Identification of a new substrate for the ribosome associated endoribonuclease Rae1 reveals a link to theB. subtilisresponse and sensitivity to chloramphenicol

Abstract

ABSTRACTRae1 is a well-conserved endoribonuclease among Gram-positive bacteria, cyanobacteria and the chloroplasts of higher plants. We have previously shown that Rae1 cleaves theBacillus subtilis yrzIoperon mRNA in a translation-dependent manner, within a short open reading frame (ORF) called S1025, encoding a 17-amino acid (aa) peptide of unknown function. Here, we map a new Rae1 cleavage site in thebmrBCDoperon mRNA encoding a multidrug transporter, within a previously unannotated 26-aa short ORF that we have namedbmrX. Similar to S1025, Rae1 cleavage withinbmrXis both translation- and reading frame-dependent. Both mRNAs were previously shown to be induced by the presence of the protein synthesis inhibitor chloramphenicol (Cm). Strikingly, arae1deletion strain shows greater resistance to Cm than the wild-type strain, while its over-expression leads to increased Cm sensitivity, suggesting a link to translation quality control. Consistent with this, we show that cleavage by Rae1 promotes ribosome rescue by the tmRNA. Globally, our data point to a role of Rae1 in mRNA surveillance by eliminating mRNAs that encounter problems with translation.