The Structural Basis for mRNA Recognition and Cleavage by the Ribosome-Dependent Endonuclease ReIE

Translational control is widely used to adjust gene expression levels. During the stringent response in bacteria, mRNA is degraded on the ribosome by the ribosome-dependent endonuclease, ReIE. The molecular basis for recognition of the ribosome and mRNA by ReIE and the mechanism of cleavage are unknown. Here, we present crystal structures of E. coli ReIE in isolation (2.5 angstrom) and bound to programmed Thermus thermophilus 70S ribosomes before (3.3 angstrom) and after (3.6 angstrom) cleavage. ReIE occupies the A site and causes cleavage of mRNA after the second nucleotide of the codon by reorienting and activating the mRNA for 2'-OH-induced hydrolysis. Stacking of A site codon bases with conserved residues in ReIE and 16S rRNA explains the requirement for the ribosome in catalysis and the subtle sequence specificity of the reaction. These structures provide detailed insight into the translational regulation on the bacterial ribosome by mRNA cleavage.