How the initiating ribosome copes with (p)ppGpp to translate mRNAs

During host colonization, bacteria use the alarmone (p)ppGpp to reshape its proteome by acting pleiotropically on RNA and protein synthesis. Here, we elucidate how the translation Initiation Factor 2 (IF2) senses the cellular ppGpp to GTP ratio and regulates the progression towards protein synthesis. Our results show that the affinity of GTP and the inhibitory concentration of ppGpp for 30S-bound IF2 vary depending on the programmed mRNA. Highly translated mRNAs enhanced GTP affinity for 30S complexes, resulting in fast transitions to elongation of protein synthesis. Less demanded mRNAs allowed ppGpp to compete with GTP for IF2, stalling 30S complexes until exchange of the mRNA enhances the affinity for GTP. Altogether, our data unveil a novel regulatory mechanism at the onset of protein synthesis that tolerates physiological concentrations of ppGpp, and that bacteria can exploit to modulate its proteome as a function of the nutritional shift happening during infection.