Structural and systems characterization of phosphorylation on metabolic enzymes identifies sex-specific metabolic reprogramming in obesity

Tigist Y Tamir; Shreya Chaudhary; Annie X Li; Sonia E Trojan; Cameron T Flower; Paula Vo; Yufei Cui; Jeffrey C Davis; Rachit Mukkamala; Francesca N Venditti; Alissandra L Hillis; Alex Toker; Matthew G Vander Heiden; Jessica B Spinelli; Norman J Kennedy; Roger J Davis; Forest M White

doi:10.1016/j.molcel.2025.05.007

Structural and systems characterization of phosphorylation on metabolic enzymes identifies sex-specific metabolic reprogramming in obesity

Mol Cell. 2025 Jun 5;85(11):2211-2229.e8. doi: 10.1016/j.molcel.2025.05.007. Epub 2025 May 28.

Authors

Tigist Y Tamir¹, Shreya Chaudhary², Annie X Li², Sonia E Trojan³, Cameron T Flower⁴, Paula Vo⁵, Yufei Cui⁶, Jeffrey C Davis⁷, Rachit Mukkamala⁶, Francesca N Venditti², Alissandra L Hillis⁸, Alex Toker⁸, Matthew G Vander Heiden⁹, Jessica B Spinelli⁵, Norman J Kennedy⁵, Roger J Davis⁵, Forest M White¹⁰

Affiliations

¹ Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. Electronic address: tytamir@med.unc.edu.
² Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
³ Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Faculty of Medicine, Chair of Medical Biochemistry, Jagiellonian University Medical College, Krakow, Poland.
⁴ Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA; Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁵ Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
⁶ Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁷ Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁸ Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
⁹ Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA.
¹⁰ Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. Electronic address: fwhite@mit.edu.

PMID: 40441152
PMCID: PMC12147527 (available on 2026-06-05)
DOI: 10.1016/j.molcel.2025.05.007

Abstract

Coordination of adaptive metabolism through signaling networks is essential for cellular bioenergetics and homeostasis. Phosphorylation of metabolic enzymes provides a rapid, efficient, and dynamic mechanism to regulate metabolic networks. Our structural analysis stratified phosphosites on metabolic enzymes based on proximity to functional and dimerization domains. Most phosphosites occur on oxidoreductases and are enriched near substrate, cofactor, active sites, or dimer interfaces. Despite low stoichiometry, phosphotyrosine (pY) is overrepresented in functional domains. Using high-fat diet (HFD)-induced obesity in C57BL/6J mice and multiomics, we measured HFD-induced sex-specific dysregulation of pY and metabolites, which was reversible with the antioxidant butylated hydroxyanisole (BHA). Computational modeling revealed predictive pY sites for HFD- or BHA-induced metabolite changes. We characterized functional roles for predictive pY sites on glutathione S-transferase pi 1 (GSTP1), isocitrate dehydrogenase 1 (IDH1), and uridine monophosphate synthase (UMPS) using CRISPR interference (CRISPRi) rescue and stable isotope tracing. Our findings reveal mechanisms whereby cellular signaling fine-tunes enzyme activity and metabolism.

Keywords: GSTP1; IDH1; UMPS; cell signaling; computational modelling; metabolism; metabolomics; obesity; oxidative stress response; phosphoproteomics.

MeSH terms

Animals
Diet, High-Fat / adverse effects
Energy Metabolism
Female
Humans
Isocitrate Dehydrogenase / chemistry
Isocitrate Dehydrogenase / genetics
Isocitrate Dehydrogenase / metabolism
Male
Metabolic Reprogramming
Mice
Mice, Inbred C57BL
Obesity* / enzymology
Obesity* / etiology
Obesity* / genetics
Obesity* / metabolism
Obesity* / pathology
Phosphorylation
Sex Factors
Signal Transduction

Substances

Isocitrate Dehydrogenase

Abstract

MeSH terms

Substances

Grants and funding