Neuronal Proteomic Analysis of the Ubiquitinated Substrates of the Disease-Linked E3 Ligases Parkin and Ube3a

Figure 1

Main intracellular quality control mechanisms: Ubiquitin-Proteasome System (UPS) and Autophagy. (a) Ubiquitin is attached to target substrates by a sequential enzymatic cascade comprised by E1 (ubiquitin-activating), E2 (ubiquitin-conjugating), and E3 (ubiquitin-ligase) enzymes. E1 hydrolyses ATP to form an Ub-adenyl intermediate that is subsequently attached to the E1 via a thioester bond. E1-Ub transfers the ubiquitin to the E2, which then interacts with an E3 to transfer the ubiquitin to the substrate. DUBs can cleave ubiquitin moieties to edit ubiquitinated substrates. Protein ubiquitination regulates many biological processes, such as proteasomal degradation, autophagy, endosomal trafficking, and signalling events, and also chromatin assembly, DNA transcription and repair, ribosome biogenesis and translation, cell cycle and division, apoptosis, immunity, and organelle biogenesis. (b) Based on cargo recognition mechanisms, autophagy can be subdivided into macroautophagy, microautophagy, and chaperone-mediated autophagy. Macroautophagy is the best-studied form of autophagy, in which a double-membrane structure expands around and engulfs large cytosolic contents or organelles, forming an autophagosome. The autophagosome then fuses with a lysosome and the contents are degraded. Microautophagy degrades smaller cytosolic cargo, such proteins and tiny pieces of organelles by lysosomal invagination. CMA is involved in the degradation of unfolded or aggregated proteins that expose a particular degradation motif (KFERQ) that is then recognised by the cytosolic chaperone heat shock cognate protein of 70 kDa (HSC70), which interacts with lysosome-associated membrane protein type 2A leading to the unfolding and translocation of the substrate into the lysosomal lumen where it is degraded. Several macroautophagy subtypes can be distinguished according to cargo: reticulophagy (ER), mitophagy (mitochondria), pexophagy (peroxisome), ribophagy (ribosome), lipophagy (lipid droplets), xenophagy (intracellular pathogens such as bacteria and virus), and aggrephagy (protein aggregates).

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