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

PLoS One. 2020 Feb 13;15(2):e0229103. doi: 10.1371/journal.pone.0229103. eCollection 2020.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin Assembly and Disassembly / genetics
  • Chromatin Assembly and Disassembly / physiology
  • DNA Repair / genetics
  • Oxidative Stress / genetics
  • Oxidative Stress / physiology
  • RNA, Transfer / metabolism*
  • Ribose / metabolism*
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • tRNA Methyltransferases / genetics
  • tRNA Methyltransferases / metabolism

Substances

  • Saccharomyces cerevisiae Proteins
  • Ribose
  • RNA, Transfer
  • Trm7 protein, S cerevisiae
  • tRNA Methyltransferases

Grants and funding

This research was completed with support from a SUNY Polytechnic Institute Seed Grant (LE, https://sunypoly.edu/sponsored-research.html) and an award from the Dr. Nuala McGann Drescher Diversity and Inclusion Leave Program (LE, https://goer.ny.gov).