biostudies-literatureJin BNatural Science Foundation of ChinaScience and Technology Commission of Shanghai Municipality ProjectNatural Science Foundation of ShanghaiMedical Engineering Cross Fund of Shanghai Jiao Tong University1119https://www.ebi.ac.uk/biostudies/studies/S-EPMC12842286biostudies-literatureUnknown27(2)Mitophagy, as a critical form of selective autophagy, plays a central role in maintaining cellular homeostasis. While the canonical PTEN-Induced Kinase 1 (PINK1)-Parkin pathway is well established, mitophagy can still be effectively induced in Parkin-deficient cells such as HeLa, indicating the existence of Parkin-independent alternative pathways. The mitochondrial matrix proteins 4-Nitrophenylphosphatase domain and non-neuronal SNAP25-like protein homolog 1 (NIPSNAP1) acts as a key effector in such pathways, yet its regulatory mechanisms remain incompletely understood. Here, we identify Ubiquitination Factor E4B (UBE4B) as an E3 ubiquitin ligase for NIPSNAP1 and demonstrate that it catalyzes NIPSNAP1 ubiquitination in both Human Embryonic Kidney 293 cells (HEK293T) and HeLa cells. Under mInternational journal of molecular sciencesUBE4B Mediates Mitophagy via NIPSNAP1 Ubiquitination and NDP52 Recruitment.PMC128422863197118720JC141120025ZR1401210YG2025ZD2482273647Xu KXu PJin BZhao BZhang YQu JWang XJiao XfalseUBE4B Mediates Mitophagy via NIPSNAP1 Ubiquitination and NDP52 Recruitment.Mitophagy, as a critical form of selective autophagy, plays a central role in maintaining cellular homeostasis. While the canonical PTEN-Induced Kinase 1 (PINK1)-Parkin pathway is well established, mitophagy can still be effectively induced in Parkin-deficient cells such as HeLa, indicating the existence of Parkin-independent alternative pathways. The mitochondrial matrix proteins 4-Nitrophenylphosphatase domain and non-neuronal SNAP25-like protein homolog 1 (NIPSNAP1) acts as a key effector in such pathways, yet its regulatory mechanisms remain incompletely understood. Here, we identify Ubiquitination Factor E4B (UBE4B) as an E3 ubiquitin ligase for NIPSNAP1 and demonstrate that it catalyzes NIPSNAP1 ubiquitination in both Human Embryonic Kidney 293 cells (HEK293T) and HeLa cells. Under m2026-01-01T00:00:00Z2026 Jan2026-06-16T03:10:04.501Z2026-06-16T03:06:51.866ZS-EPMC128422864159675910.3390/ijms27021119