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Nature Chemical Biology
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Defining the geometry of the two-component proteasome degron

Nature Chemical Biologyvolume 7, pages161–167 (2011)Cite this article

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Abstract

The eukaryotic 26S proteasome controls cellular processes by degrading specific regulatory proteins. Most proteins are targeted for degradation by a signal or degron that consists of two parts: a proteasome-binding tag, typically covalently attached polyubiquitin chains, and an unstructured region that serves as the initiation region for proteasomal proteolysis. Here we have characterized how the arrangement of the two degron parts in a protein affects degradation. We found that a substrate is degraded efficiently only when its initiation region is of a certain minimal length and is appropriately separated in space from the proteasome-binding tag. Regions that are located too close or too far from the proteasome-binding tag cannot access the proteasome and induce degradation. These spacing requirements are different for a polyubiquitin chain and a ubiquitin-like domain. Thus, the arrangement and location of the proteasome initiation region affect a protein's fate and are important in selecting proteins for proteasome-mediated degradation.

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Figure 1: Proteasome-mediated degradation depends on initiation region length.
Figure 2: Separating the proteasome-binding tag and initiation region in degradation substrates.
Figure 3: Immunoglobulin domain I27 insertions increase the distance between proteasome-binding tag and the initiation region.
Figure 4: Proteasome-mediated degradation depends on the spacing between proteasome-binding tag and initiation region.
Figure 5: Spacing requirements for the two degron parts as initiation region length varies.
Figure 6: Schematic representation of the length and spacing requirement for the initiation region.

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Acknowledgements

We thank S. Elsasser (Harvard University Medical School), D. Finley (Harvard University Medical School), B.S. Glick (University of Chicago) and Y. Saeki (Tokyo Metropolitan Institute of Medical Science) for providing plasmids and yeast strains and members of the Matouschek lab for advice and comments. The authors greatly appreciate and gratefully acknowledge N. Nukina (RIKEN) for his support and the use of his laboratory equipment. We also thank G. Leigh for editing the manuscript. The work was supported by grants R01GM063004 and U54CA143869 from the US National Institutes of Health, by Ministry of Education, Culture, Sports, Science and Technology of Japan Grant-in-Aid 22770137 (T.I.) and by the Robert H. Lurie Comprehensive Cancer Center at Northwestern University. T.I. also gratefully acknowledges a Japan Society for the Promotion of Science Postdoctoral Fellowship for Research Abroad and the RIKEN Special Postdoctoral Researchers Program.

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Authors and Affiliations

  1. Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA

    Tomonao Inobe, Susan Fishbain, Sumit Prakash & Andreas Matouschek

  2. Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA

    Tomonao Inobe, Susan Fishbain, Sumit Prakash & Andreas Matouschek

  3. Laboratory for Structural Neuropathology, RIKEN Brain Science Institute, Wako, Saitama, Japan

    Tomonao Inobe

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  1. Tomonao Inobe

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T.I., S.F., S.P. and A.M. designed and interpreted the experiments and wrote the manuscript. T.I., S.F. and S.P. performed the experiments.

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Correspondence toAndreas Matouschek.

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Inobe, T., Fishbain, S., Prakash, S.et al. Defining the geometry of the two-component proteasome degron.Nat Chem Biol7, 161–167 (2011). https://doi.org/10.1038/nchembio.521

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