Chemical Genetic Screen Identifies PSD3 as a Direct Substrate of NUAK1 that Regulates Dendritic Spine Maturation

Novel (nua) Kinase 1 (NUAK1) encodes a serine-threonine protein kinase, mutations in which are associated with autism spectrum disorder. Direct phosphorylation targets of NUAK1 have been elusive hindering mechanistic understanding of its role in brain development. Here, we characterize autism-associated NUAK1 variants and show their differential impact on catalytic activity and subcellular distribution. We engineered ATP-analog sensitive NUAK1 and utilized its specificity towards bulky analogs to identify over 30 hitherto unknown direct phosphorylation targets of NUAK1. We demonstrate that Pleckstrin Homology and Sec7-domain containing protein 3 (PSD3) is a bona fide phosphorylation target of NUAK1. A guanine exchange factor (GEF) for ARF6 GTPase, PSD3 is phosphorylated by NUAK1 at S476. Expression of phosphodeficient PSD3 leads to aberrant activation of ARF6 and generation of PI(4,5)P₂ that accumulates in intracellular vesicles. In neurons, phosphomutant PSD3 leads to enhanced spine maturation in an ARF6 dependent fashion. This study reveals direct neuronal substrates of an autism risk gene NUAK1, and delineates a mechanism by which PSD3 phosphorylation regulates ARF6 activation and spine maturation.