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Module 3 · Quality Control

ERAD & Quality Control

Misfolded proteins cannot be left to accumulate in the ER — they aggregate, titrate chaperones, and trigger UPR. The ER clears them by endoplasmic reticulum-associated degradation (ERAD): a conserved pathway that retrotranslocates misfolded substrates into the cytosol, where they are polyubiquitinated and digested by the proteasome. The machinery bridges the ER lumen, the membrane, and the cytosol and uses the ATP hydrolysis of a hexameric AAA+ ATPase as the motor.

1. Substrate Recognition

Three substrate categories, each handled by a dedicated pathway:

  • ERAD-L: lesion in the luminal domain. Handled by Hrd1 / Sel1L complex, with lectins OS-9 and XTP3-B recognising trimmed Man7GlcNAc2 glycans.
  • ERAD-M: lesion in the membrane domain. Also Hrd1-dependent but uses Derlin-1/2/3 to extract TM segments.
  • ERAD-C: lesion on the cytosolic face. Handled by a separate E3 ligase (Doa10/TEB4/MARCH6).

The Man7 signal is critical: a substrate that fails the calnexin cycle (Module 2) has mannose residues trimmed by ER mannosidases (EDEM1, EDEM2, EDEM3, Htm1/Mnl1) over ~20–60 min. The resulting Man7GlcNAc2 is recognised by OS-9/XTP3-B and committed to degradation. This is an irreversible glycan-based timer: once the mannose is trimmed, there is no way back.

2. Retrotranslocation

The Hrd1 / Sel1L complex forms the retrotranslocation channel (Schoebel 2017 cryo-EM). Hrd1 is a multi-TM E3 ligase whose TM domain creates a polar groove through which the substrate threads back to the cytosol. Sel1L stabilises the complex; Derlins provide additional channel capacity for TM substrates.

Accessory factors: Yos9/OS-9 lectins deliver luminal substrates, Herp stabilises the complex under stress, and the signal-peptide-peptidase-like (SPP/SPPL) proteases cleave membrane-embedded substrates before retrotranslocation.

3. The Cdc48 / p97 ATPase: The Motor

p97 / VCP (yeast Cdc48) is a hexameric AAA+ ATPase that extracts ubiquitinated substrates from membranes, organelles, and complexes. In ERAD, p97-Ufd1-Npl4 docks on the cytoplasmic face of the Hrd1 complex after ubiquitin chain attachment, threads the substrate through its central pore, and uses ATP hydrolysis to unfold and deliver it to the proteasome.

p97 mutations cause multisystem proteinopathy (IBMPFD: inclusion body myopathy, Paget’s bone disease, frontotemporal dementia) and ALS. p97 inhibitors (CB-5083) entered cancer trials on the logic that high secretion-demand tumours (multiple myeloma) cannot sustain ERAD without p97. Clinical trials were halted for off-target toxicity; the field continues to pursue cleaner inhibitors.

Simulation: Folding vs Degradation as a Kinetic Race

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4. Proteasomal Delivery & Degradation

p97 hands unfolded substrate to the 26S proteasome, either directly or through shuttle factors (Rad23, Dsk2, Ddi1). The proteasome processively degrades the chain into 3–15-residue peptides, recycled by aminopeptidases or loaded onto MHC class I for antigen presentation. A single round of ERAD can take 1–30 minutes, rate-limited typically by retrotranslocation rather than proteasome throughput.

5. ER-Phagy: When ERAD Is Not Enough

ERAD handles soluble clients and moderate-sized membrane proteins. For bulk clearance — whole ER cisternae, aggregated protein condensates that cannot enter a retrotranslocation channel — the cell uses ER-phagy: selective autophagy of ER fragments.

Dedicated ER-phagy receptors bind both the ER membrane and the autophagosome LC3/GABARAP:

  • FAM134B (Khaminets 2015): reticulon homology domain; curvature-sensing; essential for normal ER homeostasis. Mutations cause hereditary sensory and autonomic neuropathy.
  • RTN3: tubular ER-phagy.
  • SEC62: post-stress recovery ER-phagy.
  • CCPG1, ATL3, TEX264: additional tissue- and context-specific receptors.

ER-phagy is increasingly recognised as homeostatically important — its dysregulation contributes to neurodegeneration, fibrosis, and cancer. It is a young and rapidly developing subfield.

6. Viral Hijacking & Immune Consequences

Viruses exploit ERAD. HIV Nef protein targets CD4 via an ERAD-like pathway. HCMV US2/US11 accessory proteins recruit MHC class I to Hrd1 for degradation, preventing viral antigen presentation. Conversely, ERAD-generated peptides are a major source of MHC class I epitopes — the immune system co-opts the degradation pathway for surveillance. The interaction of secretory-pathway quality control with adaptive immunity is one of the most elegant uses of a basic cellular mechanism.

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