Fig. 5. Environmental shifts temporarily deviate from the expected growth rate vs RNA/protein ratio trend as the cell reallocates biomass to optimize growth.

Growth rate and RNA/protein mass ratio plotted over time starting in rich media, removing amino acids from the media and adding amino acids back once the cell has adjusted to the new media with all regulation (a), no mechanistic amino acid supply (b) and no ppGpp regulation (c). The blue trace is an average of 32 cell lineages with circles indicating each hour of simulation. The stringent response shows a sharply suppressed growth rate immediately after an environmental downshift with all regulation. Without modeling kinetic amino acid supply, translation is not as limited so the full stringent response will not be activated. Without ppGpp regulation, the cellular composition has limited reorganization because there is not a differential response between the RNA and protein growth rates and the effect of the stringent response can be seen in the difference in growth rate response when compared to having ppGpp regulation included. Growth rate of RNA (light purple) and protein (dark purple) fractions of the cell over time are shown for all regulation (d), no mechanistic amino acid supply (e) and no ppGpp regulation (f). A higher protein growth rate will result in a decreasing RNA/protein ratio, while a higher RNA growth rate will result in an increasing RNA/protein ratio. RNA polymerase output (g), RNA degradation rate (h), and mRNA to rRNA mass ratio (i) for simulations with all regulation included (blue) compared to simulations with no ppGpp regulation (gray). Data comes from 28 generations and 32 initial seeds.