Crustacean Protein Kinases A and C: Bioinformatic Characterization in Decapods and Other Non-Model Organisms

The AGC kinases constitute a large and ancient gene superfamily with origins that coincided with the appearance of multicellularity. Three AGC kinase families-protein kinase A (PKA), protein kinase G (PKG), and protein kinase C (PKC)-mediate the actions of neuropeptide hormones, biogenic amines, and other ligands on various physiological processes in metazoans. Metazoans express two PKG types. Jawed vertebrates express three PKA catalytic (C) subunits, four regulatory (R) subunits, and twelve PKCs, organized into conventional, novel delta-like, novel epsilon-like, atypical, and protein kinase N (PKN) subfamilies. By contrast, invertebrate PKA and PKC sequences are not well characterized. Consequently, limited database resources can result in misidentification or mischaracterization of proteins and can lead to misinterpretation of experimental data. A broad phylogenetic and sequence analysis of CrusTome transcriptome and GenBank databases was used to characterize 640 PKA-C sequences, 1122 PKA-R sequences, and 1844 PKC sequences distributed among the Annelida, Arthropoda, Chordata, Cnidaria, Nematoda, Mollusca, Echinodermata, Porifera, Platyhelminthes, and Tardigrada. Phylogenetic analysis and multiple sequence alignments revealed conservation of certain PKA-C, PKA-R and PKC isoforms across metazoans, as well as diversification of additional taxon-specific isoforms. Decapods expressed four PKA-C isoforms, designated PKA-C₁, -C_D1, -C_GLY1, and -C_GLY2; five PKA-R isoforms, designated PKA-RI₁, -RI_D1, -RII_GLY, and -RII_D1; and five PKC isoforms, designated PKN_D1-3, conventional cPKC_D1, novel nPKC_D1δ and nPKC_D1ε, and atypical aPKC_D1. PKA-C_GLY1, -C_GLY2, and -RII_GLY had glycine-rich N-terminal sequences that were unique to crustaceans. These data suggest lineage-specific diversification that retained the core catalytic function of each kinase, while regions outside of the kinase domain may provide specialized regulatory mechanisms and/or spatiotemporal subcellular localization in invertebrate tissues.