Ubiquitination and selective autophagy

Abstract

Ubiquitination has long been recognised as a key determinator of protein fate by tagging proteins for proteasomal degradation. Most recently, the ability of conjugated ubiquitin chains to confer selectivity to autophagy was demonstrated. Although autophagy was first believed to be a bulk, non-selective 'self-eating' degradative process, the molecular mechanisms of selectivity are now starting to emerge. With the discovery of autophagy receptors - which bind both ubiquitinated substrates and autophagy specific light chain 3 (LC3) modifier on the inner sheath of autophagosomes - a new pathway of selective autophagy is being unravelled. In this review, we focus on the special role of ubiquitin signals and selective autophagy receptors in sorting a variety of autophagic cargos.

Figure 1

The Ubiquitin code links between proteasomal and lysosomal degradation. A model for different degradation routes of a misfolded protein. As illustrated, a misfolded protein can be degraded by proteasome or lysosomal system. Chaperone-dependent E3-ligase CHIP or other related E3-ligases leads to ubiquitination of the misfolded protein, predominantly in a K48-linked mode, which targets for the proteasome. Under certain conditions i.e., if the capacity of the chaperone-mediated refolding machinery and the UPS is overloaded, protein aggregation occurs, which are then targeted for autophagic clearance. Thereby, ubiquitin chains on misfolded proteins can undergo remodelling by combined activity of deubiquitinating enzyme (DUB) and E3-ligases. Newly formed ubiquitin chains, i.e., K63-linked chains are then recognised by the UBD of p62, NBR1 to form inclusion bodies or by the corresponding UBD of HDAC6, which direct protein aggregates to the aggresome. Aggresomes can be degraded via the proteasome or via autophagy pathway. If degradation occurs via autophagy, targeting of the protein aggregates are determined by the LIR motif of p62 and NBR1. Autophagy takes part in distinct steps. Cytosolic components are enclosed by an isolation membrane so-called phagophore, which leads to the formation of the autophagosomes. Thereby, LC3 and other ATG proteins such as the ATG 5/12/16L complex are recruited to autophagosome. Finally, the outer membrane of the autophagosome fuses with the lysosome and the internal material is degraded in the autolysosome. LC3, mammalian LC3 modifier including all LC3 and GABARAP family protein; Ub, ubiquitin

Figure 2

Two UBL are required for autophagy. (a) In the ubiquitin system, ubiquitination takes part in three steps. First, the enzymes E1 leads to activation of ubiquitin followed by a conjugation step, which is catalysed by E2 enzyme. Finally, a ubiquitin E3-ligase process tagging of ubiquitin to a protein. Removal of ubiquitin is performed by DUB. (b) The UBLs ATG12 and LC3 have functional similarities to the ubiquitin system. Both systems utilise a E1-like enzyme (Atg7) in the first activation step. Then, the E2-like enzyme Atg10 conjugates Atg12 to Atg5 to form a complex with Atg16L, which assists as a E3 ubiquitin ligase in the ligation of PE to LC3 by Atg3 (E2-like enzyme). The corresponding deubiquitinating enzyme (DUB) ATG4 removes LC3 from PE. LC3, mammalian LC3 modifier including all LC3 and GABARAP family protein; Ub, ubiquitin

Figure 3

Non-selective and selective Autophagy. (a) Upon nutrient deprivation, autophagy catabolizes cytoplasmic components nonselectively into autophagosome and mediates recycling and global turnover of cytoplasmic materials. (b) In selective autophagy particular substrate are targeted into the autophagosome by selective autophagy receptors. The targeted cargo includes protein aggregates, damaged mitochondria or pathogens such as bacteria. 16/12/5, ATG 16/12/5 complex; LC3, mammalian LC3 modifier including all LC3 and GABARAP family protein; Ub ubiquitin

Figure 4

Hitherto identified proteins involved in selective autophagy and their domain architecture. (a) p62, NBR1, OPTN, NDP52 and c-Cbl are autophagic adaptor proteins. Excluding c-Cbl they all interact with both ubiquitin and LC3 to promote autophagic degradation. The UBD domain of c-Cbl instead seems not to be involved in autophagic degradation. (b) NIX and newly found FUNDC1 are mitochondrial membrane proteins, which bind LC3/GABARP via their LIR motifs. (c) HDAC6 has only a UBD corresponding called BUZ and binds to ubiquitin (but not to LC3), (d) whereas the proteins Alfy, Bag3 and Tecpr1 are indirectly associated with ubiquitinated proteins or with LC3. Although this may ultimately also result in bridging substrates to autophagosomes, these proteins are not referred to as autophagy receptors. Numbers indicates length of human proteins in amino acids. BEACH, BEACH domain; BH3, Bcl-2 homology 3 domain; BUZ, ubiquitin-binding zinc finger; CC, coiled coil domain; Dysf, Dysferlin domain; FYVE, Fab1,YOTB/ZK632.12, Vac1, and EEA1 domain; PH, Pleckstrin homology domain; TM, transmembrane domain; WD40, WD40 repeats; WW, WW domain; ZnF, Zinc-finger domain