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  • Review Article
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Mechanisms of substrate processing during ER-associated protein degradation

Nature Reviews Molecular Cell Biology volume 24, pages 777–796 (2023)Cite this article

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Abstract

Maintaining proteome integrity is essential for long-term viability of all organisms and is overseen by intrinsic quality control mechanisms. The secretory pathway of eukaryotes poses a challenge for such quality assurance as proteins destined for secretion enter the endoplasmic reticulum (ER) and become spatially segregated from the cytosolic machinery responsible for disposal of aberrant (misfolded or otherwise damaged) or superfluous polypeptides. The elegant solution provided by evolution is ER-membrane-bound ubiquitylation machinery that recognizes misfolded or surplus proteins or by-products of protein biosynthesis in the ER and delivers them to 26S proteasomes for degradation. ER-associated protein degradation (ERAD) collectively describes this specialized arm of protein quality control via the ubiquitin–proteasome system. But, instead of providing a single strategy to remove defective or unwanted proteins, ERAD represents a collection of independent processes that exhibit distinct yet overlapping selectivity for a wide range of substrates. Not surprisingly, ER-membrane-embedded ubiquitin ligases (ER-E3s) act as central hubs for each of these separate ERAD disposal routes. In these processes, ER-E3s cooperate with a plethora of specialized factors, coordinating recognition, transport and ubiquitylation of undesirable secretory, membrane and cytoplasmic proteins. In this Review, we focus on substrate processing during ERAD, highlighting common threads as well as differences between the many routes via ERAD.

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Fig. 1: Overview of the principal steps in ERAD.
Fig. 2: ER-E3 complexes follow different strategies for substrate recruitment.
Fig. 3: Topological organization of the Hrd1 ER-E3 complex.
Fig. 4: Polyubiquitylation drives substrate extraction from the ER through the Cdc48/VCP AAA-ATPase complex.

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Acknowledgements

The authors thank all members of the Christianson and Sommer labs, as well as P. Carvalho for helpful discussions and input to this manuscript. J.C.C. is supported by a Senior Cancer Research Fellowship from Cancer Research UK (C68569/A29217). E.J. and T.S. are supported by the German Research Foundation DFG (SPP 1365 and SFB 740/TP B05). The authors apologize to all authors whose work they were unable to directly cite or discuss in detail owing to space constraints.

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Authors and Affiliations

  1. Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK

    John C. Christianson

  2. Max-Delbrück-Centrer for Molecular Medicine in Helmholtz Association, Berlin-Buch, Germany

    Ernst Jarosch & Thomas Sommer

  3. Institute for Biology, Humboldt Universität zu Berlin, Berlin, Germany

    Thomas Sommer

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  1. John C. Christianson
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  2. Ernst Jarosch
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  3. Thomas Sommer
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Contributions

J.C.C. and E.J. researched data for the article. All authors contributed substantially to discussion of the content. J.C.C. and E.J. wrote the article. All authors reviewed and/or edited the manuscript before submission.

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Correspondence to John C. Christianson or Thomas Sommer.

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Nature Reviews Molecular Cell Biology thanks Gerardo Lederkremer, Ling Qi and the other, anonymous reviewer(s) for their contribution to the peer review of this work.

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Glossary

26S proteasomes

Ubiquitin-specific protease complexes that specifically recognize ubiquitylated proteins and cleave them into peptide fragments.

AAA-ATPases

Protein that contains a conserved motif and that is organized in multimeric (typically homo-hexameric) assemblies with a central pore; structural rearrangements within these complexes upon coordinated ATP hydrolysis thread protein substrates through the pore and unfold them, thereby extracting them from cellular structures such as protein complexes, DNA or membranes.

Ceramide

Lipid molecule built up from a N-acetylsphingosine and a fatty acid that serves as a second messenger and plays a part in the structural organization of cellular membranes.

Degron

Amino acid sequence or structural motif within a protein that targets it to an E3 enzyme for ubiquitylation and degradation; degrons are inherent elements that, when fused to a non-related protein in the same cellular compartment, confer ubiquitin–proteasome system-mediated degradation.

De-ubiquitylating enzymes (DUBs)

Ubiquitin-specific proteases that cleave ubiquitin from ubiquitylated proteins.

Dislocation

Eviction of transmembrane domain or domains from lipid bilayer during endoplasmic reticulum-associated protein degradation.

E1 enzyme

Activates ubiquitin for the transfer onto substrates by forming a thioester linkage with the C-terminal glycine residue in ubiquitin and a cysteine residue in its active site centre upon hydrolysis of ATP.

E2 enzyme

Also termed ubiquitin-conjugating enzyme; conserved group of enzymes that are charged with a ubiquitin thioester on their active site cysteine residues by E1 enzymes and either directly conjugate ubiquitin onto substrates or transfer the ubiquitin thioester onto a dedicated E3 enzyme.

E3 enzyme

Also termed ubiquitin ligase; single proteins or protein complexes that recognize substrates and either activate E2 enzymes for attaching ubiquitin onto a substrate (RING-type E3) or themselves form a thioester with ubiquitin and then transfer ubiquitin (HECT- and RBR-type E3s).

ER–lysosomal degradation (ERLAD) pathway

Collection of mechanistically diverse endoplasmic reticulum autophagy (ER-phagy) pathways that captured misfolded ER proteins in double membrane autophagosomes and deliver them to degradative organelles for proteolysis.

Lectin

Glycan-binding protein that recognizes specific carbohydrate molecule but does not harbour enzymatic activity.

Linchpin residues

Particular amino acid positions adjacent to the ultimate cysteine residue in most RING finger domains that interact with both the E2 enzyme and the ubiquitin thioester, thereby delimitating the space available for the ubiquitin thioester, and that coordinate facilitation of its conjugation to a substrate.

Mannose 6-phosphate receptor homology (MRH) domains

Regions in a protein that bind a specific structure within a high-mannose N-glycan.

Microautophagy

Highly conserved cellular process that causes the engulfment of cytoplasmic material with lysosomal or vacuolar membranes and its degradation.

Molecular glues

Typically small molecules that assist in establishing a physical association of two proteins that do not normally interact.

Really interesting new gene (RING) finger domain

A structural protein motif of about 30–60 amino acids typically containing seven cysteine and one histidine residues for complexing two zinc cations that is characteristically found in a class of E3 ubiquitylating enzymes.

Retrotranslocation

Transport of entire lumenal proteins or domains of misfolded proteins across the endoplasmic reticulum membrane into the cytoplasm during endoplasmic reticulum-associated protein degradation.

Rhomboid intramembrane proteases

Structurally conserved family of integral membrane serine proteases that mostly target membrane proteins and cleave them at sites within or close to the lipid bilayer.

Sec61 translocon complex

An endoplasmic reticulum (ER)-resident protein complex composed of Sec61α, Sec61β and Sec61γ subunits that forms a polypeptide-conducting channel through the ER membrane for the import of secretory proteins from the cytoplasm into the ER.

Ubiquitin–proteasome system

(UPS). Sum of all proteins involved in the generation, decoding and processing of ubiquitin and ubiquitylated proteins.

Unfolded protein response (UPR)

A set of intracellular signal transduction pathways elicited in order to alleviate proteotoxic stress in the ER and restore organelle homeostasis.

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Christianson, J.C., Jarosch, E. & Sommer, T. Mechanisms of substrate processing during ER-associated protein degradation. Nat Rev Mol Cell Biol 24, 777–796 (2023). https://doi.org/10.1038/s41580-023-00633-8

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