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The ubiquitin conjugation system. Through the function of three enzymes, called ubiquitin activating enzymes (E1), ubiquitin conjugating enzymes (E2), and ubiquitin ligases (E3), ubiquitin is conjugated to target proteins that are specifically recognized by E3s. Once an ubiquitin is conjugated to the target protein, additional ubiquitins are conjugated successively onto the terminal ubiquitin already conjugated to the target protein to form polyubiquitin chains. The polyubiquitin chains have been velieved to be generated by iso-peptide bond formation between the C-terminal carboxyl group of one ubiquitin and an ε-amino group of one of seven Lys residues in another ubiquitin. In the case of the ubiquitin proteolytic pathway, polyubiquitin chains are conjugated via K48. K63 conjugated chains are involved in signaling or DNA repair without the conjugated protein being subject to degradation. However, the linear ubiquitin chain, as reviewed here, is unique because it is generated by peptide bond formation between the C-terminus of one ubiquitin and the α-amino group of Met1 residues in another ubiquitin. Conjugated ubiquitins are cleaved by deubiquitinating enzymes (DUBs). The function of conjugated proteins is modulated via specific recognition of conjugated polyubiquitin chains

A) Regulation of induction: In yeast, the Tor kinase and its effectors regulate the induction of autophagy. UNC-51 is the C. elegans Atg1 ortholog, however, it is not clear if there are similar regulatory proteins to Atg17 or Atg13.
B) Vesicle nucleation requires a lipid kinase complex, which includes the class III phosphatidylinositol 3-kinase (PI3K), Vps34 (in C. elegans LET-512). In yeast, Vps34 activation depends on its binding partners, Atg6, Atg14, and Vps15 (Kihara et al., 2001). In C. elegans, the ATG6 ortholog is bec-1, however, orthologs to ATG14 and VPS15 appear to be missing in the C. elegans genome. The interaction between the antiapoptotic protein CED-9 and BEC-1 is conserved in C. elegans (Takács-Vellai et al., 2005). A similar interaction between the mammalian proteins Bcl-2 and Beclin 1, inhibits autophagy (Maiuri et al., 2007a; Maiuri et al., 2007b; Pattingre et al., 2005).
C) Two novel ubiquitin-like conjugation pathways: the Atg12 conjugation system (Atg5, Atg12, and Atg16), and the Atg8 lipidation system (Atg8, Atg3, and Atg7) mediate vesicle expansion, and vesicle completion. Orthologs to all the members of these two complexes have been found in C. elegans, where they are named ATG-3, ATG-4, ATG-5, ATG-7, ATG-16, LGG-1/Atg8 and LGG-3/Atg12. In yeast, Atg8 undergoes two posttranslational processing events resulting in conjugation to phosphatidylethanolamine (PE) and recruitment to the PAS membrane. ATG-7 is an E1 ubiquitin activating enzyme required for the activation of of LGG-1. LGG-3-ATG-5 oligomerize with ATG-16 to allow for the formation of the multimeric complex. ATG-3 and ATG-10 are E2-like ubiquitin conjugating enzymes and ATG-4 is a cysteine protease. As for its yeast ortholog, LGG-1 appears to remain in the completed autophagosome and thus is an excellent marker for early and late autophagosomal structures.
D) The retrieval of the integral membrane protein ATG-9 from the phagophore assembly site (PAS) involves ATG-2 and ATG-18, two interacting peripheral proteins.