Critical factors for precise and efficient RNA cleavage by RNase Y inStaphylococcus aureus

Abstract

Cellular processes require precise and specific gene regulation, in which continuous mRNA degradation is a major element. The mRNA degradation mechanisms should be able to degrade a wide range of different RNA substrates with high efficiency, but should at the same time be limited, to avoid killing the cell by elimination of all cellular RNA. RNase Y is a major endoribonuclease in found most Firmicutes, includingBacillus subtilisandStaphylococcus aureus. However, the molecular interactions that direct RNase Y to cleave the correct RNA molecules at the correct position remain unknown. In this work we have identified transcripts that are homologs inS. aureusandB. subtilis, and are RNase Y targets in both bacteria. Two such transcript pairs were used as models to show a functional overlap between theS. aureusand theB. subtilisRNase Y, which highlighted the importance of the nucleotide sequence of the RNA molecule itself in the RNase Y targeting process. We then truncated one model transcript to identify 103 nucleotides that are sufficient for this targeting, and detailed analyses of this region revealed sequence and structural elements that drive cleavage efficiency and fine-tune the positioning of the cleavage to a specific nucleotide bond.