{"id":{"repo_id":"dundee","oai_identifier":"oai:discovery.dundee.ac.uk:studenttheses/32e734c5-198d-4c8a-9f56-7d5d19d1ef3d"},"canonical_url":"https://search.dev.ndltd.org/etd/dundee/oai:discovery.dundee.ac.uk:studenttheses/32e734c5-198d-4c8a-9f56-7d5d19d1ef3d","repository":{"repo_id":"dundee","name":"University of Dundee","base_url":"https://discovery.dundee.ac.uk/ws/oai"},"display":{"title":"A systems biology approach unravels the biological function of two tRNA wobble base modifications in fine-tuning translation and the response to environmental stress","abstract":"tRNA molecules undergo extensive post-transcriptional modifications to produce several variations of the four canonical nucleotides. Despite the huge number of nucleotide modifications that have been identified in tRNAs, to date their biological roles and regulations continue to be poorly understood. The uridines at the wobble position of the eukaryotic cytoplasmic tRNAs tKUUU, tQUUG and tEUUC are methoxycarbonylmethylated and thiolated to form mcm5s2U34 by the ELP- and URM1-pathways, respectively. Several in vitro experiments have implicated these modifications in modulating wobbling capacity. Moreover, mutations in the ELP- and URM1-pathway genes have been associated with physiological defects in several organisms, including complex neurological disorders in humans. In this thesis we used a systems biology approach to study the in vivo functional relevance of mcm5s2U34. A sensitive, robust and quantitative proteomics workflow was developed and applied to investigate differential proteome composition in budding yeast mutants deficient in U34 modifications. We find that, in vivo and under normal conditions, mcm5s2U34 fine tunes proteome composition by ensuring efficient translation of mRNAs biased for AAA, CAA and GAA codons. Importantly, our results connect these tRNA modifications with various cellular stress response pathways. Follow up analyses of yeast cells subjected to environmental stresses were conducted and led to the discovery that the biosynthesis of mcm5s2U34 is dynamically regulated in response to growth conditions in a URM1-pathway dependent fashion. We propose that this regulation allows the cells to adjust their translational capacity during unfavourable growth conditions and contributes to the management of the environmental stress response.
Overall, this thesis presents the first extensive investigation of the functional relevance of tRNA nucleotide modifications and reports one of the few known cases wherein cells regulate the levels of modified nucleotides to fine tune their metabolism in response to environmental cues. We expect that dynamic modulation of RNA modifications will prove to be a more general regulatory mechanism of cellular processes. The experimental and analytical approaches presented in this dissertation will provide a general framework for future studies in this field.","abstract_html":"tRNA molecules undergo extensive post-transcriptional modifications to produce several variations of the four canonical nucleotides. Despite the huge number of nucleotide modifications that have been identified in tRNAs, to date their biological roles and regulations continue to be poorly understood. The uridines at the wobble position of the eukaryotic cytoplasmic tRNAs tK<sup>UUU</sup>, tQ<sup>UUG</sup> and tE<sup>UUC</sup> are methoxycarbonylmethylated and thiolated to form mcm<sup>5</sup>s<sup>2</sup>U<sub>34</sub> by the <i>ELP</i>- and <i>URM1</i>-pathways, respectively. Several <i>in vitro</i> experiments have implicated these modifications in modulating wobbling capacity. Moreover, mutations in the <i>ELP</i>- and <i>URM1</i>-pathway genes have been associated with physiological defects in several organisms, including complex neurological disorders in humans. In this thesis we used a systems biology approach to study the <i>in vivo</i> functional relevance of mcm<sup>5</sup>s<sup>2</sup>U<sub>34</sub>. A sensitive, robust and quantitative proteomics workflow was developed and applied to investigate differential proteome composition in budding yeast mutants deficient in U<sub>34</sub> modifications. We find that, <i>in vivo</i> and under normal conditions, mcm<sup>5</sup>s<sup>2</sup>U<sub>34</sub> fine tunes proteome composition by ensuring efficient translation of mRNAs biased for AAA, CAA and GAA codons. Importantly, our results connect these tRNA modifications with various cellular stress response pathways. Follow up analyses of yeast cells subjected to environmental stresses were conducted and led to the discovery that the biosynthesis of mcm<sup>5</sup>s<sup>2</sup>U<sub>34</sub> is dynamically regulated in response to growth conditions in a <i>URM1</i>-pathway dependent fashion. We propose that this regulation allows the cells to adjust their translational capacity during unfavourable growth conditions and contributes to the management of the environmental stress response.<br/>Overall, this thesis presents the first extensive investigation of the functional relevance of tRNA nucleotide modifications and reports one of the few known cases wherein cells regulate the levels of modified nucleotides to fine tune their metabolism in response to environmental cues. We expect that dynamic modulation of RNA modifications will prove to be a more general regulatory mechanism of cellular processes. The experimental and analytical approaches presented in this dissertation will provide a general framework for future studies in this field.","abstract_has_math":false,"creators":["Tyagi, Kshitiz"],"institution":"University of Dundee","degree_name":"Doctor of Philosophy","degree_level":"Doctoral Thesis","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2014,"date_issued":"2014","date_published":"2014","updated_at":"2026-07-24T02:07:59Z","subjects":[],"languages":["eng"],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["oai:discovery.dundee.ac.uk:studenttheses/32e734c5-198d-4c8a-9f56-7d5d19d1ef3d"],"render_values":[{"text":"oai:discovery.dundee.ac.uk:studenttheses/32e734c5-198d-4c8a-9f56-7d5d19d1ef3d","href":null,"code":true}]}]},"links":{"outbound_url":"https://discovery.dundee.ac.uk/en/studentTheses/32e734c5-198d-4c8a-9f56-7d5d19d1ef3d","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:creator","label":"Author","values":["Tyagi, Kshitiz"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2014"]},{"key":"dc:date.issued","label":"Date","values":["2014"]},{"key":"dc:publisher.department","label":"Dc Publisher Department","values":["Scottish Institute for ceLL Signalling"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Dundee"]},{"key":"dc:relation.isreferencedby","label":"Dc Relation Isreferencedby","values":["https://discovery.dundee.ac.uk/en/studentTheses/32e734c5-198d-4c8a-9f56-7d5d19d1ef3d"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Doctoral Thesis"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["Doctor of Philosophy"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]},{"key":"dc:rights.embargodate","label":"Dc Rights Embargodate","values":["2018-01-15"]},{"key":"dc:rights.embargoreason","label":"Dc Rights Embargoreason","values":["/dk/atira/pure/core/document/studentthesisembargoreason/commercialexploitation"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["oai:discovery.dundee.ac.uk:studenttheses/32e734c5-198d-4c8a-9f56-7d5d19d1ef3d","https://discovery.dundee.ac.uk/en/studentTheses/32e734c5-198d-4c8a-9f56-7d5d19d1ef3d"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://discovery.dundee.ac.uk/files/6180350/full_thesis_formatted_final.pdf"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["tRNA molecules undergo extensive post-transcriptional modifications to produce several variations of the four canonical nucleotides. Despite the huge number of nucleotide modifications that have been identified in tRNAs, to date their biological roles and regulations continue to be poorly understood. The uridines at the wobble position of the eukaryotic cytoplasmic tRNAs tKUUU, tQUUG and tEUUC are methoxycarbonylmethylated and thiolated to form mcm5s2U34 by the ELP- and URM1-pathways, respectively. Several in vitro experiments have implicated these modifications in modulating wobbling capacity. Moreover, mutations in the ELP- and URM1-pathway genes have been associated with physiological defects in several organisms, including complex neurological disorders in humans. In this thesis we used a systems biology approach to study the in vivo functional relevance of mcm5s2U34. A sensitive, robust and quantitative proteomics workflow was developed and applied to investigate differential proteome composition in budding yeast mutants deficient in U34 modifications. We find that, in vivo and under normal conditions, mcm5s2U34 fine tunes proteome composition by ensuring efficient translation of mRNAs biased for AAA, CAA and GAA codons. Importantly, our results connect these tRNA modifications with various cellular stress response pathways. Follow up analyses of yeast cells subjected to environmental stresses were conducted and led to the discovery that the biosynthesis of mcm5s2U34 is dynamically regulated in response to growth conditions in a URM1-pathway dependent fashion. We propose that this regulation allows the cells to adjust their translational capacity during unfavourable growth conditions and contributes to the management of the environmental stress response.
Overall, this thesis presents the first extensive investigation of the functional relevance of tRNA nucleotide modifications and reports one of the few known cases wherein cells regulate the levels of modified nucleotides to fine tune their metabolism in response to environmental cues. We expect that dynamic modulation of RNA modifications will prove to be a more general regulatory mechanism of cellular processes. The experimental and analytical approaches presented in this dissertation will provide a general framework for future studies in this field."]},{"key":"dc:title","label":"Title","values":["A systems biology approach unravels the biological function of two tRNA wobble base modifications in fine-tuning translation and the response to environmental stress"]}]}],"canonical_facts":{"dc:creator":["Tyagi, Kshitiz"],"dc:date":["2014"],"dc:date.issued":["2014"],"dc:description.abstract":["tRNA molecules undergo extensive post-transcriptional modifications to produce several variations of the four canonical nucleotides. Despite the huge number of nucleotide modifications that have been identified in tRNAs, to date their biological roles and regulations continue to be poorly understood. The uridines at the wobble position of the eukaryotic cytoplasmic tRNAs tKUUU, tQUUG and tEUUC are methoxycarbonylmethylated and thiolated to form mcm5s2U34 by the ELP- and URM1-pathways, respectively. Several in vitro experiments have implicated these modifications in modulating wobbling capacity. Moreover, mutations in the ELP- and URM1-pathway genes have been associated with physiological defects in several organisms, including complex neurological disorders in humans. In this thesis we used a systems biology approach to study the in vivo functional relevance of mcm5s2U34. A sensitive, robust and quantitative proteomics workflow was developed and applied to investigate differential proteome composition in budding yeast mutants deficient in U34 modifications. We find that, in vivo and under normal conditions, mcm5s2U34 fine tunes proteome composition by ensuring efficient translation of mRNAs biased for AAA, CAA and GAA codons. Importantly, our results connect these tRNA modifications with various cellular stress response pathways. Follow up analyses of yeast cells subjected to environmental stresses were conducted and led to the discovery that the biosynthesis of mcm5s2U34 is dynamically regulated in response to growth conditions in a URM1-pathway dependent fashion. We propose that this regulation allows the cells to adjust their translational capacity during unfavourable growth conditions and contributes to the management of the environmental stress response.
Overall, this thesis presents the first extensive investigation of the functional relevance of tRNA nucleotide modifications and reports one of the few known cases wherein cells regulate the levels of modified nucleotides to fine tune their metabolism in response to environmental cues. We expect that dynamic modulation of RNA modifications will prove to be a more general regulatory mechanism of cellular processes. The experimental and analytical approaches presented in this dissertation will provide a general framework for future studies in this field."],"dc:identifier":["oai:discovery.dundee.ac.uk:studenttheses/32e734c5-198d-4c8a-9f56-7d5d19d1ef3d","https://discovery.dundee.ac.uk/en/studentTheses/32e734c5-198d-4c8a-9f56-7d5d19d1ef3d"],"dc:identifier.uri":["https://discovery.dundee.ac.uk/files/6180350/full_thesis_formatted_final.pdf"],"dc:language":["eng"],"dc:publisher.department":["Scottish Institute for ceLL Signalling"],"dc:publisher.institution":["University of Dundee"],"dc:relation.isreferencedby":["https://discovery.dundee.ac.uk/en/studentTheses/32e734c5-198d-4c8a-9f56-7d5d19d1ef3d"],"dc:rights.embargodate":["2018-01-15"],"dc:rights.embargoreason":["/dk/atira/pure/core/document/studentthesisembargoreason/commercialexploitation"],"dc:title":["A systems biology approach unravels the biological function of two tRNA wobble base modifications in fine-tuning translation and the response to environmental stress"],"dc:type":["Thesis"],"dc:type.qualificationlevel":["Doctoral Thesis"],"dc:type.qualificationname":["Doctor of Philosophy"]},"updated_at":"2026-07-24T02:07:59Z"}