Endonucleolytic cleavage within polycistronic mRNAs can lead to differential stability, and thus discordant abundance, among cotranscribed genes. RNase Y, the major endonuclease for mRNA decay in Bacillus subtilis, was originally identified for its cleavage activity toward the cggR-gapA operon, an event that differentiates the synthesis of a glycolytic enzyme from its transcriptional regulator. A three-protein Y-complex (YlbF, YmcA, and YaaT) was recently identified as also being 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 posttranscriptionally 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 also affects riboswitch abundance in B. subtilis. In contrast, noncoding RNA maturation by RNase Y often does 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 conserved in Staphylococcus aureus.

多顺反子mRNA中的核酸内切裂解可导致共转录基因之间的差异稳定性，从而导致丰度不一致。RNase Y是枯草芽孢杆菌中导致mRNA降解的主要核酸内切酶，最初被鉴定为其对cggR-gapA的切割活性。操纵子，将糖酵解酶的合成与其转录调节子区分开的事件。最近发现，在体内进行这种裂解还需要三蛋白Y复合物（YlbF，YmcA和YaaT），这增加了它是调节RNase Y的辅助因子的可能性。 RNase Y的活性广泛需要未知。在这里，我们使用了末端富集RNA测序（Rend-seq）来全局识别通过RNase Y和Y-复合物转录后成熟的操纵子mRNA。我们发现Y-复合物是大多数RNase Y介导的mRNA成熟事件所必需的，并且还影响枯草芽孢杆菌中核糖开关的丰度。。相反，RNase Y的非编码RNA成熟通常不需要Y复合物。此外，与Y复合物的缺失相比，RNase Y的缺失对转录组和细胞生长具有更多的多效性作用。我们建议Y复合物是RNase Y的特异性因子，有证据表明其在金黄色葡萄球菌中的作用是保守的。