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Specificity for latent C termini links the E3 ubiquitin ligase CHIP to caspases

Nature Chemical Biology volume 15, pages 786–794 (2019)Cite this article

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Abstract

Protein–protein interactions between E3 ubiquitin ligases and protein termini help shape the proteome. These interactions are sensitive to proteolysis, which alters the ensemble of cellular N and C termini. Here we describe a mechanism wherein caspase activity reveals latent C termini that are then recognized by the E3 ubiquitin ligase CHIP. Using expanded knowledge of CHIP’s binding specificity, we predicted hundreds of putative interactions arising from caspase activity. Subsequent validation experiments confirmed that CHIP binds the latent C termini at tauD421 and caspase-6D179. CHIP binding to tauD421, but not tauFL, promoted its ubiquitination, while binding to caspase-6D179 mediated ubiquitin-independent inhibition. Given that caspase activity generates tauD421 in Alzheimer’s disease (AD), these results suggested a concise model for CHIP regulation of tau homeostasis. Indeed, we find that loss of CHIP expression in AD coincides with the accumulation of tauD421 and caspase-6D179. These results illustrate an unanticipated link between caspases and protein homeostasis.

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Fig. 1: CHIP function is rooted in the recognition of C termini.
Fig. 2: Structural basis for CHIP TPR domain specificity.
Fig. 3: Proteome-wide prediction of CHIP TPR interactions with C termini.
Fig. 4: TauD421 specifically recruits CHIP.
Fig. 5: CHIP specifically binds and inhibits mature caspase-6.
Fig. 6: CHIP interactions at latent C termini suggest a role in the progression of AD.

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Data availability

All structural data has been deposited in the PDB (PDB ID 6EFK and 6NSV). All predicted CHIP binders and relevant scores are provided in the Supplementary Information. Additional data supporting the findings of this manuscript are available from the corresponding author upon reasonable request.

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Acknowledgements

This work is dedicated to R. Raines on the occasion of his 60th birthday. This work was supported by grants from the Tau Consortium and NIH no. R01059690 (to J.E.G.), nos. P41CA196276 and P50GM082250 (to C.S.C.), no. K24 AG053435 (to L.T.G.) Alzheimer Association grant no. AARG-16-441514 (to L.T.G. and M.A.). Additional support included an NSF GRFP fellowship (to K.A.O.-N.), an ARCS Foundation fellowship (to M.R.), institutional grant nos. UL1 TR001872 and K01AG053433 (to P.T.) and a Program for Breakthrough Biomedical Science funded by the Sandler Foundation (to C.S.C.). The authors thank the laboratories of K.M. Scaglione (Medical College of Wisconsin) and J. A. Wells (University of California San Francisco) for technical support, as well as S.-A. Mok for input on the manuscript.

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Authors and Affiliations

  1. Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA

    Matthew Ravalin, Koli Basu, Kwadwo A. Opoku-Nsiah, Victoria A. Assimon, Daniel Medina-Cleghorn, Yi-Fan Chen, Markus F. Bohn, Michelle Arkin, Charles S. Craik & Jason E. Gestwicki

  2. Department of Neurology, Memory and Aging Center, University of California at San Francisco, San Francisco, CA, USA

    Panagiotis Theofilas & Lea T. Grinberg

  3. University of California San Francisco Summer Research Training Program, San Francisco, CA, USA

    Yi-Fan Chen

  4. Sandler Neuroscience Center, University of California at San Francisco, San Francisco, CA, USA

    Lea T. Grinberg & Jason E. Gestwicki

  5. Department of Pathology, University of California at San Francisco, San Francisco, CA, USA

    Lea T. Grinberg

  6. Global Brain Health Institute, University of California at San Francisco, San Francisco, CA, USA

    Lea T. Grinberg

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Contributions

M.R., C.S.C. and J.E.G. designed the studies and wrote the manuscript. M.R., K.A.O.-N., V.A.A., Y.-F.C. and D.M.-C. conducted biochemistry experiments and generated necessary reagents. K.B., M.F.B. and M.R. designed and executed structural and computational studies. M.R. and D.M.-C. designed and conducted cell biology experiments. P.T. and L.T.G designed and conducted the immunohistochemistry experiments. J.E.G., C.S.C., M.A. and L.T.G. provided funding.

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Correspondence to Charles S. Craik or Jason E. Gestwicki.

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Supplementary information

Supplementary Tables 1–5, Supplementary Figures 1–9

Supplementary Tables 1–5, Supplementary Figs. 1–9

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Supplementary Table S5

List of caspase substrates that include potential, cryptic CHIP-binding sequences.

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Ravalin, M., Theofilas, P., Basu, K. et al. Specificity for latent C termini links the E3 ubiquitin ligase CHIP to caspases. Nat Chem Biol 15, 786–794 (2019). https://doi.org/10.1038/s41589-019-0322-6

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