Palmitoylation targets the calcineurin phosphatase to the phosphatidylinositol 4-kinase complex at the plasma membrane

Calcineurin - the Ca2+ regulated phosphatase and target of immunosuppressants - regulates GPCR-mediated phospholipid signaling at the plasma membrane. Here the authors show that CNA beta 1 (a poorly studied isoform of the calcineurin catalytic subunit) is targeted to the plasma membrane through palmitoylation to dephosphorylate and promote PI4KA complex activity. Calcineurin, the conserved protein phosphatase and target of immunosuppressants, is a critical mediator of Ca2+ signaling. Here, to discover calcineurin-regulated processes we examined an understudied isoform, CNA beta 1. We show that unlike canonical cytosolic calcineurin, CNA beta 1 localizes to the plasma membrane and Golgi due to palmitoylation of its divergent C-terminal tail, which is reversed by the ABHD17A depalmitoylase. Palmitoylation targets CNA beta 1 to a distinct set of membrane-associated interactors including the phosphatidylinositol 4-kinase (PI4KA) complex containing EFR3B, PI4KA, TTC7B and FAM126A. Hydrogen-deuterium exchange reveals multiple calcineurin-PI4KA complex contacts, including a calcineurin-binding peptide motif in the disordered tail of FAM126A, which we establish as a calcineurin substrate. Calcineurin inhibitors decrease PI4P production during Gq-coupled GPCR signaling, suggesting that calcineurin dephosphorylates and promotes PI4KA complex activity. In sum, this work discovers a calcineurin-regulated signaling pathway which highlights the PI4KA complex as a regulatory target and reveals that dynamic palmitoylation confers unique localization, substrate specificity and regulation to CNA beta 1.

Automated summary

Calcineurin, a phosphatase regulated by calcium and targeted by immunosuppressants, is involved in regulating GPCR-mediated phospholipid signaling. A less-studied isoform of calcineurin, CNA beta 1, was found to localize to the plasma membrane through palmitoylation and promote the activity of PI4KA complex. This work reveals a calcineurin-regulated signaling pathway involving the PI4KA complex and highlights the importance of dynamic palmitoylation in conferring unique localization and regulation to CNA beta 1.