ubiquitin-proteasome pathway

**Mechanism** 1. **Ubiquitin**: a small (76-amino-acid) highly conserved protein. 2. **E1 (ubiquitin-activating enzyme)**: uses ATP to activate ubiquitin and forms a thioester bond with it. 3. **E2 (ubiquitin-conjugating enzyme)**: receives the activated ubiquitin from E1. 4. **E3 (ubiquitin ligase)**: confers substrate specificity. It binds the target protein and transfers ubiquitin from E2 to a lysine on the substrate. There are hundreds of E3s, versus only a few E1s and E2s. 5. **Polyubiquitination**: a chain of ≥4 ubiquitins linked through **Lys48** targets the protein to the proteasome. Monoubiquitination or Lys63-linked chains instead signal other processes (endocytosis, DNA repair, signaling). 6. **26S proteasome**: a barrel-shaped complex made of a **20S core** (catalytic, protease activity) and **19S regulatory caps**. The 19S cap recognizes ubiquitinated proteins, removes the ubiquitin (deubiquitinases, which recycle it), unfolds the substrate (ATPases), and feeds it into the 20S core. The substrate is cleaved into short peptides (~7–9 amino acids).

**Physiologic roles** - Quality control: degrades misfolded or damaged proteins (e.g., from the ER via ERAD). - Cell cycle control: degrades cyclins and CDK inhibitors. The **APC/C** (anaphase-promoting complex) is an E3 ligase that degrades securin and cyclin B to allow anaphase and mitotic exit. - Regulation of transcription: IκB is phosphorylated and then ubiquitinated and degraded, which releases **NF-κB** to enter the nucleus. - **p53 regulation**: **MDM2** is an E3 ligase that ubiquitinates p53 and keeps its levels low. Stress inhibits MDM2 and stabilizes p53. - **MHC class I antigen presentation**: cytosolic proteins are degraded by the proteasome (the immunoproteasome, with IFN-γ-induced subunits). The peptides are transported into the ER by TAP and loaded onto MHC I. - HIF-1α: under normoxia, hydroxylation allows **VHL** (an E3 ligase component) to bind and ubiquitinate it for degradation. - Muscle wasting (cachexia, sepsis): the pathway is upregulated and degrades muscle proteins.

**Clinical correlations** - **Multiple myeloma / mantle cell lymphoma**: **bortezomib** and carfilzomib (proteasome inhibitors). Myeloma cells make large amounts of immunoglobulin, so they are especially sensitive to the buildup of misfolded protein and the resulting ER stress. They also have blocked NF-κB activation because IκB isn't degraded. Bortezomib toxicity includes **peripheral neuropathy** and herpes zoster reactivation (give acyclovir prophylaxis). - **Von Hippel-Lindau disease**: VHL mutation prevents HIF-1α degradation, so HIF-1α accumulates and drives VEGF/PDGF. This leads to hemangioblastomas, clear cell renal cell carcinoma, and pheochromocytoma. - **Parkinson disease**: mutations in **parkin** (an E3 ligase; autosomal recessive juvenile Parkinson) impair degradation of misfolded proteins. Lewy bodies (α-synuclein) are ubiquitin-positive. - **Neurodegenerative inclusions**: ubiquitin-tagged aggregates are seen in Lewy bodies, Pick bodies, neurofibrillary tangles, Mallory-Denk bodies (alcoholic hepatitis), and Huntington inclusions. - **Angelman syndrome**: loss of maternal **UBE3A** (an E3 ligase) in the brain (15q11-13). Findings are severe intellectual disability, ataxia, seizures, inappropriate laughter ("happy puppet"). - **Cystic fibrosis (ΔF508)**: misfolded CFTR is retained in the ER and degraded by the proteasome, so there is no CFTR at the membrane. Correctors such as lumacaftor and tezacaftor help folding and trafficking. - **HPV**: E6 protein recruits E6-AP (an E3 ligase) to degrade p53, and E7 inactivates Rb. These promote cervical cancer. - **MDM2 amplification**: p53 is excessively degraded, which is seen in sarcomas. - Targeted protein degraders (PROTACs) and immunomodulatory drugs (**thalidomide, lenalidomide**) work by redirecting the **cereblon** E3 ligase to degrade specific proteins (e.g., IKZF1/3 in myeloma).

**High-yield contrast** - **Ubiquitin-proteasome**: selective, ATP-dependent, for cytosolic/nuclear proteins. - **Lysosomal degradation/autophagy**: for extracellular and membrane proteins (endocytosed) and for organelles and aggregates. Autophagy is regulated by mTOR, and Beclin-1 helps initiate it.

**Mnemonic**: E1 **activates**, E2 **conjugates**, E3 **ligates and gives specificity**. "Lys48 = kill (degradation); Lys63 = signaling."