Spatial Organization in Protein Kinase A Signaling Emerged at the Base of Animal Evolution

In
phosphorylation-directed signaling, spatial and temporal control
is organized by complex interaction networks that diligently direct
kinases toward distinct substrates to fine-tune specificity. How these
protein networks originate and evolve into complex regulatory machineries
are among the most fascinating research questions in biology. Here,
spatiotemporal signaling is investigated by tracing the evolutionary
dynamics of each functional domain of cAMP-dependent protein kinase
(PKA) and its diverse set of A-kinase anchoring proteins (AKAPs).
Homologues of the catalytic (PKA-C) and regulatory (PKA-R) domains
of the (PKA-R)2–(PKA-C)2 holoenzyme were
found throughout evolution. Most variation was observed in the RIIa
of PKA-R, crucial for dimerization and docking to AKAPs. The RIIa
domain was not observed in all PKA-R homologues. In the fungi and
distinct protist lineages, the RIIa domain emerges within PKA-R, but
it displays large sequence variation. These organisms do not harbor
homologues of AKAPs, suggesting that efficient docking to direct spatiotemporal
PKA activity evolved in multicellular eukaryotes. To test this in silico hypothesis, we experimentally screened organisms
with increasing complexity by cAMP-based chemical proteomics to reveal
that the occurrence of PKA–AKAP interactions indeed coincided
and expanded within vertebrates, suggesting a crucial role for AKAPs
in the advent of metazoan multicellularity.