m5U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs

Abstract

Transfer RNA (tRNA) molecules contain various post-transcriptional modifications that are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation to gene expression control and cellular stress response. Recent evidence indicates that tsRNAs are also modified, however, the impact of tRNA epitranscriptome deregulation on tsRNAs generation is only now beginning to be uncovered. The 5-methyluridine (m5U) modification at position 54 of cytosolic tRNAs is one of the most common and conserved tRNA modifications among species. The tRNA methyltransferase TRMT2A catalyzes this modification, but its biological role remains mostly unexplored. Here, we show that TRMT2A knockdown in human cells induces m5U54 tRNA hypomodification and tsRNA formation. More specifically, m5U54 hypomodification is followed by overexpression of the ribonuclease angiogenin (ANG) that cleaves tRNAs near the anticodon, resulting in accumulation of 5′tRNA-derived stress-induced RNAs (5′tiRNAs), namely 5′tiRNA-GlyGCC and 5′tiRNA-GluCTC, among others. Additionally, transcriptomic analysis confirms that down-regulation of TRMT2A and consequently m5U54 hypomodification impacts the cellular stress response and RNA stability, which is often correlated with tiRNA generation. Accordingly, exposure to oxidative stress conditions induces TRMT2A down-regulation and tiRNA formation in mammalian cells. These results establish a link between tRNA hypomethylation and ANG-dependent tsRNAs formation and unravel m5U54 as a tRNA cleavage protective mark.

Deciphering the tRNA-derived small RNAs: origin, development, and future

“…The accumulated 5’ tRNAs were shown to be able to activate the uncapped translational repressor program [ 58 , 59 ], resulting in reduced protein synthesis [ 58 ]. As a tRNA methyltransferase, TRMT2A can catalyze 5-methyluridine (m 5 U) modification at position 54 of cytoplasmic tRNAs [ 60 ]. TRMT2A knockdown promoted m 5 U54 tRNA hypomodification and enhanced ANG-dependent production of 5’tiRNA-GlyGCC and 5’tiRNA-GluCTC.…”

“…Furthermore, Pereira M et al found that silencing TRMT2A inhibited global protein synthesis, however, they did not establish whether TRMT2A-induced 5’ tiRNA can directly modulate protein synthesis (Fig. 2A ) [ 60 ]. In pancreatic β-cells, the methylation transferase, TRMT10A, is responsible for methylating guanosine at the tRNA-Gln and tRNA iniMeth position 9 (m 1 G9) [ 61 – 63 ].…”

tRNA derived small RNAs—Small players with big roles

“…The size of tRFs can vary between 10–50 nucleotides ( Ma et al, 2021 ; Yuan et al, 2021 ). Since then, more comprehensive naming systems have been proposed for tRFs ( Megel et al, 2015 ; Xie et al, 2020 ; Pereira et al, 2021 ). Among the five categories, tRFs derived from mature tRNAs are more predominant ( Keam and Hutvagner, 2015 ).…”

“…The extent of posttranscriptional modifications of parent tRNA has been shown to influence the biogenesis of tRFs ( Pereira et al, 2021 ). Queuosine (Q) modification in the wobble anticodon position of some tRNAs was found to inhibit cleavage by endonuclease Angiogenin and alter the pool of tRFs in human cells ( Wang et al, 2018 ).…”

“…M5U54 tRNA hypomodification was observed in TRMT2A mutant human cells followed by an increase in angiogenin-dependent tRFs production. Interestingly, oxidative stress has been shown to downregulate TRMT2A in mammalian cells linking oxidative stress to increased tRFs production ( Pereira et al, 2021 ).…”