Usp9X Controls Ankyrin-Repeat Domain Protein Homeostasis during Dendritic Spine Development

Variants in the ANK3 gene encoding ankyrin-G are associated with neurodevelopmental disorders, including intellectual disability, autism, schizophrenia, and bipolar disorder. However, no upstream regulators of ankyrin-G at synapses are known. Here, we show that ankyrin-G interacts with Usp9X, a neurodevelopmental-disorder-associated deubiquitinase (DUB). Usp9X phosphorylation enhances their interaction, decreases ankyrin-G polyubiquitination, and stabilizes ankyrin-G to maintain dendritic spine development. In forebrain-specific Usp9X knockout mice (Usp9X–/Y), ankyrin-G as well as multiple ankyrin-repeat domain (ANKRD)-containing proteins are transiently reduced at 2 but recovered at 12 weeks postnatally. However, reduced cortical spine density in knockouts persists into adulthood. Usp9X–/Y mice display increase of ankyrin-G ubiquitination and aggregation and hyperactivity. USP9X mutations in patients with intellectual disability and autism ablate its catalytic activity or ankyrin-G interaction. Our data reveal a DUB-dependent mechanism of ANKRD protein homeostasis, the impairment of which only transiently affects ANKRD protein levels but leads to persistent neuronal, behavioral, and clinical abnormalities. [Display omitted] •Ankyrin-G interaction with Usp9X regulates spine development•Usp9X controls ankyrin-repeat domain protein homeostasis•Usp9X knockout mice show synaptic abnormalities, ankyrin-G aggregates, and hyperactivity•USP9X mutations in patients ablate its catalytic activity or ankyrin-G interaction Yoon et al. show that deubiquitination of proteins containing ankyrin-repeat domains is essential for the correct developmental trajectory of cortical synapses, with disruption of the deubiquitinase Usp9X resulting in deficient synaptic structural plasticity as well as behavioral and clinical abnormalities.