Large-scale PTM analysis reveals that the E3 ligase, Anaphase promoting complex, APC/C, is a master regulator of protein complexes containing GIGYF2.

GIGYF2 is one of several uncertain candidates in Parkinson’s disease (PD) since follow-on studies did not confirm the findings from large scale genetics analyses. This report shows that post translational modifications (PTMs) of GIGYF2 and additional proteins or PD candidates with which it complexes are regulated by the E3 ligase Anaphase promoting complex (APC/C) in HEK293T cells. A large-scale screen for PTMs indicates that APC/C employs three distinct modes for recruiting substrates for ubiquitination, including GIGYF2. E3L-tagging interactions of APC/C with HUWE1, UBR4, and CRL4 E3 ligases expands the substrate repertoire to over a thousand proteins. Ubiquitination of enzymes involved in PTMs by APC/C extends its influence over a large section of the proteome. A fifth E3 ligase competes with APC/C for ubiquitination of common substrates, including many proteins implicated in PD. The findings suggest that structural polymorphism of these proteins and the biological environments in which their mutually exclusive complexes function may be responsible for the observed pleiotropy. Consequently, the phenotypic manifestations of GIGYF2 mutations may lie at the intersection of protein structure-function alterations by PTMs and genetic changes involving additional PD candidates. The implications of these findings for target validation and the potential to target APC/C substrates for clinical benefit in PD are discussed.