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

Owens, D. D. G.; Maitland, M. E. R.; Khalili Yazdi, A.; Song, X.; Schwalm, M. P.; Machado, R. A. C.; Bauer, N.; Wang, X.; Szewczyk, M. M.; Dong, C.; Dong, A.; Loppnau, P.; Calabrese, M.; Dowling, M. S.; Lee, J.; Montgomery, J. I.; O'Connell, T. N.; Subramanyam, C.; Wang, F.; Schapira, M.; Knapp, S.; Vedadi, M.; Min, J.; Lajoie, G. A.; Barsyte-Lovejoy, D.; Owen, D. R.; Schild-Poulter, C.; Arrowsmith, C. H.

doi:10.1101/2023.01.17.524225

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bioRxiv · 10.1101/2023.01.17.524225

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

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Abstract

The CTLH complex is a multi-subunit ubiquitin ligase complex that recognizes substrates with Pro/N-degrons via the substrate receptor GID4. Recently, focus has turned to this complex as a potential mediator of targeted protein degradation, but the role GID4-mediated substrate ubiquitylation and proteasomal degradation plays in humans has thus far remained 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 enabled the identification of dozens of endogenous GID4-interacting proteins that bind via the GID4 substrate binding pocket, only a subset of which possess canonical Pro/N-degron sequences. GID4 interactors are enriched for nuclear and nucleolar proteins including RNA helicases. GID4 antagonism by PFI-7 altered protein levels of several proteins including RNA helicases as measured by label-free quantitative proteomics, defining proteins that are regulated by GID4 and the CTLH complex in humans. Interactions with GID4 via Pro/N-degron pathway did not result in proteasomal degradation, demonstrating that CTLH interactors are regulated through a combination of degradative and non-degradative functions. The lack of degradation of GID4 interactors highlights potential challenges in utilizing GID4-recruiting bifunctional molecules for targeted protein degradation. Going forward, PFI-7 will be a valuable research tool for defining CTLH complex biology and honing targeted protein degradation strategies.

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Owens, D. D. G., Maitland, M. E. R., Khalili Yazdi, A., Song, X., Schwalm, M. P., Machado, R. A. C., Bauer, N., Wang, X., Szewczyk, M. M., Dong, C., Dong, A., Loppnau, P., Calabrese, M., Dowling, M. S., Lee, J., Montgomery, J. I., O'Connell, T. N., Subramanyam, C., Wang, F., Schapira, M., Knapp, S., Vedadi, M., Min, J., Lajoie, G. A., Barsyte-Lovejoy, D., Owen, D. R., Schild-Poulter, C., Arrowsmith, C. H.. 2023-01-18. A chemical probe to modulate human GID4 Pro/N-degron interactions. https://doi.org/10.1101/2023.01.17.524225

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