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Substrate selection by the proteasome during degradation of protein complexes

Nature Chemical Biology volume 5, pages 29–36 (2009)Cite this article

A Correspondence to this article was published on 01 March 2009

Abstract

The proteasome controls the turnover of many cellular proteins. Two structural features are typically required for proteins to be degraded: covalently attached ubiquitin polypeptides that allow binding to the proteasome and an unstructured region in the targeted protein that initiates proteolysis. Here, we have tested the degradation of model proteins to further explore how the proteasome selects its substrates. Using purified yeast proteasome and mammalian proteasome in cell lysate, we have demonstrated that the two structural features can act in trans when separated onto different proteins in a multisubunit complex. In such complexes, the location of the unstructured initiation site and its chemical properties determine which subunit is degraded. Thus, our findings reveal the molecular basis of subunit specificity in the degradation of protein complexes. In addition, our data provide a plausible explanation for how adaptor proteins can bind to otherwise stable proteins and target them for degradation.

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Figure 1: Proteasome substrates and N-degron–mediated degradation.
Figure 2: The proteasome degrades an unubiquitinated subunit in a heterodimeric complex.
Figure 3: trans initiation by the proteasome.
Figure 4: Substrate selection in reticulocyte lysate.
Figure 5: Substrate selection by the purified proteasome.
Figure 6: Subunit-specific degradation by the proteasome.

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Acknowledgements

We thank R.W. Carthew, A.C. Rosenzweig, J. Widom and members of the Matouschek lab (Northwestern University), as well as R.J. Deshaies (Caltech), for advice and comments, and we thank G. Leigh for editing the manuscript. The work was supported by grant R01GM64003 from the US National Institutes of Health, by the Leukemia and Lymphoma Society and by the Robert H. Lurie Comprehensive Cancer Center at Northwestern University. T.I. gratefully acknowledges a Japan Society for the Promotion of Science Postdoctoral Fellowship for Research Abroad.

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Authors and Affiliations

  1. Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, 60208, Illinois, USA

    Sumit Prakash, Tomonao Inobe, Ace Joseph Hatch & Andreas Matouschek

  2. Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 303 East Superior Street L3-125, Chicago, 60611, Illinois, USA

    Sumit Prakash, Tomonao Inobe, Ace Joseph Hatch & Andreas Matouschek

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Contributions

S.P., T.I. and A.M. designed the experiments and wrote the manuscript. S.P. and T.I. performed most of the experiments. A.J.H. assisted S.P. in performing some of the degradation experiments, in purifying proteins and in constructing many of the genes.

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Correspondence to Andreas Matouschek.

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Prakash, S., Inobe, T., Hatch, A. et al. Substrate selection by the proteasome during degradation of protein complexes. Nat Chem Biol 5, 29–36 (2009). https://doi.org/10.1038/nchembio.130

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