The Ubiquitin Proteasome Pathway (UPP)

The Ubiquitin Proteasome Pathway (UPP) is the principal mechanism for protein catabolism in the mammalian cytosol and nucleus. The highly regulated UPP affects a wide variety of cellular processes and substrates and defects in the system can result in the pathogenesis of several important human diseases. The central role of the UPP in biology has been recognized with the Nobel Prize for Chemistry which was awarded to Avram Hershko, Aaron Ciechanover and Irwin Rose in 2004. The UPP is central to the regulation of almost all cellular processes including:

  • Antigen processing
  • Apoptosis
  • Biogenesis of organelles
  • Cell cycle and division
  • DNA transcription and repair
  • Differentiation and development
  • Immune response and inflammation
  • Neural and muscular degeneration
  • Morphogenesis of neural networks
  • Modulation of cell surface receptors, ion channels and the secretory pathway
  • Response to stress and extracellular modulators
  • Ribosome biogenesis
  • Viral infection

Degradation of a protein via the Ubiquitin Proteasome Pathway (UPP) involves two discrete and successive steps: tagging of the substrate protein by the covalent attachment of multiple ubiquitin molecules (Conjugation); and the subsequent degradation of the tagged protein by the 26S proteasome, composed of the catalytic 20S core and the 19S regulator (Degradation). This classical function of ubiquitin is associated with housekeeping functions, regulation of protein turnover and antigeni‑peptide generation.

More recently, it has become evident that protein modification by ubiquitin also has unconventional (non-degradative) functions such as the regulation of DNA repair and endocytosis. These non-traditional functions are dictated by the number of ubiquitin units attached to proteins (mono versus poly-ubiquitination) and also by the type of ubiquitin chain linkage that is present.

Conjugation

Ubiquitin becomes covalently linked to itself and/or other proteins either as a single molecule or as poly-ubiquitin chains. The attachment of ubiquitin to the ε-amine of lysine residues of target proteins requires a series of ATP-dependent enzymatic steps by E1 (ubiquitin activating), E2 (ubiquitin conjugating) and E3 (ubiquitin ligating) enzymes. E3 binds to substrate proteins and also to an E2 to form an E2-E3-substrate complex. It is the recognition and formation of said complex that has the highest level of substrate specificity for the conjugation cascade. The C‑terminal Gly75-Gly76 residues of ubiquitin are the key residues that function in the diverse chemistry of ubiquitin reactions. Ubiquitin can be conjugated to itself via specific lysine (K6, K11, K27, K29, K33, K48 or K63) residues which results in diverse types of chain linkages.

Deubiquitination (Deconjugation)

The covalent ubiquitin bonds (isopeptide linkages) between ubiquitin and a target protein as well as between ubiquitin molecules in a chain can be reversed by specific deubiquitinating enzymes (DUBs). Recent studies have revealed that DUBs are dynamic enzymes that partner with various interacting proteins to facilitate both substrate selection and DUB activity. Assembly of individual DUBs into distinct protein complexes has allowed for the diversification of DUB activity that is needed to process the increasingly diverse assemblages of monoubiquitin and polyubiquitin marks on substrates. This dynamic regulation in the ubiquitin proteasome system is underscored by the increasing evidence that many DUBs are part of ubiquitin ligase complexes, which enables DUBs to regulate the activity and abundance of both the ligase and the substrate. A subset of DUBs and their associated complexes are displayed below, along with the cellular pathways in which they act. 

Ubiquitin-Like Modifiers (UBLs)

Although ubiquitin is the most well understood post- translation modifier, there is a growing family of ubiquitin-like proteins (UBLs) that modify cellular targets in a pathway that is parallel to, but distinct from that of ubiquitin. These alternative modifiers include: SUMO, NEDD8, ISG15, APG8, APG12, FAT10, Ufm1, URM1, and Hub1. These related molecules have novel functions and influence diverse biological processes. There is also cross-regulation between the various conjugation pathways since some proteins can become modified by more than one UBL and sometimes even at the same lysine residue.  For instance, SUMO modification often acts antagonistically to that of ubiquitination and serves to stabilize protein substrates. Proteins conjugated to UBLs are typically not targeted for degradation by the proteasome, but rather function in diverse regulatory activities. Attachment of UBLs might alter substrate conformation, affect the affinity for ligands or other interacting molecules, alter substrate localization and influence protein stability. UBLs are structurally similar to ubiquitin and are processed, activated, conjugated and released from conjugates by enzymatic steps that are similar to the corresponding mechanisms for ubiquitin. UBLs are also translated with C‑terminal extensions that are processed to expose the invariant C‑terminal LRGG. These modifiers have their own specific E1 (activating), E2 (conjugating) and E3 (ligating) enzymes that conjugate the UBLs to intracellular targets. These conjugates can be reversed by UBL-specific isopeptidases that have similar mechanisms to that of the deubiquitinating enzymes.