The Atg8 and Atg12 ubiquitin-like conjugation systems in macroautophagy. 'Protein modifications: beyond the usual suspects' review series

Abstract

As a lysosomal/vacuolar degradative pathway that is conserved in eukaryotic organisms, autophagy mediates the turnover of long-lived proteins and excess or aberrant organelles. The main characteristic of autophagy is the formation of a double-membrane vesicle, the autophagosome, which envelops part of the cytoplasm and delivers it to the lysosome/vacuole for breakdown and eventual recycling of the degradation products. Among the approximately 30 autophagy-related (Atg) genes identified so far, there are two ubiquitin-like proteins, Atg12 and Atg8. Analogous to ubiquitination, Atg12 is conjugated to Atg5 by Atg7--an E1-like protein--and Atg10--an E2-like protein. Similarly, Atg7 and Atg3 are the respective E1-like and E2-like proteins that mediate the conjugation of Atg8 to phosphatidylethanolamine. Both Atg12-Atg5 and Atg8 localize to the developing autophagosome. The Atg12-Atg5 conjugate facilitates the lipidation of Atg8 and directs its correct subcellular localization. Atg8-phosphatidylethanolamine is probably a scaffold protein that supports membrane expansion and the amount present correlates with the size of autophagosomes.

Figure 1

Structural comparisons of ubiquitin, LC3 and AtAtg12. (A) Ribbon diagrams of ubiquitin (Vijay-Kumar et al, 1987; Protein Data Bank (PDB) code ), LC3 (Sugawara et al, 2004; PDB code ) and AtAtg12 (Suzuki et al, 2005; PDB code ) are shown in the same orientation; α-helices are shown in purple, 3₁₀ helices in blue, β-strands in yellow, β-turns in cyan and unstructured loops in white. (B) Superimposition of ubiquitin (red), LC3 (blue) and AtAtg12 (green). A multiple structural alignment was constructed using MAMMOTH-mult (http://ub.cbm.uam.es/mammoth/mult; Lupyan et al, 2005) and the structures were visualized with the Visual Molecular Dynamics (VMD) program (http://www.ks.uiuc.edu/Research/vmd). At, Arabidopsis thaliana; Atg, autophagy-related; LC3, microtubule-associated protein 1 light chain 3.

Figure 2

Conjugation processes in yeast. (A) Ubiquitin. (B) Atg12. (C) Atg8. See text for details. Atg, autophagy-related; PE, phosphatidylethanolamine; PPi, pyrophosphate; Ubi, ubiquitin; Ubl, ubiquitin-like.

Figure 3

Atg12 and Atg8 conjugation systems in vesicle formation. The initiation of the early-stage phagophore is independent of the presence of the Atg12–Atg5 conjugate, and the Atg12–Atg5-Atg16 complex is subsequently recruited to this structure. Atg12–Atg5-Atg16 redistributes mostly to the outer surface of the phagophore and directs additional Atg8 to this site. The presence of Atg8 on the phagophore supports its expansion. On completion of the autophagosome, the Atg12–Atg5-Atg16 complex dissociates from the vesicle, and Atg4 proteolytically releases the Atg8 that is present on the external surface. Atg, autophagy-related; LC3, microtubule-associated protein 1 light chain 3.

Jiefei Geng

Daniel J. Klionsky