Stress-induced ribosome degradation in Bacillus subtilis is mediated by the RNase Y-specificity complex

Limiting ribosome synthesis and activity is crucial for adaptation to stresses, such as heat or nutrient starvation. In Bacillus subtilis, this can be achieved through the coordinated action of the alarmones (p)ppGpp and the transcription factor Spx. Here, we performed a genetic screen to identify novel factors that contribute to the heat shock response in B. subtilis. We identified the Y-complex, which confers specificity to the endonuclease RNase Y, as a critical player under stress conditions, such as heat or transition into the stationary phase. This protein complex is required for the targeting and processing of diverse RNAs, notably the maturation of mRNAs encoding proteins involved in translation and metabolism. We further demonstrate that the Y-complex and RNase Y initiate the degradation of rRNAs of mature ribosomes, lowering their abundance. We propose that the Y-complex is a regulatory hub that modulates gene expression, adjusts protein synthesis and resource allocation.