Charting unknown metabolic reactions by mass spectrometry-resolved stable-isotope tracing metabolomics

Yang Gao, Mingdu Luo, Hongmiao Wang, Zhiwei Zhou, Yandong Yin, Ruohong Wang, Beizi Xing, Xiaohua Yang, Yuping Cai () and Zheng-Jiang Zhu ()
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Yang Gao: Chinese Academy of Sciences
Mingdu Luo: Chinese Academy of Sciences
Hongmiao Wang: Chinese Academy of Sciences
Zhiwei Zhou: Chinese Academy of Sciences
Yandong Yin: Chinese Academy of Sciences
Ruohong Wang: Chinese Academy of Sciences
Beizi Xing: Chinese Academy of Sciences
Xiaohua Yang: Chinese Academy of Sciences
Yuping Cai: Chinese Academy of Sciences
Zheng-Jiang Zhu: Chinese Academy of Sciences

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: Abstract Metabolic reactions play important roles in organisms such as providing energy, transmitting signals, and synthesizing biomacromolecules. Charting unknown metabolic reactions in cells is hindered by limited technologies, restricting the holistic understanding of cellular metabolism. Using mass spectrometry-resolved stable-isotope tracing metabolomics, we develop an isotopologue similarity networking strategy, namely IsoNet, to effectively deduce previously unknown metabolic reactions. The strategy uncovers ~300 previously unknown metabolic reactions in living cells and mice. Specifically, we elaborately chart the metabolic reaction network related to glutathione, unveiling three previously unreported reactions nestled within glutathione metabolism. Among these, a transsulfuration reaction, synthesizing γ-glutamyl-seryl-glycine directly from glutathione, underscores the role of glutathione as a sulfur donor. Functional metabolomics studies systematically characterize biochemical effects of previously unknown reactions in glutathione metabolism, showcasing their diverse functions in regulating cellular metabolism. Overall, these newly uncovered metabolic reactions fill gaps in the metabolic network maps, facilitating exploration of uncharted territories in cellular biochemistry.

Date: 2025
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DOI: 10.1038/s41467-025-60258-7

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