‘Tuning’ of ribosome levels mediated by RNase I and hibernating ribosomes

Ribosomes consume vast energy to synthesize proteins, so controlling the ribosome abundance is a significant concern for cells. Ribonucleases mediate ribosome degradation in response to stresses, while some ribosomes deactivate translational activity and protect themselves from degradation, called ribosome hibernation. RNase T2 is an endoribonuclease found in almost all organisms, and they are thought to be involved in the degradation of ribosomal RNA. Although it was recently reported that the activity of Escherichia coli RNase T2, called RNase I, depends on the environmental conditions, the regulation mechanism remains elusive. Here, we report how rRNA degradation by RNase I is regulated by hibernating ribosomes. Combining the biochemical, cryo-electron microscopy, and single-molecule analyses, we found that hibernating ribosome is an inhibitor by forming a complex with RNase I. Moreover, RNase I does not bind to the translating ribosome, so rRNA is protected. On the other hand, RNase I degrades the rRNA of each subunit dissociated from stalled ribosomes on aberrant mRNA by trans -translation. Under stress conditions, and even in the actively growing phase, some ribosomes are stalling or pausing. Although such ribosomes were thought to be recycled after being rescued, our results add a new insight that they are not recycled but degraded. These findings have broad implications for understanding the regulation of ribosome levels, which is critical for cellular homeostasis and response to environmental stresses.