Unconventional mRNA processing and degradation pathways for the polycistronic yrzI mRNA in B. subtilis

The ribosome-associated endoribonuclease Rae1 cleaves the Bacillus subtilis yrzI operon mRNA in a translation-dependent manner. This operon encodes up to four small peptides, S1027, YrzI, S1025 and S1024, whose functions were unknown. We show that YrzI is toxic at high concentrations, but co-expression with S1025 abolishes its toxicity. We show that a highly stable mRNA species containing the YrzI and S1025 open reading frames results from endoribonucleolytic cleavage upstream of the yrzI ORF followed by 5-exoribonucleolytic processing arrested by ribosomes bound to its exceptionally strong Shine-Dalgarno sequence. Degradation of this mRNA requires either translation-dependent cleavage within S1025 by Rae1 or direct attack from the structured 3-end by 3-exoribonucleases. Both pathways are atypical for a B. subtilis mRNA.