RNA degradation is an essential process that allows bacteria to control gene expression and adapt to various environmental conditions. It is usually initiated by endoribonucleases (endoRNases), which produce intermediate fragments that are subsequently degraded by exoribonucleases (exoRNases). However, global studies of the coordinated action of these enzymes are lacking. Here, we compare the targetome of endoRNase Y with the targetomes of 3′-to-5′ exoRNases from Streptococcus pyogenes, namely, PNPase, YhaM, and RNase R. We observe that RNase Y preferentially cleaves after guanosine, generating substrate RNAs for the 3′-to-5′ exoRNases. We demonstrate that RNase Y processing is followed by trimming of the newly generated 3′ ends by PNPase and YhaM. Conversely, the RNA 5′ ends produced by RNase Y are rarely further trimmed. Our strategy enables the identification of processing events that are otherwise undetectable. Importantly, this approach allows investigation of the intricate interplay between endo- and exoRNases on a genome-wide scale.

RNA降解是使细菌能够控制基因表达并适应各种环境条件的重要过程。它通常由核糖核酸内切酶（endoRNases）引发，产生的中间片段随后被核糖核酸外切酶（exoRNases）降解。但是，缺乏对这些酶的协同作用的整体研究。在这里，我们比较了endoRNase Y的靶基因组和化脓性链球菌的3'至5'exoRNase的靶基因组。，即PNPase，YhaM和RNaseR。我们观察到RNase Y在鸟苷后优先裂解，生成3'至5'exoRNase的底物RNA。我们证明了RNase Y处理之后是通过PNPase和YhaM修剪新生成的3'末端。相反，由RNase Y产生的RNA 5'末端很少被进一步修剪。我们的策略可以识别原本无法检测到的处理事件。重要的是，这种方法可以在全基因组范围内研究内切酶与外切酶之间的复杂相互作用。