Drosophila UBE3A regulates substrates associated with gliopathic seizures through direct ubiquitination of translation initiation and ubiquitin-proteasome proteins

UBE3A encodes a HECT-type E3 ubiquitin ligase essential for neurodevelopment. Loss of maternal UBE3A causes Angelman syndrome (AS), while maternal duplications of 15q11.2–q13.1 (including UBE3A) lead to Dup15q syndrome, both characterized by severe neurological impairment and epilepsy. Despite its importance, few disease-relevant substrates have been identified due to the transient and low-stoichiometric nature of E3–substrate interactions. To address this, we adapted the Ubiquitin-Activated Interaction Trap (UBAIT) system for in vivo use in Drosophila melanogaster, enabling enrichment for potential Dube3a substrates. Using GAL4/UAS drivers, we expressed Dube3a-UBAIT in neurons and glia, followed by LC-MS/MS quantification to identify cell-type-specific candidate substrates. Distinct interactomes emerged, with strong enrichment in glia for RNA surveillance and translation-related pathways. Functional screening of 163 candidates using Drosophila RNAi lines identified eight genes that induced seizure phenotypes upon knockdown, primarily in glia and linked to RNA processing. Biochemical validation in HEK-293T UBE3A knockout cells confirmed Dube3a-dependent polyubiquitination of five substrates: Sap47, emb, Dpm1, tio, and Nedd4. These findings define a set of cell-type-specific Dube3a substrates and implicate glial RNA regulation as a key contributor to seizure susceptibility in UBE3A-related disorders. An in vivo Drosophila UBAIT approach identifies neuronal and glial Dube3a substrates, implicating glial RNA-processing pathways as potential contributors to seizure phenotypes in Dup15q syndrome.