Ribosomes Regulate the Stability and Action of the Exoribonuclease RNase R

Background: Cells require mechanisms to regulate the potentially destructive action of RNases. Results: RNase R is largely bound to ribosomes in growing cells dependent on tmRNA-SmpB and nonstop mRNA. Conclusion: Ribosome binding stabilizes RNase R and sequesters it away from action on many functional RNAs. Significance: This work defines a previously unknown mechanism by which ribosomes regulate a deleterious enzyme. Ribonucleases play an important role in RNA metabolism. Yet, they are also potentially destructive enzymes whose activity must be controlled. Here we describe a novel regulatory mechanism affecting RNase R, a 3 to 5 exoribonuclease able to act on essentially all RNAs including those with extensive secondary structure. Most RNase R is sequestered on ribosomes in growing cells where it is stable and participates in trans-translation. In contrast, the free form of the enzyme, which is deleterious to cells, is extremely unstable, turning over with a half-life of 2 min. RNase R binding to ribosomes is dependent on transfer-messenger RNA (tmRNA)-SmpB, nonstop mRNA, and the modified form of ribosomal protein S12. Degradation of the free form of RNase R also requires tmRNA-SmpB, but this process is independent of ribosomes, indicating two distinct roles for tmRNA-SmpB. Inhibition of RNase R binding to ribosomes leads to slower growth and a massive increase in RNA degradation. These studies indicate a previously unknown role for ribosomes in cellular homeostasis.