2025
Vicente, Alexandre Magno; Hencel, Katarzyna; Schicktanz, Jannick; Hammann, Christian; Akay, Alper; Kaiser, Stefanie
NAIL-MS Elucidates Crucial tRNA U34 Modifications in Response to Heat Stress across Eukaryotes and Prokaryotes Journal Article
In: Journal of Molecular Biology, pp. 169228, 2025, ISSN: 0022-2836.
Abstract | Links | BibTeX | Tags: global warming, mass spectrometry, NAIL-MS, translation, tRNA modification reprogramming
@article{vicente_nail-ms_2025,
title = {NAIL-MS Elucidates Crucial tRNA U34 Modifications in Response to Heat Stress across Eukaryotes and Prokaryotes},
author = {Alexandre Magno Vicente and Katarzyna Hencel and Jannick Schicktanz and Christian Hammann and Alper Akay and Stefanie Kaiser},
url = {https://www.sciencedirect.com/science/article/pii/S0022283625002943},
doi = {10.1016/j.jmb.2025.169228},
issn = {0022-2836},
year = {2025},
date = {2025-06-01},
urldate = {2025-06-02},
journal = {Journal of Molecular Biology},
pages = {169228},
abstract = {Global warming leads to rising temperatures, necessitating organismal adaptation at the cellular level. One potential mechanism for maintaining proteome integrity during stress is the adaptation of tRNA modifications. While tRNA modification reprogramming has been well-studied under chemical stressors, its role in heat stress remains unclear. To address this, we performed a comparative analysis of tRNA modifications in Arabidopsis thaliana, Saccharomyces cerevisiae, Caenorhabditis elegans, Dictyostelium discoideum, and Escherichia coli under heat stress. We assessed the abundance of 30 modified nucleosides using isotope dilution mass spectrometry under control conditions. A. thaliana showed a similar diversity and abundance of tRNA modifications compared to other eukaryotes, suggesting conservation across species. Under heat stress, overall tRNA modification levels were largely stable, with no significant changes in modifications such as dihydrouridine and N4-acetylcytidine. However, one to four modifications per organism were altered, with uridine modifications at position 34 (U34) being the most prominent change. Here, pulse-chase NAIL-MS (nucleic acid isotope labeling coupled mass spectrometry) experiments in E. coli and S. cerevisiae revealed that changes in U34 modifications occurred not only in pre-existing tRNAs but also in newly transcribed tRNAs. These results suggest that existing tRNAs adapt as an early response to heat stress, while newly transcribed tRNAs are reprogrammed to ensure long-term survival under prolonged heat. Our findings highlight the potential role of tRNA modification reprogramming in heat stress adaptation.},
keywords = {global warming, mass spectrometry, NAIL-MS, translation, tRNA modification reprogramming},
pubstate = {published},
tppubtype = {article}
}
Global warming leads to rising temperatures, necessitating organismal adaptation at the cellular level. One potential mechanism for maintaining proteome integrity during stress is the adaptation of tRNA modifications. While tRNA modification reprogramming has been well-studied under chemical stressors, its role in heat stress remains unclear. To address this, we performed a comparative analysis of tRNA modifications in Arabidopsis thaliana, Saccharomyces cerevisiae, Caenorhabditis elegans, Dictyostelium discoideum, and Escherichia coli under heat stress. We assessed the abundance of 30 modified nucleosides using isotope dilution mass spectrometry under control conditions. A. thaliana showed a similar diversity and abundance of tRNA modifications compared to other eukaryotes, suggesting conservation across species. Under heat stress, overall tRNA modification levels were largely stable, with no significant changes in modifications such as dihydrouridine and N4-acetylcytidine. However, one to four modifications per organism were altered, with uridine modifications at position 34 (U34) being the most prominent change. Here, pulse-chase NAIL-MS (nucleic acid isotope labeling coupled mass spectrometry) experiments in E. coli and S. cerevisiae revealed that changes in U34 modifications occurred not only in pre-existing tRNAs but also in newly transcribed tRNAs. These results suggest that existing tRNAs adapt as an early response to heat stress, while newly transcribed tRNAs are reprogrammed to ensure long-term survival under prolonged heat. Our findings highlight the potential role of tRNA modification reprogramming in heat stress adaptation.
2017
Delft, Pieter; Akay, Alper; Huber, Sabrina M; Bueschl, Christoph; Rudolph, Konrad L M; Domenico, Tomás Di; Schuhmacher, Rainer; Miska, Eric A; Balasubramanian, Shankar
The Profile and Dynamics of RNA Modifications in Animals Journal Article
In: Chembiochem, vol. 18, no. 11, pp. 979–984, 2017, ISSN: 1439-4227.
Abstract | Links | BibTeX | Tags: Caenorhabditis elegans, isotopic labeling, mass spectrometry, RNA modifications, stress response, tRNA
@article{van_delft_profile_2017,
title = {The Profile and Dynamics of RNA Modifications in Animals},
author = {Pieter Delft and Alper Akay and Sabrina M Huber and Christoph Bueschl and Konrad L M Rudolph and Tomás Di Domenico and Rainer Schuhmacher and Eric A Miska and Shankar Balasubramanian},
url = {http://dx.doi.org/10.1002/cbic.201700093},
doi = {10.1002/cbic.201700093},
issn = {1439-4227},
year = {2017},
date = {2017-06-01},
journal = {Chembiochem},
volume = {18},
number = {11},
pages = {979–984},
abstract = {More than a hundred distinct modified nucleosides have been identified in
RNA, but little is known about their distribution across different
organisms, their dynamic nature and their response to cellular and
environmental stress. Mass-spectrometry-based methods have been at the
forefront of identifying and quantifying modified nucleosides. However,
they often require synthetic reference standards, which do not exist in
the case of many modified nucleosides, and this therefore impedes their
analysis. Here we use a metabolic labelling approach to achieve rapid
generation of bio-isotopologues of the complete Caenorhabditis elegans
transcriptome and its modifications and use them as reference standards to
characterise the RNA modification profile in this multicellular organism
through an untargeted liquid-chromatography tandem high-resolution mass
spectrometry (LC-HRMS) approach. We furthermore show that several of these
RNA modifications have a dynamic response to environmental stress and
that, in particular, changes in the tRNA wobble base modification
5-methoxycarbonylmethyl-2-thiouridine (mcm5 s2 U) lead to codon-biased
gene-expression changes in starved animals.},
keywords = {Caenorhabditis elegans, isotopic labeling, mass spectrometry, RNA modifications, stress response, tRNA},
pubstate = {published},
tppubtype = {article}
}
More than a hundred distinct modified nucleosides have been identified in
RNA, but little is known about their distribution across different
organisms, their dynamic nature and their response to cellular and
environmental stress. Mass-spectrometry-based methods have been at the
forefront of identifying and quantifying modified nucleosides. However,
they often require synthetic reference standards, which do not exist in
the case of many modified nucleosides, and this therefore impedes their
analysis. Here we use a metabolic labelling approach to achieve rapid
generation of bio-isotopologues of the complete Caenorhabditis elegans
transcriptome and its modifications and use them as reference standards to
characterise the RNA modification profile in this multicellular organism
through an untargeted liquid-chromatography tandem high-resolution mass
spectrometry (LC-HRMS) approach. We furthermore show that several of these
RNA modifications have a dynamic response to environmental stress and
that, in particular, changes in the tRNA wobble base modification
5-methoxycarbonylmethyl-2-thiouridine (mcm5 s2 U) lead to codon-biased
gene-expression changes in starved animals.
RNA, but little is known about their distribution across different
organisms, their dynamic nature and their response to cellular and
environmental stress. Mass-spectrometry-based methods have been at the
forefront of identifying and quantifying modified nucleosides. However,
they often require synthetic reference standards, which do not exist in
the case of many modified nucleosides, and this therefore impedes their
analysis. Here we use a metabolic labelling approach to achieve rapid
generation of bio-isotopologues of the complete Caenorhabditis elegans
transcriptome and its modifications and use them as reference standards to
characterise the RNA modification profile in this multicellular organism
through an untargeted liquid-chromatography tandem high-resolution mass
spectrometry (LC-HRMS) approach. We furthermore show that several of these
RNA modifications have a dynamic response to environmental stress and
that, in particular, changes in the tRNA wobble base modification
5-methoxycarbonylmethyl-2-thiouridine (mcm5 s2 U) lead to codon-biased
gene-expression changes in starved animals.