Atlas of stress-induced changes in yeast tRNA modification levels
- 1University of Helsinki
Abstract
Transfer RNA (tRNA) modifications are essential for accurate translation and cellular adaptation to environmental changes. Although short-term modification dynamics are well documented, the impact of prolonged stress exposure on the global tRNA landscape remains largely unexplored. Here, we provide the first systematic profiling of tRNA modifications in Saccharomyces cerevisiae following long-term exposure to distinct stress types, including heat, suboptimal pH, oxidative stress (paraquat and diamide), osmotic stress (NaCl and KCl), and genotoxic stress (MMS). Using our broad-range UPLC-MS protocol, we characterized relative nucleoside modification changes across the global tRNA landscape, revealing that long-term stress triggers a global reprogramming of the tRNA epitranscriptome in a stress-specific and time-dependent manner. Remarkably, we identified that pH stress and paraquat induce a near-complete loss of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U34) modification, and we observe an increase in the non-thiolated 5-methoxycarbonylmethyl (mcm5U) precursor at pH 7. This coupled response is akin to that previously reported for temperature-dependent thiolation deficiency. However, the impact on thiolation is transient in the case of pH stress, but not with paraquat, suggesting two distinct stress-dependent impairment mechanisms of the thiolation pathway. To further integrate our results, we sought to normalize changes in nucleoside modification levels against potential alterations in the tRNA pool. Thus, we performed MarathonRT-based tRNA sequencing and devised the modification deviation (MDm) index. This established that the observed modification changes occurred independently of tRNA isoacceptor abundance, implying that tRNA modification levels are predominantly affected by other factors. Together, this study provides a comprehensive atlas of tRNA modification dynamics under prolonged stress, addressing a critical gap in our understanding of RNA-based translational control. Furthermore, we present the MDm index as a robust quantitative framework to decouple the influence of tRNA abundance from global modification signals, providing a necessary metric for the field to interpret epitranscriptomic reprogramming.
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BibTeX
@misc{radesic2026atlas,
title = {{Atlas of stress-induced changes in yeast tRNA modification levels}},
author = {M. Radesic and J. K. Pedor and M. S. Qasim and A.-E. Rajaveraja and N. Sipari and P. Sarin},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.17.745200},
url = {https://www.biorxiv.org/content/10.64898/2026.08.17.745200v2},
note = {CC BY},
}
RIS
TY - UNPB
TI - Atlas of stress-induced changes in yeast tRNA modification levels
AU - M. Radesic
AU - J. K. Pedor
AU - M. S. Qasim
AU - A.-E. Rajaveraja
AU - N. Sipari
AU - P. Sarin
PY - 2026
DA - 2026/08/17
PB - bioRxiv
DO - 10.64898/2026.08.17.745200
UR - https://www.biorxiv.org/content/10.64898/2026.08.17.745200v2
AB - Transfer RNA (tRNA) modifications are essential for accurate translation and cellular adaptation to environmental changes. Although short-term modification dynamics are well documented, the impact of prolonged stress exposure on the global tRNA landscape remains largely unexplored. Here, we provide the first systematic profiling of tRNA modifications in Saccharomyces cerevisiae following long-term exposure to distinct stress types, including heat, suboptimal pH, oxidative stress (paraquat and diamide), osmotic stress (NaCl and KCl), and genotoxic stress (MMS). Using our broad-range UPLC-MS protocol, we characterized relative nucleoside modification changes across the global tRNA landscape, revealing that long-term stress triggers a global reprogramming of the tRNA epitranscriptome in a stress-specific and time-dependent manner. Remarkably, we identified that pH stress and paraquat induce a near-complete loss of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U34) modification, and we observe an increase in the non-thiolated 5-methoxycarbonylmethyl (mcm5U) precursor at pH 7. This coupled response is akin to that previously reported for temperature-dependent thiolation deficiency. However, the impact on thiolation is transient in the case of pH stress, but not with paraquat, suggesting two distinct stress-dependent impairment mechanisms of the thiolation pathway. To further integrate our results, we sought to normalize changes in nucleoside modification levels against potential alterations in the tRNA pool. Thus, we performed MarathonRT-based tRNA sequencing and devised the modification deviation (MDm) index. This established that the observed modification changes occurred independently of tRNA isoacceptor abundance, implying that tRNA modification levels are predominantly affected by other factors. Together, this study provides a comprehensive atlas of tRNA modification dynamics under prolonged stress, addressing a critical gap in our understanding of RNA-based translational control. Furthermore, we present the MDm index as a robust quantitative framework to decouple the influence of tRNA abundance from global modification signals, providing a necessary metric for the field to interpret epitranscriptomic reprogramming.
ER -