Maturation of polycistronic mRNA by RNase Y and its associated Y-complex in Gram-positive bacteria

Endonucleolytic cleavage within polycistronic mRNAs can lead to differential stability and discordant abundance among co-transcribed genes. RNase Y, the major endonuclease for mRNA decay in Bacillus subtilis, was originally identified for its cleavage activity towards the cggR-gapA operon, an event that differentiates the expression of a glycolytic enzyme from its transcriptional regulator. A three-protein Y-complex (YlbF, YmcA, and YaaT) was recently identified that is also required for this cleavage in vivo, raising the possibility that it is an accessory factor acting to regulate RNase Y. However, whether the Y-complex is broadly required for RNase Y activity is unknown. Here we used end-enrichment RNA sequencing (Rend-seq) to globally identify operon mRNAs that undergo maturation post-transcriptionally by RNase Y and the Y-complex. We found that the Y-complex is required for the majority of RNase Y-mediated mRNA maturation events and affects riboswitch abundance in B. subtilis. In contrast, noncoding RNA maturation by RNase Y often do not require the Y-complex. Furthermore, deletion of RNase Y has more pleiotropic effects on the transcriptome and cell growth than deletions of the Y-complex. We propose that the Y-complex is a specificity factor for RNase Y, with evidence that its role is broadly distributed across low-GC Firmicutes. Overall design: 16 Rend-seq experiments in B. subtilis and Staphylococcus aureus