Transfer RNA halves are found as nicked tRNAs in cells: evidence that nicked tRNAs regulate expression of an RNA repair operon

Transfer RNA fragments are proposed to regulate numerous processes in eukaryotes, including translation inhibition, epigenetic inheritance, and cancer. In the bacterium Salmonella enterica serovar Typhimurium, 5 ' tRNA halves ending in 2 ',3 ' cyclic phosphate are proposed to bind the RtcR transcriptional activator, resulting in transcription of an RNA repair operon. However, since 5 ' and 3 ' tRNA halves can remain base paired after cleavage, the 5 ' tRNA halves could potentially bind RtcR as nicked tRNAs. Here we report that nicked tRNAs are ligands for RtcR. By isolating RNA from bacteria under conditions that preserve base pairing, we show that many tRNA halves are in the form of nicked tRNAs. Using a circularly permuted tRNA that mimics a nicked tRNA, we show that nicked tRNA ending in 2 ',3 ' cyclic phosphate is a better ligand for RtcR than the corresponding 5 ' tRNA half. In human cells, we show that some tRNA halves similarly remain base paired as nicked tRNAs following cleavage by anticodon nucleases. Our work supports a role for the RNA repair operon in repairing nicked tRNAs and has implications for the functions proposed for tRNA fragments in eukaryotes.

Automated summary

Transfer RNA fragments play important roles in regulating various processes in eukaryotes and bacteria. In Salmonella enterica serovar Typhimurium, nicked tRNAs ending in 2',3' cyclic phosphate are ligands for the RtcR transcriptional activator and contribute to RNA repair. Similarly, in human cells, tRNA fragments can also remain as nicked tRNAs after cleavage. This research provides insights into the function of tRNA fragments in both bacteria and eukaryotes.