Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
Department of Molecular Biology, University of Geneva, Geneva, Switzerland.
Elife. 2023 Jan 4;12:e84295. doi: 10.7554/eLife.84295.
Although the genetic code of the yeast 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, 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.
尽管酵母的遗传密码在 25 年前就已经被测序，但对其基因功能的描述还远远不够完整。缺乏对基因功能的完整映射阻碍了对细胞生物学的系统理解。高通量代谢组学的出现提供了一种独特的方法，可以通过具有成本效益、稳健性和广泛适用性的优势来揭示基因功能。在这里，我们使用流动注射飞行时间质谱法，在雷帕霉素处理的时间过程中对 164 个 TOR 和受体或受体样基因的功能丧失突变体进行动态代谢组学分析，生成了一个包含超过 7000 个代谢组学测量值的数据集。为了向更广泛的社区提供资源，这些数据可通过在 https://rapamycin-yeast.ethz.ch 上托管的交互式数据可视化应用程序进行浏览。我们证明，与稳态响应相比，雷帕霉素的动态代谢物响应在恢复已知的 TOR 信号调节剂，以及识别新的调节剂时更具信息量。删除一组新基因的一部分会导致对雷帕霉素的表型和蛋白质组响应，这进一步表明它们与 TOR 信号有关。我们发现，其中一个基因与 URA10 通过嘧啶生物合成的调节有关。这些结果表明，该方法对于标记新的潜在 TOR 信号相关基因是有效的，并强调了在使用功能代谢组学提供生物学见解时，动态扰动的实用性。
