Research ResourceBiochemistry

Tracing the origin and evolution of pseudokinases across the tree of life

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Science Signaling  23 Apr 2019:
Vol. 12, Issue 578, eaav3810
DOI: 10.1126/scisignal.aav3810

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Hunting pseudokinases

Pseudokinases generally have a similar structure to that of kinases but without the catalytic function. Rather, they serve alternative, some as yet unknown, functions across various signaling niches in many cell and tissue types. Kwon et al. performed an evolutionary analysis of pseudokinases across species and classified both known and previously unknown pseudokinases into groups and families. Their analysis reveals that pseudokinases are more prevalent than was previously appreciated and shows how pseudokinase structures may have evolved to confer advantageous functions in bacteria, plants, and animals. The classification is part of a new online, mineable resource called ProKinO.

Abstract

Protein phosphorylation by eukaryotic protein kinases (ePKs) is a fundamental mechanism of cell signaling in all organisms. In model vertebrates, ~10% of ePKs are classified as pseudokinases, which have amino acid changes within the catalytic machinery of the kinase domain that distinguish them from their canonical kinase counterparts. However, pseudokinases still regulate various signaling pathways, usually doing so in the absence of their own catalytic output. To investigate the prevalence, evolutionary relationships, and biological diversity of these pseudoenzymes, we performed a comprehensive analysis of putative pseudokinase sequences in available eukaryotic, bacterial, and archaeal proteomes. We found that pseudokinases are present across all domains of life, and we classified nearly 30,000 eukaryotic, 1500 bacterial, and 20 archaeal pseudokinase sequences into 86 pseudokinase families, including ~30 families that were previously unknown. We uncovered a rich variety of pseudokinases with notable expansions not only in animals but also in plants, fungi, and bacteria, where pseudokinases have previously received cursory attention. These expansions are accompanied by domain shuffling, which suggests roles for pseudokinases in plant innate immunity, plant-fungal interactions, and bacterial signaling. Mechanistically, the ancestral kinase fold has diverged in many distinct ways through the enrichment of unique sequence motifs to generate new families of pseudokinases in which the kinase domain is repurposed for noncanonical nucleotide binding or to stabilize unique, inactive kinase conformations. We further provide a collection of annotated pseudokinase sequences in the Protein Kinase Ontology (ProKinO) as a new mineable resource for the signaling community.

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