A research team led by Professor Tsutomu Suzuki and Assistant Professor Takayuki Ohira at the University of Tokyo has uncovered an unexpected role for precursor transfer RNAs (pre-tRNAs) in regulating protein synthesis. The study demonstrates that pre-tRNAs are not merely intermediates in tRNA maturation but can function as regulatory molecules that help cells adapt to environmental stress and may contribute to heat-stress sensing.

Transfer RNAs (tRNAs) are essential adaptor molecules that decipher genetic information carried by messenger RNAs (mRNAs) into proteins. Before becoming mature tRNAs, they are synthesized as precursor molecules (pre-tRNAs) that undergo multiple processing steps. Although pre-tRNAs have long been regarded as transient intermediates, their physiological significance has remained largely unexplored.

The research team previously discovered that some pre-tRNAs carry a 5′ cap structure, a modification typically associated with RNA polymerase II transcripts such as mRNAs (Ohira and Suzuki, Nature Chemical Biology, 2016). In the present study, the researchers investigated the biological role of this phenomenon, termed pre-tRNA capping, in budding yeast.

To comprehensively analyze capped pre-tRNAs, the team developed a new sequencing method, CaSh-seq (Capped Short RNA sequencing), which combines anti-cap immunoprecipitation with next-generation sequencing. Using this approach, they found that capped pre-tRNAs are generated from all yeast tRNA genes and that the abundance of capped pre-tRNAs increases markedly under heat-stress conditions. The analysis also revealed the transcription-units of all yeast tRNA genes with a single nucleotide-resolution.

Proposed mechanism of translation initiation regulation by pre-tRNA capping under heat stress

Further experiments revealed that capped pre-tRNAs interact with eIF4E, a cap-binding protein that is a component of translation initiation complex. In vitro translation assays showed that capped pre-tRNAs selectively inhibit cap-dependent translation, whereas decapped pre-tRNAs do not. Cellular reporter assays further demonstrated that accumulation of pre-tRNAs suppresses cap-dependent protein synthesis in vivo.

These findings suggest that capped pre-tRNAs compete with mRNAs for access to eIF4E, thereby reducing translation initiation during heat stress. Because elevated temperature appears to relax the 5′-terminal structure of pre-tRNAs and promote their capping, pre-tRNAs may themselves act as molecular sensors that couple temperature changes to translation control. The study uncovers a previously unrecognized mechanism linking environmental stress to translational control and expands the biological significance of RNA capping beyond its established roles in mRNA metabolism.

Source – University of Tokyo

Availability – All original code is available from a public GitHub repository https://github.com/ITKKC/cashseqcalc.