Ancestral resurrection to understand kinase regulation in the CMGC family

We have successfully completed the first ancestral reconstruction (see background) of a major kinase group, the CMGC kinases. We then resurrected 8 ancestros, beginning with the deep ancestor of the CDK, MAPK, GSK and Ime2 kinase families from >2-billion years ago, to determine mechanisms of specificity evolution.

We are now extending this study to determine the mechanisms of regulation of Mitogen Activated Protein Kinases (MAPKs) and Cyclin Dependent Kinases (CDKs).

See Howard et al. for more details.
See also Ignite talk for a 5-minute talk on the principles of ancestral resurrection

Background: Ancestral reconstruction and resurrection

Ancestral reconstruction is the inference of ancestral protein sequences from protein sequence information that exists today. The recent explosion in genomics data means that can now identify homologous sequences for a given protein from hundreds of diverse species. We can then perform multiple sequence alignments to place these sequences on a tree. From this starting point, we can use the phylogenetic relationships between these proteins together with a model of evolution to infer the sequences of ancestral proteins that gave rise to this set of modern proteins. The model of evolution takes into account the probabilities of amino acid substitutions, deletions and insertions. For example, histidines can mutate to glutamine as the result of a single DNA base pair change making this event far more likely than a histidine to methionine mutation, which requires three base substitutions. Given this information, we can use a maximum likelihood algorithm to infer the most likely amino acid identity at every ancestral node (Figure 1). Ancestral resurrection is the synthesis of DNA encoding these computationally deduced sequences and the recombinant expression of the ancestral protein to allow direct biochemical analysis of protein evolution.