM) (ref. 25 - pink dash-dotted line). A Dynamics of the instantaneous growth rate. Our model is the only one that predicts an overshoot of the growth rate. B Size of the amount of charged tRNAs, which is not predicted by the FCR model. For the prediction of our model, given that [tRNAc] ∝ ψA we have normalized ψA to have the same pre-shift value as the FPM prediction. C ppGpp concentration G across the shift. This can be predicted with all three models, combining the FCR framework with Eq. (6), from ref. 16 (see Supplementary Note 6 for the upgraded FCR model definition). The discrepancies between the steady-state predictions are due to the different values of the parameters used. The figure shows that of all the models tested, just our framework predicts the oscillatory response to the nutrient shift, and this is due to the presence of the incoherent feedback between amino acids levels and the ribosomal sector.
