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

• Published in: RNA (Cambridge) Vol. 29; no. 8; pp. 1108 - 1116
• Main Authors: Deves, Valentin, Trinquier, Aude, Gilet, Laetitia, Alharake, Jawad, Condon, Ciarán, Braun, Frédérique
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.08.2023
• Subjects: Antibiotics; Chloroplasts; Endoribonucleases - genetics; Endoribonucleases - metabolism; Gene expression; Gram-positive bacteria; Life Sciences; Membrane Transport Proteins - genetics; Membrane Transport Proteins - metabolism; Open Reading Frames; Protein Biosynthesis; Ribosomes - genetics; Ribosomes - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; TmRNA; Translation; translation; RNA processing and decay; Bacillus subtilis; Rae1; chloramphenicol resistance; RNA processing and decay translation Rae1 chloramphenicol resistance Bacillus subtilis
• ISSN: 1355-8382; 1469-9001; 1469-9001
• DOI: 10.1261/rna.079692.123

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. Similar to , Rae1 cleavage within is both translation- and reading frame-dependent. Consistent with this, we show that translation-dependent cleavage by Rae1 promotes ribosome rescue by the tmRNA.