Shutdown of multidrug transporter mRNA expression mediated by the ribosome-associated endoribonuclease (Rae1) cleavage in a new cryptic ORF.

Rae1 is a well-conserved endoribonuclease among Gram-positive bacteria, cyanobacteria, and the chloroplasts of higher plants. We have previously shown that Rae1 cleaves the operon mRNA in a translation-dependent manner within a short open reading frame (ORF) called , encoding a 17-amino acid (aa) peptide of unknown function. Here, we map a new Rae1 cleavage site in the operon mRNA encoding a multidrug transporter, within an unannotated 26-aa cryptic ORF that we have named Expression of the portion of the mRNA is ensured by an antibiotic-dependent ribosome attenuation mechanism within the upstream ORF Cleavage by Rae1 within suppresses expression that escapes attenuation control in the absence of antibiotics.