Escherichia coli regulates its metabolism to adapt to changes in the environment, in particular to stressful downshifts in nutrient quality. Such shifts elicit the so-called stringent response coordinated by the alarmone guanosine tetra- and pentaphosphate [(p)ppGpp]. At sudden amino-acid (aa) starvation, RelA [(p)ppGpp synthetase I] activity is stimulated by binding of uncharged tRNAs to a vacant ribosomal site; the (p)ppGpp level increases dramatically and peaks within the time scale of a few minutes. The decrease of (p)ppGpp level after the peak is mediated by the decreased production of mRNA by (p)ppGpp associated transcriptional regulations, which reduces the vacant ribosomal A-site and thus constitutes a negative feedback to the RelA dependent (p)ppGpp synthesis. Here we showed that, at a sudden isoleucine starvation, this peak was higher in an E. coli strain that lacks the 10 known mRNase-encoding TA modules present in the wt strain. This observation suggested that toxins are part of the negative feedback to control the (p)ppGpp level during early stringent response. We built a ribosome trafficking model to evaluate the fold of increase in the RelA activity just after the onset of aa starvation. Combining this with a feedback model between the (p)ppGpp level and the mRNA level, we obtained reasonable fits to the experimental data for both strains. The analysis revealed that toxins are activated rapidly within a minute after the onset of starvation, reducing the mRNA half-life by ∼30 %.

IMPORTANCE: The early stringent response elicited by amino-acid starvation is controlled by a sharp increase of the cellular (p)ppGpp level. Toxin-antitoxin encoded mRNases are activated by (p)ppGpp through enhanced degradation of antitoxins. The present work shows that this activation happens at a very short time scale, and the activated mRNases negatively affects the (p)ppGpp level. The proposed mathematical model of (p)ppGpp regulation through mRNA level highlights the importance of several feedback loops in the early (p)ppGpp regulation.