Ubiquitin/Proteasome

The ubiquitin proteasome pathway, conserved from yeast to mammals, is required for the targeted degradation of most shortlived proteins in the eukaryotic cell. Targets include cell cycle regulatory proteins, whose timely destruction is vital for controlled cell division, as well as proteins unable to fold properly within the endoplasmic reticulum.

Ubiquitin modification is an ATP-dependent process carried out by three classes of enzymes. A “ubiquitin activating enzyme” (E1) forms a thio-ester bond with ubiquitin, a highly conserved 76-amino acid protein. This reaction allows subsequent binding of ubiquitin to a “ubiquitin conjugating enzyme” (E2), followed by the formation of an isopeptide bond between the carboxy-terminus of ubiquitin and a lysine residue on the substrate protein. The latter reaction requires a “ubiquitin ligase” (E3). E3 ligases can be single- or multi-subunit enzymes. In some cases, the ubiquitin-binding and substrate binding domains reside on separate polypeptides brought together by adaptor proteins or cullins. Numerous E3 ligases provide specificity in that each can modify only a subset of substrate proteins. Further specificity is achieved by post-translational modification of substrate proteins, including, but not limited to, phosphorylation.

Effects of monoubiquitination include a role in endocytosis and DNA damage, as well as changes in subcellular protein localization and trafficking. However, multiple ubiquitination cycles resulting in a polyubiquitin chain are required for targeting a protein to the proteasome for degradation. The multisubunit 26S proteasome recognizes, unfolds, and degrades polyubiquitinated substrates into small peptides. The reaction occurs within the cylindrical core of the proteasome complex, and peptide bond hydrolysis employs a core threonine residue as the catalytic nucleophile. Polyubiquitin chains are also indicated in diverse cellular processes including DNA damage response, mitochondrial maintenance and mitophagy, lysosomal degradation, T Cell Receptor signaling, and NF-κB signaling.

Ubiquitinating enzymes (UBEs) catalyze protein ubiquitination, a reversible process countered by deubiquitinating enzyme (DUB) action. Five DUB subfamilies are recognized, including the USP, UCH, OTU, MJD, and JAMM enzymes. In humans, there are three proteasomal DUBs: PSMD14 (POH1/RPN11), UCH37 (UCH-L5), and Ubiquitin-Specific Protease 14, which is also known as the 60 kDa subunit of tRNA-guanine transglycosylase (USP14/TGT60 kDa).

Selected Reviews:

• Amm I, Sommer T, Wolf DH (2014) Protein quality control and elimination of protein waste: the role of the ubiquitin-proteasome system. Biochim. Biophys. Acta 1843(1), 182–96.
• Budhidarmo R, Nakatani Y, Day CL (2012) RINGs hold the key to ubiquitin transfer. Trends Biochem. Sci. 37(2), 58–65.
• Burrows JF, Johnston JA (2012) Regulation of cellular responses by deubiquitinating enzymes: an update. Front Biosci (Landmark Ed) 17, 1184–200.
• Campello S, Strappazzon F, Cecconi F (2014) Mitochondrial dismissal in mammals, from protein degradation to mitophagy. Biochim. Biophys. Acta 1837(4), 451–60.
• Corn JE, Vucic D (2014) Ubiquitin in inflammation: the right linkage makes all the difference. Nat. Struct. Mol. Biol. 21(4), 297–300.
• Hammond-Martel I, Yu H, Affar el B (2012) Roles of ubiquitin signaling in transcription regulation. Cell. Signal. 24(2), 410–21.
• Hildebrand JM, Yi Z, Buchta CM, Poovassery J, Stunz LL, Bishop GA (2011) Roles of tumor necrosis factor receptor associated factor 3 (TRAF3) and TRAF5 in immune cell functions. Immunol. Rev. 244(1), 55–74.
• Hurley JH, Schulman BA (2014) Atomistic autophagy: the structures of cellular self-digestion. Cell 157(2), 300–11.
• Ruggiano A, Foresti O, Carvalho P (2014) Quality control: ER-associated degradation: protein quality control and beyond. J. Cell Biol. 204(6), 869–79.
• Tokunaga F (2013) Linear ubiquitination-mediated NF-κB regulation and its related disorders. J. Biochem. 154(4), 313–23.
• Weissman AM, Shabek N, Ciechanover A (2011) The predator becomes the prey: regulating the ubiquitin system by ubiquitylation and degradation. Nat. Rev. Mol. Cell Biol. 12(9), 605–20.
• Zhao Y, Brickner JR, Majid MC, Mosammaparast N (2014) Crosstalk between ubiquitin and other post-translational modifications on chromatin during double-strand break repair. Trends Cell Biol. 24(7), 426–34.

We would like to thank Prof. Wenyi Wei, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA for reviewing this diagram.

created September 2004

revised July 2014