The Stress-Dependent Dynamics of <i>Saccharomyces cerevisiae</i> tRNA and rRNA Modification Profiles
RNAs are key players in the cell, and to fulfil their functions, they are enzymatically modified. These modifications have been found to be dynamic and dependent on internal and external factors, such as stress. In this study we used nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS)...
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MDPI AG
2021-08-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/9/1344 |
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| author | Yasemin Yoluç Erik van de Logt Stefanie Kellner-Kaiser |
| author_facet | Yasemin Yoluç Erik van de Logt Stefanie Kellner-Kaiser |
| author_sort | Yasemin Yoluç |
| collection | DOAJ |
| description | RNAs are key players in the cell, and to fulfil their functions, they are enzymatically modified. These modifications have been found to be dynamic and dependent on internal and external factors, such as stress. In this study we used nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS) to address the question of which mechanisms allow the dynamic adaptation of RNA modifications during stress in the model organism <i>S. cerevisiae</i>. We found that both tRNA and rRNA transcription is stalled in yeast exposed to stressors such as H<sub>2</sub>O<sub>2</sub>, NaAsO<sub>2</sub> or methyl methanesulfonate (MMS). From the absence of new transcripts, we concluded that most RNA modification profile changes observed to date are linked to changes happening on the pre-existing RNAs. We confirmed these changes, and we followed the fate of the pre-existing tRNAs and rRNAs during stress recovery. For MMS, we found previously described damage products in tRNA, and in addition, we found evidence for direct base methylation damage of 2′O-ribose methylated nucleosides in rRNA. While we found no evidence for increased RNA degradation after MMS exposure, we observed rapid loss of all methylation damages in all studied RNAs. With NAIL-MS we further established the modification speed in new tRNA and 18S and 25S rRNA from unstressed <i>S. cerevisiae</i>. During stress exposure, the placement of modifications was delayed overall. Only the tRNA modifications 1-methyladenosine and pseudouridine were incorporated as fast in stressed cells as in control cells. Similarly, 2′-O-methyladenosine in both 18S and 25S rRNA was unaffected by the stressor, but all other rRNA modifications were incorporated after a delay. In summary, we present mechanistic insights into stress-dependent RNA modification profiling in <i>S. cerevisiae</i> tRNA and rRNA. |
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| format | Article |
| id | doaj.art-26f97050f9be424c8f8ea05be977b5b0 |
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| language | English |
| last_indexed | 2024-03-10T07:38:25Z |
| publishDate | 2021-08-01 |
| publisher | MDPI AG |
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| series | Genes |
| spelling | doaj.art-26f97050f9be424c8f8ea05be977b5b02023-11-22T13:13:37ZengMDPI AGGenes2073-44252021-08-01129134410.3390/genes12091344The Stress-Dependent Dynamics of <i>Saccharomyces cerevisiae</i> tRNA and rRNA Modification ProfilesYasemin Yoluç0Erik van de Logt1Stefanie Kellner-Kaiser2Department of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, GermanyDepartment of Chemistry, Ludwig-Maximilians University Munich, 81377 Munich, GermanyDepartment of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, GermanyRNAs are key players in the cell, and to fulfil their functions, they are enzymatically modified. These modifications have been found to be dynamic and dependent on internal and external factors, such as stress. In this study we used nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS) to address the question of which mechanisms allow the dynamic adaptation of RNA modifications during stress in the model organism <i>S. cerevisiae</i>. We found that both tRNA and rRNA transcription is stalled in yeast exposed to stressors such as H<sub>2</sub>O<sub>2</sub>, NaAsO<sub>2</sub> or methyl methanesulfonate (MMS). From the absence of new transcripts, we concluded that most RNA modification profile changes observed to date are linked to changes happening on the pre-existing RNAs. We confirmed these changes, and we followed the fate of the pre-existing tRNAs and rRNAs during stress recovery. For MMS, we found previously described damage products in tRNA, and in addition, we found evidence for direct base methylation damage of 2′O-ribose methylated nucleosides in rRNA. While we found no evidence for increased RNA degradation after MMS exposure, we observed rapid loss of all methylation damages in all studied RNAs. With NAIL-MS we further established the modification speed in new tRNA and 18S and 25S rRNA from unstressed <i>S. cerevisiae</i>. During stress exposure, the placement of modifications was delayed overall. Only the tRNA modifications 1-methyladenosine and pseudouridine were incorporated as fast in stressed cells as in control cells. Similarly, 2′-O-methyladenosine in both 18S and 25S rRNA was unaffected by the stressor, but all other rRNA modifications were incorporated after a delay. In summary, we present mechanistic insights into stress-dependent RNA modification profiling in <i>S. cerevisiae</i> tRNA and rRNA.https://www.mdpi.com/2073-4425/12/9/1344stress dependent RNA modification dynamicsabsolute quantification of RNA modificationsisotope labelingmass spectrometry<i>Saccharomyces cerevisiae</i> |
| spellingShingle | Yasemin Yoluç Erik van de Logt Stefanie Kellner-Kaiser The Stress-Dependent Dynamics of <i>Saccharomyces cerevisiae</i> tRNA and rRNA Modification Profiles Genes stress dependent RNA modification dynamics absolute quantification of RNA modifications isotope labeling mass spectrometry <i>Saccharomyces cerevisiae</i> |
| title | The Stress-Dependent Dynamics of <i>Saccharomyces cerevisiae</i> tRNA and rRNA Modification Profiles |
| title_full | The Stress-Dependent Dynamics of <i>Saccharomyces cerevisiae</i> tRNA and rRNA Modification Profiles |
| title_fullStr | The Stress-Dependent Dynamics of <i>Saccharomyces cerevisiae</i> tRNA and rRNA Modification Profiles |
| title_full_unstemmed | The Stress-Dependent Dynamics of <i>Saccharomyces cerevisiae</i> tRNA and rRNA Modification Profiles |
| title_short | The Stress-Dependent Dynamics of <i>Saccharomyces cerevisiae</i> tRNA and rRNA Modification Profiles |
| title_sort | stress dependent dynamics of i saccharomyces cerevisiae i trna and rrna modification profiles |
| topic | stress dependent RNA modification dynamics absolute quantification of RNA modifications isotope labeling mass spectrometry <i>Saccharomyces cerevisiae</i> |
| url | https://www.mdpi.com/2073-4425/12/9/1344 |
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