tRNA is a key connecting molecule in protein synthesis, responsible for converting the genetic information of mRNA into amino acid information of proteins. tRNA contains various post-transcriptional modifications, which play a crucial role in the efficiency and fidelity of genetic information transmission.
In a study published in Nature Communications, a research team led by Prof. ZHOU Xiao-Long from the Center for Excellence in Molecular Cell Science (Shanghai Institute of Biochemistry and Cell Biology) of the Chinese Academy of Sciences demonstrated the critical role of mammalian tRNA acetylation in determining translation efficiency and tRNA quality control.
N4-acetylcytidine (ac4C) was first discovered in tRNAs in the 1960s. In bacteria, it is exclusively found at the wobble position (position 34, ac4C34) of elongator tRNAMet. Its biological function is to ensure accurate recognition of AUG Met codons by avoiding misreading of near-cognate AUA Ile codons, thus maintaining translational fidelity.
In archaea, ac4C can be found in diverse positions of multiple tRNAs. ac4C accumulates in a temperature-dependent manner across all archaeal RNA species and is necessary for growth at higher temperatures.In eukaryotes, tRNA ac4C is exclusively found in C12 (ac4C12) of tRNASer and tRNALeu. Over the past 60 years, the biological function of ac4C12 in higher eukaryotes remains unclear.
In this work, researchers identified the interaction domains of Nat10 and Thumpd1. Subsequently, they purified the Thumpd1 and confirmed that Thumpd1 can directly bind to the substrate tRNA.Under physiological conditions, in WT cells, Nat10 and Thumpd1 mediated ac4C12 biogenesis in tRNALeu and tRNASer, which were then charged by cytoplasmic leucyl-tRNA synthetase and seryl-tRNA synthetase, respectively.
The generated Leu-tRNALeu and Ser-tRNASer ensured translational efficiency of ribosomal protein synthesis. They constructed a Thumpd1-deficient NIH/3T3 cell line by CRISPR-Cas9 gene editing system. Deletion of Thumpd1 led to ac4C12-hypomodification and reduced charging level of both tRNAs.They elucidated that the decoding efficiency of Leu and Ser codons was significantly impaired, particularly those with two U-A base pairs in mRNA-tRNA interaction.
ac4C12 hypomodification selectively generated rapid tRNALeu(CAG) turnover under heat stress. They demonstrated that tRNALeu(CAG) was degraded by Xrn1/Xrn2-mediated 5-3’ exonuclease digestion and modulated by Bpnt1/Bpnt2 due to regulation of intracellular 3,5’-diphosphate (pAp) level. The researchers designated this finely regulated tRNA degradation mechanism as mammalian rapid tRNA decay (mRTD).
Taken together, this comprehensive study reveals a new mechanism for the regulation of tRNA aminoacylation and translation efficiency in mammalian cells under physiological conditions through tRNA ac4C12 modification. It also clarifies the critical role of ac4C12 modification in the stability of tRNA under heat stress conditions, establishing a new pathway for the quality control of tRNA in mammalian cells. The above results further deepen our understanding of the multi-dimensional regulation of tRNA modification on mRNA translation rate and fidelity.
Reference: https://www.nature.com/articles/s41467-025-60723-3
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