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

Nat Chem Biol. 2024 Sep;20(9):1164-1175. doi: 10.1038/s41589-024-01618-0. Epub 2024 May 21.

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.

MeSH terms

  • DEAD-box RNA Helicases / metabolism
  • Degrons
  • HEK293 Cells
  • Humans
  • Molecular Probes / chemistry
  • Molecular Probes / metabolism
  • Protein Binding*
  • Proteolysis
  • Receptors, Interleukin-17
  • Ubiquitin-Protein Ligases / metabolism

Substances

  • IL17RB protein, human
  • Molecular Probes
  • DEAD-box RNA Helicases
  • Ubiquitin-Protein Ligases
  • Receptors, Interleukin-17