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A conserved processing mechanism regulates the activity of transcription factors Cubitus interruptus and NF-κB

Nature Structural & Molecular Biology volume 12, pages 1045–1053 (2005)Cite this article

Abstract

The proteasome degrades some proteins, such as transcription factors Cubitus interruptus (Ci) and NF-κB, to generate biologically active protein fragments. Here we have identified and characterized the signals in the substrate proteins that cause this processing. The minimum signal consists of a simple sequence preceding a tightly folded domain in the direction of proteasome movement. The strength of the processing signal depends primarily on the complexity of the simple sequence rather than on amino acid identity, the resistance of the folded domain to unraveling by the proteasome and the spacing between the simple sequence and folded domain. We show that two unrelated transcription factors, Ci and NF-κB, use this mechanism to undergo partial degradation by the proteasome in vivo. These findings suggest that the mechanism is conserved evolutionarily and that processing signals may be widespread in regulatory proteins.

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Figure 1: A GRR in combination with a folded domain inhibits progression of proteasomal degradation.
Figure 2: Progression of proteasomal degradation can be inhibited by simple sequences.
Figure 3: The spacing of the simple sequence inserts relative to the folded domain determines fragment formation.
Figure 4: Simple sequence inserts can inhibit proteasome progression in both directions of degradation.
Figure 5: Processing of Ci by the proteasome in vitro.
Figure 6: Processing of Ci in vivo.
Figure 7: Processing of NF-κB precursor p105 depends on the presence of a folded Rel-homology domain and a GRR.

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Acknowledgements

This work is dedicated to Irving M. Klotz. We thank R.W. Carthew and M. Feller for help and advice with the Ci cell culture experiments and C. Horvath and J.-P. Parisien for help with the NF-κB cell culture experiments. We also thank J. Widom, R.W. Carthew, C. Horvath, S. Prakash and S. Fishbain for advice. We are grateful to N. Shah and C. Malalis for constructing several plasmids. The work was supported by grant GM063004 from the US National Institutes of Health.

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

    Lin Tian, Robert A Holmgren & Andreas Matouschek

  2. Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, 60611, Illinois, USA

    Lin Tian, Robert A Holmgren & Andreas Matouschek

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Supplementary information

Supplementary Fig. 1

Degradation depends on ubiquitin proteasome pathway. (PDF 89 kb)

Supplementary Fig. 2

Gel filtration. (PDF 42 kb)

Supplementary Fig. 3

Spacing requirement. (PDF 25 kb)

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Tian, L., Holmgren, R. & Matouschek, A. A conserved processing mechanism regulates the activity of transcription factors Cubitus interruptus and NF-κB. Nat Struct Mol Biol 12, 1045–1053 (2005). https://doi.org/10.1038/nsmb1018

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