2'-O-ribose methylation of transfer RNA promotes recovery from oxidative stress in Saccharomyces cerevisiae.

Lauren Endres,Taylor Rahn,Daniele Fabris,Bethany Lee,Rebecca E Rose,Frank Doyle,Jessica Seaman,William D Mcintyre,Thomas Preiss

doi:10.1371/journal.pone.0229103

Lauren Endres, Taylor Rahn + Show 7 more

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https://doi.org/10.1371/journal.pone.0229103

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Abstract

Chemical modifications that regulate protein expression at the translational level are emerging as vital components of the cellular stress response. Transfer RNAs (tRNAs) are significant targets for methyl-based modifications, which are catalyzed by tRNA methyltransferases (Trms). Here, Saccharomyces cerevisiae served as a model eukaryote system to investigate the role of 2'-O-ribose tRNA methylation in the cell's response to oxidative stress. Using 2'-O-ribose deletion mutants for trms 3, 7, 13, and 44, in acute and chronic exposure settings, we demonstrate a broad cell sensitivity to oxidative stress-inducing toxicants (i.e., hydrogen peroxide, rotenone, and acetic acid). A global analysis of hydrogen peroxide-induced tRNA modifications shows a complex profile of decreased, or undetectable, 2'-O-ribose modification events in 2'-O-ribose trm mutant strains, providing a critical link between this type of modification event and Trm status post-exposure. Based on the pronounced oxidative stress sensitivity observed for trm7 mutants, we used a bioinformatic tool to identify transcripts as candidates for regulation by Trm7-catalyzed modifications (i.e., enriched in UUC codons decoded by tRNAPheGmAA). This screen identified transcripts linked to diverse biological processes that promote cellular recovery after oxidative stress exposure, including DNA repair, chromatin remodeling, and nutrient acquisition (i.e., CRT10, HIR3, HXT2, and GNP1); moreover, these mutants were also oxidative stress-sensitive. Together, these results solidify a role for TRM3, 7, 13, and 44, in the cellular response to oxidative stress, and implicate 2'-O-ribose tRNA modification as an epitranscriptomic strategy for oxidative stress recovery.

Highlights

Transfer RNAs are fundamental biological molecules that read cognate codons in mRNA to complete the flow of genetic information from DNA to protein
Using a bioinformatics approach [30], we identified UUC-enriched transcripts in S. cerevisiae as potential Trm7-influenced translational targets and found several with biological functions linked to the oxidative stress response
In light of recent evidence that trm7 mutants activate the general amino acid control (GAAC) response pathway [31], we propose that attenuated codon-biased translation of GNP1 is a component of this response, contributing to the oxidative stress sensitivity phenotype of the trm7 mutants, which is a focus for future study

Summary

Introduction

Transfer RNAs are fundamental biological molecules that read cognate codons in mRNA to complete the flow of genetic information from DNA to protein. Methylation of tRNA at the 2’-OH position of the ribose sugar is generally thought to increase the stability of tRNA via mechanisms that protect against spontaneous hydrolysis or nuclease digestion (e.g., in non-helical regions) and reinforce intra-loop interactions that stabilize the tertiary structure of the molecule [11, 19]] Such stabilization strategies are essential for thermophilic organisms where tRNAs must carry out protein translation at denaturing temperatures, an idea supported by observations in diverse archaea that show an abundance of 2’-O-methylated nucleosides among global populations of modified tRNAs [20,21,22,23]. This work solidifies a role for 2’-O-ribose methylation in the oxidative stress response and supports a model in which S. cerevisiae uses this type of modification event in an epitranscriptomic strategy that combines increased tRNA stability and enhanced translational effects post-exposure

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