Dissection of the mechanism for the stringent factor ReIA

During conditions of nutrient deprivation, ribosomes are blocked by uncharged tRNA at the A site. The stringent factor ReIA binds to blocked ribosomes and catalyzes synthesis of (p)ppGpp, a secondary messenger that induces the stringent response. We demonstrate that binding of ReIA and (p)ppGpp synthesis are inversely coupled, i.e., (p)ppGpp synthesis decreases the affinity of ReIA for the ribosome. ReIA binding to ribosomes is governed primarily by mRNA, but independently of ribosomal protein L11, while (p)ppGpp synthesis strictly requires uncharged tRNA at the A site and the presence of L11. A model is proposed whereby ReIA hops between blocked ribosomes, providing an explanation for how low intracellular concentrations of ReIA (1/200 ribosomes) can synthesize (p)ppGpp at levels that accurately reflect the starved ribosome population.