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How do the metabolites, GTP and (p)ppGpp, simultaneously control the occurrence of translational errors and resource allocation in bacteria?

Abstract : Even though diverse mechanisms cooperate to prevent protein synthesis errors in bacteria, missense and translational frameshift errors (TFEs) can occur . In particular, TFEs were detected at low levels in the exponential growth phase and at higher levels in the stationary phase in both Escherichia coli and Bacillus subtilis. This observation led researchers to revisit the role of the “stringent response” in the occurrence of TFEs since it is the key mechanism involved in the bacterial adaptation to nutritional downshifts. It relies on the interaction between the RelA/SpoT proteins and the translating ribosomes, which leads to the detection of uncharged tRNAs and to the production of an alarmone called (p)ppGpp. In a relA mutant strains unable to synthesize (p)ppGpp, translational errors are highly increased.In this context, the main goal of our work was to revisit the role of the stringent response in the translational error control and to clarify the role of the two key, antagonistic metabolites GTP and (p)ppGpp. Indeed, while GTP enhances translation initiation (targeting the initiation factor IF2) and elongation (targeting the elongation factor EF-Tu) , (p)ppGpp inhibits GTP biosynthesis (reducing the enzyme activity of Gmk, HprT and GuaB) and translation initiation (competing with GTP on IF2).For this purpose, we used the Gram positive model bacterium B. subtilis, designed three distinct reporter systems to detect TFEs and built a strain unable to synthesize (p)ppGpp (called “(p)ppGpp0”). We observed that during growth in poor media TFEs were increased in the absence of (p)ppGpp in the exponential phase (i.e. steady-state growth) and that by contrast to the wild type, the (p)ppGpp0 strain exhibited a TFE burst during the transition in rich medium to the stationary phase. By controlling intracellular levels of GTP in the (p)ppGpp0 strain, we showed that GTP abundance is the trigger factor of TFEs occurrence. Nevertheless, upon a "weak" induction of GTP biosynthesis leading to sub-optimal growth rates, the TFEs rate still peaked during the transition to the stationary phase, which demonstrated that the mode of action of (p)ppGpp to prevent TFEs occurrence did not only rely on its inhibition of GTP biosynthesis. We then focused on the (p)ppGpp inhibitory effect on IF2 and mimicked its action by injecting drugs known to inhibit translation initiation. Hence, we demonstrated that by reducing translation initiation (injecting drugs) upon aminoacyl-tRNAs depletion (p)ppgGp0 wild-strain type cells is are able to optimally control the rate of TFEs in the transition to the stationary phase. The same conclusion is obtained even in presence of a high GTP level.In a second part, we studied how transcription and translation are affected by variations in GTP and (p)ppGpp abundances. We observed that genes possessing a transcription start site (TSS) made of two guanines were more importantly transcribed at higher growth rates than genes possessing a TSS made of two adenines. This difference was even more pronounced for (p)ppGpp0 strains grown in rich medium upon guanosine addition (leading to a high level of GTP). Moreover, the ribosomal RNAs (rrns; for which the TSS is a guanine) synthesis level seemed to be positively correlated to GTP levels during exponential growth in poor and rich media as observed by the modulation of GTP biosynthesis.In conclusion, we demonstrated that (p)ppGpp controls the occurrence of translational errors during steady-state growth by decreasing GTP levels and during a nutritional downshift by specifically inhibiting translation initiation ensuring a parsimonious , which also globally affects resource allocation.
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Claire Baudier. How do the metabolites, GTP and (p)ppGpp, simultaneously control the occurrence of translational errors and resource allocation in bacteria?. Molecular biology. Université Paris Saclay (COmUE), 2018. English. ⟨NNT : 2018SACLS202⟩. ⟨tel-02887100⟩

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