ATG-3 is the C. elegans ortholog of yeast Atg3 and mammalian ATG3, the E2-like conjugating enzyme of the Atg8 lipidation system. It receives the Atg8-family proteins LGG-1 and LGG-2 from the E1-like enzyme ATG-7 as a thioester and, with the E3-like LGG-3/ATG12-ATG-5-ATG-16 complex, transfers them to phosphatidylethanolamine on forming autophagosomal membranes. ATG-3 acts in the cytosol and at sites of autophagosome formation and is essential for autophagosome biogenesis; atg-3 mutant embryos fail to degrade the aggrephagy substrates SQST-1/p62, EPG-7 and other autophagy cargo, which accumulate as aggregates.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000045 autophagosome assembly | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that ATG-3 participates in autophagosome assembly. Reason: ATG-3 catalyses the final transfer step of Atg8-family lipidation that autophagosome biogenesis depends on. In C. elegans, atg-3 mutants are a reference strain for complete block of aggrephagy. Supporting Evidence: PMID:24185444 The ubiquitin-like protein Atg8 is activated by the E1-like enzyme Atg7 and then transferred to the E2-like conjugating enzyme Atg3 and finally conjugated to phosphatidylethanolamine (PE). PMID:27046254 Lipidation of LGG-1 and LGG-2 is mediated by 2 enzymes, ATG-7 and ATG-3. |
| GO:0000407 phagophore assembly site | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that ATG-3 acts at the phagophore assembly site, from yeast Atg3. Reason: Conserved site of Atg8 lipidation; no evidence of divergence in C. elegans. |
| GO:0000422 autophagy of mitochondrion | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic inference of autophagy of mitochondrion, sourced from yeast Atg3. Reason: Mitophagy depends on the general lipidation machinery, but this is not a core function of ATG-3 and is untested for C. elegans atg-3. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of cytosolic activity. Reason: ATG3 orthologs are soluble cytosolic E2-like enzymes that are recruited transiently to membranes; appropriate location. |
| GO:0016236 macroautophagy | IDA PMID:23530068 The scaffold protein EPG-7 links cargo-receptor complexes wi... | ACCEPT | Summary: Lin et al. used atg-3 mutants as an autophagy-null reference: SQST-1, EPG-7 and other autophagy substrates accumulate at dramatically elevated levels and form aggregates in atg-3 mutant embryos and larvae. Reason: Directly shows that atg-3 is required for autophagic (aggrephagy) degradation in C. elegans. The evidence is a loss-of-function phenotype (closer to IMP than IDA), but the macroautophagy term is correct. Supporting Evidence: PMID:23530068 levels of SQST-1 are dramatically elevated in atg-3 and epg-7 mutant embryos in an immunoblotting assay PMID:23530068 Levels of EPG-7 are dramatically elevated and a large number of EPG-7 aggregates are formed in atg-3 mutants. |
| GO:0019787 ubiquitin-like protein transferase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro (Atg3/Atg10 family) mapping to ubiquitin-like protein transferase activity. Reason: Correct but general; ATG-3 is specifically the Atg8-family E2 (the Atg3/Atg10 InterPro entry covers both E2s, so it cannot resolve the substrate). Replace with the specific child term already asserted by IBA. Proposed replacements: Atg8-family conjugating enzyme activity Supporting Evidence: PMID:27046254 Lipidation of LGG-1 and LGG-2 is mediated by 2 enzymes, ATG-7 and ATG-3. |
| GO:0044804 nucleophagy | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic inference of a role in nucleophagy, sourced from yeast Atg3. Reason: Nucleophagy is one cargo-specific output of core autophagy machinery and is not documented for ATG-3 in C. elegans; retained as a non-core inherited annotation. |
| GO:0061723 glycophagy | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic inference of glycophagy, from Drosophila Atg3. Reason: Glycophagy is a cargo-specific output of the general machinery; not documented in C. elegans. Non-core. |
| GO:0141046 Atg8-family conjugating enzyme activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that ATG-3 is the Atg8-family conjugating (E2-like) enzyme, from human and rat ATG3. Reason: Core molecular function. ATG-3 is a member of the ATG3 family (PTHR12866:SF2) and C. elegans data show that ATG-7 and ATG-3 mediate LGG-1 and LGG-2 lipidation, with LGG-1 and LGG-2 differing in their affinities for ATG-3. Supporting Evidence: PMID:27046254 Lipidation of LGG-1 and LGG-2 is mediated by 2 enzymes, ATG-7 and ATG-3. PMID:27046254 LGG-1 and LGG-2 have different affinities for ATG-7 and ATG-3 |
| GO:0006501 C-terminal protein lipidation | IMP PMID:27046254 Small differences make a big impact: Structural insights int... | NEW | Summary: ATG-3, with ATG-7, mediates the PE conjugation of LGG-1 and LGG-2 in C. elegans. Reason: ATG-3 catalyses the transfer of LGG-1/LGG-2 to phosphatidylethanolamine, so it performs the step (participation test passed). Comparator check: yeast Atg3 (P40344) carries C-terminal protein lipidation (GO:0006501) by IDA/IMP, and human ATG7's IDA row on the precomposed child GO:0061739 is decomposed to this genus. The autophagosome-assembly context is carried by the core functions (GO:0000045). C. elegans ATG-3 otherwise has no lipidation process term. Supporting Evidence: PMID:27046254 Lipidation of LGG-1 and LGG-2 is mediated by 2 enzymes, ATG-7 and ATG-3. |
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Experiment: In vitro LGG-1 versus LGG-2 lipidation with recombinant ATG-7 and ATG-3 on liposomes, with and without the ATG-5-LGG-3-ATG-16 complex, to quantify the affinity differences reported in vivo.
Type: in vitro reconstitution
atg-3 encodes an ortholog of the autophagic budding yeast protein Atg3p,and of human ATG3 (OMIM:609606); ATG-3 is expressed in larval and adultpharynx and body wall muscle, and in adult reproductive system, vulvalmuscle, spermetheca, and seam cells; ATG-3 has no obvious phenotype inmass RNAi assays.
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