Covariation MS uncovers a protein that controls cysteine catabolism

• 成果类型: Article
• 署名作者: Xiao, Haopeng; Ordonez, Martha; Fink, Emma C.; Covington, Taylor A.; Woldemichael, Hilina B.; Chen, Junyi; Jain, Mika Sarkin; Rohatgi, Milan H.; Wei, Shelley M.; Burger, Nils; Sharif, Muneeb A.; Jan, Julius; Wang, Yaoyu; Petrocelli, Jonathan J.; Blackmore, Katherine; Smythers, Amanda L.; Zhang, Bingsen; Gilbert, Matthew; Cheong, Hakyung; Khetarpal, Sumeet A.; Smith, Arianne; Bogoslavski, Dina; Lei, Yu; Vaites, Laura Pontano; Mcallister, Fiona E.; Van Bruggen, Nick; Donovan, Katherine A.; Huttlin, Edward L.; Mills, Evanna L.; Fischer, Eric S.; Chouchani, Edward T.
• 署名单位: Harvard University; Harvard University Medical Affiliates; Dana-Farber Cancer Institute; Harvard University; Harvard Medical School; Stanford Medicine; Stanford University; Stanford University; Stanford Cancer Institute; Stanford Medicine; Harvard University; Harvard University Medical Affiliates; Dana-Farber Cancer Institute; Harvard University; Harvard Medical School; Stanford University; Harvard University; Harvard Medical School; Harvard University; Harvard University Medical Affiliates; Dana-Farber Cancer Institute; Harvard University; Harvard Medical School; Howard Hughes Medical Institute
• 刊物名称: NATURE
• ISSN/ISSBN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-025-09535-5
• 发表日期: 2025-11-06
• 关键词: false discovery rate; quantitative proteomics; energy-expenditure; adipose-tissue; metabolism; database; liver; taurine; thermogenesis; ms/ms

摘要

The regulation of metabolic processes by proteins is fundamental to biology and yet is incompletely understood. Here we develop a mass spectrometry (MS)-based approach that leverages genetic diversity to nominate functional relationships between 285 metabolites and 11,868 proteins in living tissues. This method recapitulates protein-metabolite functional relationships mediated by direct physical interactions and local metabolic pathway regulation while nominating 3,542 previously undescribed relationships. With this foundation, we identify a mechanism of regulation over liver cysteine utilization and cholesterol handling, regulated by the poorly characterized protein LRRC58. We show that LRRC58 is the substrate adaptor of an E3 ubiquitin ligase that mediates proteasomal degradation of CDO1, the rate-limiting enzyme of the catabolic shunt of cysteine to taurine1. Cysteine abundance regulates LRRC58-mediated CDO1 degradation, and depletion of LRRC58 is sufficient to stabilize CDO1 to drive consumption of cysteine to produce taurine. Taurine has a central role in cholesterol handling, promoting its excretion from the liver2, and we show that depletion of LRRC58 in hepatocytes increases cysteine flux to taurine and lowers hepatic cholesterol in mice. Uncovering the mechanism of LRRC58 control over cysteine catabolism exemplifies the utility of covariation MS to identify modes of protein regulation of metabolic processes.