Dynamic metabolome profiling uncovers potential TOR signaling genes
Although the genetic code of the yeast Saccharomyces cerevisiae was sequenced 25 years ago, the characterization of the roles of genes within it is far from complete. The lack of a complete mapping of functions to genes hampers systematic understanding of the biology of the cell. The advent of high-...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2023-01-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/84295 |
| _version_ | 1797961724556476416 |
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| author | Stella Reichling Peter F Doubleday Tomas Germade Ariane Bergmann Robbie Loewith Uwe Sauer Duncan Holbrook-Smith |
| author_facet | Stella Reichling Peter F Doubleday Tomas Germade Ariane Bergmann Robbie Loewith Uwe Sauer Duncan Holbrook-Smith |
| author_sort | Stella Reichling |
| collection | DOAJ |
| description | Although the genetic code of the yeast Saccharomyces cerevisiae was sequenced 25 years ago, the characterization of the roles of genes within it is far from complete. The lack of a complete mapping of functions to genes hampers systematic understanding of the biology of the cell. The advent of high-throughput metabolomics offers a unique approach to uncovering gene function with an attractive combination of cost, robustness, and breadth of applicability. Here, we used flow-injection time-of-flight mass spectrometry to dynamically profile the metabolome of 164 loss-of-function mutants in TOR and receptor or receptor-like genes under a time course of rapamycin treatment, generating a dataset with >7000 metabolomics measurements. In order to provide a resource to the broader community, those data are made available for browsing through an interactive data visualization app hosted at https://rapamycin-yeast.ethz.ch. We demonstrate that dynamic metabolite responses to rapamycin are more informative than steady-state responses when recovering known regulators of TOR signaling, as well as identifying new ones. Deletion of a subset of the novel genes causes phenotypes and proteome responses to rapamycin that further implicate them in TOR signaling. We found that one of these genes, CFF1, was connected to the regulation of pyrimidine biosynthesis through URA10. These results demonstrate the efficacy of the approach for flagging novel potential TOR signaling-related genes and highlight the utility of dynamic perturbations when using functional metabolomics to deliver biological insight. |
| first_indexed | 2024-04-11T01:02:13Z |
| format | Article |
| id | doaj.art-9a801935c2f74edba40a0ca0cbdc6ed9 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-11T01:02:13Z |
| publishDate | 2023-01-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-9a801935c2f74edba40a0ca0cbdc6ed92023-01-04T15:32:43ZengeLife Sciences Publications LtdeLife2050-084X2023-01-011210.7554/eLife.84295Dynamic metabolome profiling uncovers potential TOR signaling genesStella Reichling0Peter F Doubleday1https://orcid.org/0000-0002-1784-1282Tomas Germade2https://orcid.org/0000-0002-5144-1266Ariane Bergmann3Robbie Loewith4https://orcid.org/0000-0002-2482-603XUwe Sauer5Duncan Holbrook-Smith6https://orcid.org/0000-0003-0787-3165Institute of Molecular Systems Biology, ETH Zurich, Zurich, SwitzerlandInstitute of Molecular Systems Biology, ETH Zurich, Zurich, SwitzerlandInstitute of Molecular Systems Biology, ETH Zurich, Zurich, SwitzerlandDepartment of Molecular Biology, University of Geneva, Geneva, SwitzerlandDepartment of Molecular Biology, University of Geneva, Geneva, SwitzerlandInstitute of Molecular Systems Biology, ETH Zurich, Zurich, SwitzerlandInstitute of Molecular Systems Biology, ETH Zurich, Zurich, SwitzerlandAlthough the genetic code of the yeast Saccharomyces cerevisiae was sequenced 25 years ago, the characterization of the roles of genes within it is far from complete. The lack of a complete mapping of functions to genes hampers systematic understanding of the biology of the cell. The advent of high-throughput metabolomics offers a unique approach to uncovering gene function with an attractive combination of cost, robustness, and breadth of applicability. Here, we used flow-injection time-of-flight mass spectrometry to dynamically profile the metabolome of 164 loss-of-function mutants in TOR and receptor or receptor-like genes under a time course of rapamycin treatment, generating a dataset with >7000 metabolomics measurements. In order to provide a resource to the broader community, those data are made available for browsing through an interactive data visualization app hosted at https://rapamycin-yeast.ethz.ch. We demonstrate that dynamic metabolite responses to rapamycin are more informative than steady-state responses when recovering known regulators of TOR signaling, as well as identifying new ones. Deletion of a subset of the novel genes causes phenotypes and proteome responses to rapamycin that further implicate them in TOR signaling. We found that one of these genes, CFF1, was connected to the regulation of pyrimidine biosynthesis through URA10. These results demonstrate the efficacy of the approach for flagging novel potential TOR signaling-related genes and highlight the utility of dynamic perturbations when using functional metabolomics to deliver biological insight.https://elifesciences.org/articles/84295metabolomicschemical geneticsTOR signalingsystems biologychemical biology |
| spellingShingle | Stella Reichling Peter F Doubleday Tomas Germade Ariane Bergmann Robbie Loewith Uwe Sauer Duncan Holbrook-Smith Dynamic metabolome profiling uncovers potential TOR signaling genes eLife metabolomics chemical genetics TOR signaling systems biology chemical biology |
| title | Dynamic metabolome profiling uncovers potential TOR signaling genes |
| title_full | Dynamic metabolome profiling uncovers potential TOR signaling genes |
| title_fullStr | Dynamic metabolome profiling uncovers potential TOR signaling genes |
| title_full_unstemmed | Dynamic metabolome profiling uncovers potential TOR signaling genes |
| title_short | Dynamic metabolome profiling uncovers potential TOR signaling genes |
| title_sort | dynamic metabolome profiling uncovers potential tor signaling genes |
| topic | metabolomics chemical genetics TOR signaling systems biology chemical biology |
| url | https://elifesciences.org/articles/84295 |
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