Cycles of autoubiquitination and deubiquitination regulate the ERAD ubiquitin ligase Hrd1

  1. Brian G Peterson
  2. Morgan L Glaser
  3. Tom A Rapoport
  4. Ryan D Baldridge  Is a corresponding author
  1. University of Michigan Medical School, United States
  2. Harvard Medical School, United States

Abstract

Misfolded proteins in the lumen of the endoplasmic reticulum (ER) are retrotranslocated into the cytosol and polyubiquitinated before being degraded by the proteasome. The multi-spanning ubiquitin ligase Hrd1 forms the retrotranslocation channel and associates with three other membrane proteins (Hrd3, Usa1, Der1) of poorly defined function. The Hrd1 channel is gated by autoubiquitination, but how Hrd1 escapes degradation by the proteasome and returns to its inactive ground state is unknown. Here, we show that autoubiquitination of Hrd1 is counteracted by Ubp1, a deubiquitinating enzyme that requires its N-terminal transmembrane segment for activity towards Hrd1. The Hrd1 partner Hrd3 serves as a brake for autoubiquitination, while Usa1 attenuates Ubp1's deubiquitination activity through an inhibitory effect of its UBL domain. These results lead to a model in which the Hrd1 channel is regulated by cycles of autoubiquitination and deubiquitination, reactions that are modulated by the other components of the Hrd1 complex.

Data availability

Data generated or analysed during this study are included in the manuscript.

Article and author information

Author details

  1. Brian G Peterson

    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6871-2336
  2. Morgan L Glaser

    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Tom A Rapoport

    Department of Cell Biology, Harvard Medical School, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9911-4216
  4. Ryan D Baldridge

    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, United States
    For correspondence
    ryanbald@med.umich.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7158-7812

Funding

National Institute of General Medical Sciences (R35GM128592)

  • Ryan D Baldridge

National Institute of General Medical Sciences (R01GM052586)

  • Tom A Rapoport

Damon Runyon Cancer Research Foundation (DRG-2184-14)

  • Ryan D Baldridge

Damon Runyon Cancer Research Foundation (DFS-26-18)

  • Ryan D Baldridge

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2019, Peterson et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 3,332
    views
  • 558
    downloads
  • 43
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Brian G Peterson
  2. Morgan L Glaser
  3. Tom A Rapoport
  4. Ryan D Baldridge
(2019)
Cycles of autoubiquitination and deubiquitination regulate the ERAD ubiquitin ligase Hrd1
eLife 8:e50903.
https://doi.org/10.7554/eLife.50903

Share this article

https://doi.org/10.7554/eLife.50903

Further reading

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease
    Stephanie M Stuteley, Ghader Bashiri
    Insight

    In the bacterium M. smegmatis, an enzyme called MftG allows the cofactor mycofactocin to transfer electrons released during ethanol metabolism to the electron transport chain.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Cristina Paissoni, Sarita Puri ... Carlo Camilloni
    Research Article

    Both immunoglobulin light-chain (LC) amyloidosis (AL) and multiple myeloma (MM) share the overproduction of a clonal LC. However, while LCs in MM remain soluble in circulation, AL LCs misfold into toxic-soluble species and amyloid fibrils that accumulate in organs, leading to distinct clinical manifestations. The significant sequence variability of LCs has hindered the understanding of the mechanisms driving LC aggregation. Nevertheless, emerging biochemical properties, including dimer stability, conformational dynamics, and proteolysis susceptibility, distinguish AL LCs from those in MM under native conditions. This study aimed to identify a2 conformational fingerprint distinguishing AL from MM LCs. Using small-angle X-ray scattering (SAXS) under native conditions, we analyzed four AL and two MM LCs. We observed that AL LCs exhibited a slightly larger radius of gyration and greater deviations from X-ray crystallography-determined or predicted structures, reflecting enhanced conformational dynamics. SAXS data, integrated with molecular dynamics simulations, revealed a conformational ensemble where LCs adopt multiple states, with variable and constant domains either bent or straight. AL LCs displayed a distinct, low-populated, straight conformation (termed H state), which maximized solvent accessibility at the interface between constant and variable domains. Hydrogen-deuterium exchange mass spectrometry experimentally validated this H state. These findings reconcile diverse experimental observations and provide a precise structural target for future drug design efforts.