A chemical probe to modulate human GID4 Pro/N-degron interactions

  • Nat Chem Biol. 2024 May 21. doi: 10.1038/s41589-024-01618-0.
Dominic D G Owens  #  1 ,  Matthew E R Maitland  #  1  2  3  4 ,  Aliakbar Khalili Yazdi  1 ,  Xiaosheng Song  1 ,  Viviane Reber  5 ,  Martin P Schwalm  6  7 ,  Raquel A C Machado  1 ,  Nicolas Bauer  6  7 ,  Xu Wang  2 ,  Magdalena M Szewczyk  1 ,  Cheng Dong  1 ,  Aiping Dong  1 ,  Peter Loppnau  1 ,  Matthew F Calabrese  8 ,  Matthew S Dowling  8 ,  Jisun Lee  8 ,  Justin I Montgomery  8 ,  Thomas N O'Connell  8 ,  Chakrapani Subramanyam  8 ,  Feng Wang  8 ,  Ella C Adamson  1 ,  Matthieu Schapira  1  9 ,  Matthias Gstaiger  5 ,  Stefan Knapp  6  7 ,  Masoud Vedadi  1  9 ,  Jinrong Min  1  10  11 ,  Gilles A Lajoie  3  4 ,  Dalia Barsyte-Lovejoy  1  9 ,  Dafydd R Owen  8 ,  Caroline Schild-Poulter  2  3 ,  Cheryl H Arrowsmith  12  13  14
Affiliations
  • 1. Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
  • 2. Robarts Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada.
  • 3. Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada.
  • 4. Don Rix Protein Identification Facility, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada.
  • 5. Institute of Molecular Systems Biology at ETH Zurich, Zurich, Switzerland.
  • 6. Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Frankfurt am Main, Germany.
  • 7. Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
  • 8. Development and Medical, Pfizer Worldwide Research, Groton, CT, USA.
  • 9. Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.
  • 10. Department of Physiology, University of Toronto, Toronto, Ontario, Canada.
  • 11. Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China.
  • 12. Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada. [email protected].
  • 13. Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [email protected].
  • 14. Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. [email protected].
  • # Contributed equally.
PMID: 38773330 DOI: 10.1038/s41589-024-01618-0
Abstract

The C-terminal to LisH (CTLH) complex is a ubiquitin Ligase complex that recognizes substrates with Pro/N-degrons via its substrate receptor Glucose-Induced Degradation 4 (GID4), but its function and substrates in humans remain unclear. Here, we report PFI-7, a potent, selective and cell-active chemical probe that antagonizes Pro/N-degron binding to human GID4. Use of PFI-7 in proximity-dependent biotinylation and quantitative proteomics enabled the identification of GID4 interactors and GID4-regulated proteins. GID4 interactors are enriched for nucleolar proteins, including the Pro/N-degron-containing RNA Helicases DDX21 and DDX50. We also identified a distinct subset of proteins whose cellular levels are regulated by GID4 including HMGCS1, a Pro/N-degron-containing metabolic enzyme. These data reveal human GID4 Pro/N-degron targets regulated through a combination of degradative and nondegradative functions. Going forward, PFI-7 will be a valuable research tool for investigating CTLH complex biology and facilitating development of targeted protein degradation strategies that highjack CTLH E3 Ligase activity.

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