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  2. Function-guided proximity mapping unveils electrophilic-metabolite sensing by proteins not present in their canonical locales

Function-guided proximity mapping unveils electrophilic-metabolite sensing by proteins not present in their canonical locales

  • Proc Natl Acad Sci U S A. 2022 Feb 1;119(5):e2120687119. doi: 10.1073/pnas.2120687119.
Yi Zhao 1 2 3 Pierre A Miranda Herrera 1 2 Dalu Chang 1 2 Romain Hamelin 4 Marcus J C Long 5 6 Yimon Aye 7 2
Affiliations

Affiliations

  • 1 Institute of Chemical Sciences and Engineering, School of Basic Sciences, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland.
  • 2 National Centre of Competence in Research Chemical Biology, University of Geneva, 1211 Geneva, Switzerland.
  • 3 BayRay Innovation Center, Shenzhen Bay Laboratory, Shenzhen 518055, Guangdong, China.
  • 4 Proteomics Core Facility, School of Life Sciences, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland.
  • 5 National Centre of Competence in Research Chemical Biology, University of Geneva, 1211 Geneva, Switzerland; [email protected] [email protected].
  • 6 Department of Biochemistry, Faculty of Biology and Medicine, University of Lausanne, 1066 Epalinges, Switzerland.
  • 7 Institute of Chemical Sciences and Engineering, School of Basic Sciences, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland; [email protected] [email protected].
Abstract

Enzyme-assisted posttranslational modifications (PTMs) constitute a major means of signaling across different cellular compartments. However, how nonenzymatic PTMs-despite their direct relevance to covalent drug development-impinge on cross-compartment signaling remains inaccessible as current target-identification (target-ID) technologies offer limited spatiotemporal resolution, and proximity mapping tools are also not guided by specific, biologically-relevant, ligand chemotypes. Here we establish a quantitative and direct profiling platform (Localis-rex) that ranks responsivity of compartmentalized subproteomes to nonenzymatic PTMs. In a setup that contrasts nucleus- vs. cytoplasm-specific responsivity to reactive-metabolite modification (hydroxynonenylation), ∼40% of the top-enriched protein sensors investigated respond in compartments of nonprimary origin or where the canonical activity of the protein sensor is inoperative. CDK9-a primarily nuclear-localized kinase-was hydroxynonenylated only in the cytoplasm. Site-specific CDK9 hydroxynonenylation-which we identified in untreated cells-drives its nuclear translocation, downregulating RNA-polymerase-II activity, through a mechanism distinct from that of commonly used CDK9 inhibitors. Taken together, this work documents an unmet approach to quantitatively profile and decode localized and context-specific signaling/signal-propagation programs orchestrated by reactive covalent ligands.

Keywords

electrophile signaling; function-guided proximity mapping; reactive metabolites.

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  • HY-12214A
    99.20%, CDK9 Inhibitor