A cellular atlas of calcineurin signaling

Abstract

Intracellular Ca²⁺ signals are temporally controlled and spatially restricted. Signaling occurs adjacent to sites of Ca²⁺ entry and/or release, where Ca²⁺-dependent effectors and their substrates co-localize to form signaling microdomains. Here we review signaling by calcineurin, the Ca²⁺/calmodulin regulated protein phosphatase and target of immunosuppressant drugs, Cyclosporin A and FK506. Although well known for its activation of the adaptive immune response via NFAT dephosphorylation, systematic mapping of human calcineurin substrates and regulators reveals unexpected roles for this versatile phosphatase throughout the cell. We discuss calcineurin function, with an emphasis on where signaling occurs and mechanisms that target calcineurin and its substrates to signaling microdomains, especially binding of cognate short linear peptide motifs (SLiMs). Calcineurin is ubiquitously expressed and regulates events at the plasma membrane, other intracellular membranes, mitochondria, the nuclear pore complex and centrosomes/cilia. Based on our expanding knowledge of localized CN actions, we describe a cellular atlas of Ca²⁺/calcineurin signaling.

Keywords: Calcineurin; Calcium; Phosphatase; Phosphorylation; SLiMs; Signaling.

Fig. 1.. Calcineurin domain structure and activation.

(A) Schematic of canonical (α, β2 and γ) and β1 catalytic subunit (CNA) and regulatory (CNB) subunits of calcineurin. CNB binding helix (BBH); calmodulin (CaM)-binding domains (CBD); autoinhibitory sequence (AIS); autoinhibitory domain (AID); EF-hand Ca²⁺ -binding sites (EF1 and EF2 are low-affinity, EF3 and EF4 are high affinity sites) are represented in the cartoons. (B) Cartoons of activation mechanisms for canonical (α, β2 and γ) and non-canonical calcineurin-β1 (CN- β1) isozymes. CN is inactive under resting conditions. For canonical isozymes, Ca²⁺ binding to CNB and CaM binding to CNA relieves the autoinhibition by the AIS (purple) and AID (blue). Under pathophysiological conditions, cleavage of the regulatory domain can produce a constitutively active enzyme (boxed). CN-β1 is only partially activated by Ca²⁺ and CaM binding due persistent occlusion of a substrate-binding grove by the LAVP sequence (green) found within the non-canonical carboxy terminal. Full activation may involve tethering of the inhibitory tail to membranes via palmitoylation of two cysteines (red).

Fig. 2.. CN signaling occurs in localized microdomains throughout the cell.

CN substrates and scaffolds in different subcellular locations are shown as discussed in the text. (A) Plasma Membrane. (B) Endocytic compartments. Endosomes, Lysosome and the Golgi Apparatus are shown. (C) Mitochondria (D) Endoplasmic Reticulum and Nucleus. In the nucleus the nuclear pore complex (NPC) is shown. (E) Centrosome and Cilia. All figures were created with BioRender.com.