Defining human ERAD networks through an integrative mapping strategy

Abstract

Proteins that fail to correctly fold or assemble into oligomeric complexes in the endoplasmic reticulum (ER) are degraded by a ubiquitin- and proteasome-dependent process known as ER-associated degradation (ERAD). Although many individual components of the ERAD system have been identified, how these proteins are organized into a functional network that coordinates recognition, ubiquitylation and dislocation of substrates across the ER membrane is not well understood. We have investigated the functional organization of the mammalian ERAD system using a systems-level strategy that integrates proteomics, functional genomics and the transcriptional response to ER stress. This analysis supports an adaptive organization for the mammalian ERAD machinery and reveals a number of metazoan-specific genes not previously linked to ERAD.

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Figure 1: Hierarchical cluster analysis of CompPASS-identified high-confidence candidate interaction proteins (HCIPs).
Figure 2: The INfERAD.
Figure 3: shRNA-mediated refinement of ERAD E3 ligase subnetworks.
Figure 4: Functional genomic screen to identify essential substrate-specific ERAD components.
Figure 5: Coordinated ER stress response of ERAD genes.
Figure 6: Characterization of the Hrd1-binding partner FAM8A1.
Figure 7: Characterization of UBAC2, a ubiquitin-binding ERAD component.
Figure 8: Functional integration of mammalian ERAD networks.

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Acknowledgements

This work was supported by grants from the NIH to R.R.K. and J.W.H. J.C.C. was supported by funding from the Ludwig Institute for Cancer Research. J.A.O. and R.E.T were supported by NRSA fellowships from NIH. E.J.B. was supported by a fellowship from the Damon Runyon Cancer Research Foundation (DRG 1974-08). We thank the members of the Kopito laboratory for helpful discussion, and M. Pearce, J. Hwang and C. Beveridge for critical reading of the manuscript.

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The manuscript was written collectively by J.C.C., J.A.O. and R.R.K. Experiments and data analysis were carried out by J.A.O. and J.C.C. with assistance from C.M.R. R.E.T. and E.J.G. LC–MS/MS analysis was carried out by T.A.S. CompPASS analysis was carried out by M.E.S. and E.J.B with support from J.W.H.

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Correspondence to Ron R. Kopito.

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Christianson, J., Olzmann, J., Shaler, T. et al. Defining human ERAD networks through an integrative mapping strategy. Nat Cell Biol 14, 93–105 (2012). https://doi.org/10.1038/ncb2383

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