Transcriptome-Wide Analyses of 5′-Ends in RNase J Mutants of a Gram-Positive Pathogen Reveal a Role in RNA Maturation, Regulation and Degradation

RNA decay and maturation have in recent years been recognised as major regulatory mechanisms in bacteria. In contrast to Escherichia coli, the Firmicute (Gram-positive) bacteria often do not encode the well-studied endonuclease RNase E, but instead rely on the endonucleases RNase Y, RNase J1 and RNase J2, of which the latter two have additionally been shown to have 5' to 3' exonucleolytic activity. We have previously demonstrated that these RNases could be deleted individually in the pathogenic Firmicute Staphylococcus aureus; however, we here present that, outside a narrow permissive window of growth conditions, deleting one or both of the RNase J genes presents serious difficulties for the cell. Moreover, an active site mutant of RNase J1 behaved like a deletion, whereas no phenotypes were detected for the RNase J2 active site mutant. Furthermore, in order to study the in vivo enzymatic activity of RNase J1 and J2, a method was developed to map the exact 5'-ends of mature and processed RNA, on a global scale. An enrichment of 5' RNA ends could be seen in the RNase J mutants, suggesting that their exonucleolytic activity is crucial for normal degradation of bulk RNA. Using the data to examine specific RNAs, we demonstrated that RNase J activity is needed for correct 5' maturation of both the 16S rRNA and the RNase P ribozyme, and can also inactivate the latter, possibly as quality control. Additional examples show that RNase J perform initial cleavages, apparently competing with ribosomes for access to mRNAs. The novel 5' mapping assay offers an exceptionally detailed view of RNase activity, and reveals that the roles of RNase J proteins are diverse, ranging from maturation and post-transcriptional regulation to degradation.