Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity

Protein kinases have evolved diverse specificities to enable cellular information processing. To gain insight into the mechanisms underlying kinase diversification, we studied the CMGC protein kinases using ancestral reconstruction. Within this group, the cyclin dependent kinases (CDKs) and mitogen activated protein kinases (MAPKs) require proline at the +1 position of their substrates, while Ime2 prefers arginine. The resurrected common ancestor of CDKs, MAPKs, and Ime2 could phosphorylate substrates with +1 proline or arginine, with preference for proline. This specificity changed to a strong preference for +1 arginine in the lineage leading to Ime2 via an intermediate with equal specificity for proline and arginine. Mutant analysis revealed that a variable residue within the kinase catalytic cleft, DFGx, modulates +1 specificity. Expansion of Ime2 kinase specificity by mutation of this residue did not cause dominant deleterious effects in vivo. Tolerance of cells to new specificities likely enabled the evolutionary divergence of kinases.

DOI:http://dx.doi.org/10.7554/eLife.04126.001

All living things have enzymes called protein kinases that transfer chemical tags called phosphates onto other proteins. Adding a phosphate to a protein can change the protein's activity—for example, by switching it on or off—and many biological processes involve large networks of kinases that phosphorylate hundreds of proteins.

Humans have approximately 500 different protein kinases, which can each phosphorylate many proteins, and so human cells are regulated by tens of thousands of different phosphorylation sites. This raises a number of questions: how have these different kinases evolved over evolutionary history? And how have they come to recognize, and phosphorylate, so many different sites?

Howard, Hanson-Smith et al. studied members of a large family of protein kinases called the CMGC group. These enzymes are found in all organisms that have a cell nucleus, including animals, plants, and fungi. All proteins, including kinases, are built up of a chain of smaller molecules called amino acids, and the ability of a kinase to phosphorylate a protein depends on the kinase recognizing a short string of amino acids known as a motif. The phosphate is added in the middle of this motif at the so-called ‘0’ position. Howard, Hanson-Smith et al. found that all of the CMGC protein kinases tested ‘preferred’ an arginine or proline amino acid at the ‘+1’ position of this motif. However, some kinases preferred motifs with an arginine amino acid at this position, and others preferred a proline instead.

Howard, Hanson-Smith et al. predicted how the ancestors of a number of CMGC protein kinases might have looked and then ‘resurrected’ them by producing them in yeast cells. When the preference of these ancestral enzymes was tested, the oldest ancestor was found to slightly prefer motifs that had a proline amino acid at the +1 position. Testing six more recent ancestors showed that, over a billion years of evolution, this amino acid preference became broader to include both proline and arginine—and that some modern protein kinases subsequently evolved and specialized to prefer arginine at the +1 position, thus creating a new specificity.

Kinases are sometimes likened to microchips in complex electronic networks. In this analogy, expanding the specificity of a kinase could be like creating many ‘loose wires’ and cause short-circuits. From their evolutionary analysis, Howard, Hanson-Smith et al. were able to identify a structural change in the enzyme that causes an expansion of kinase specificity, which allowed them to directly test this idea in cells. Expanding the specificity of a protein kinase that controls sexual cell division in yeast cells did not stop the yeast from dividing to produce spores, suggesting that these changes are more readily tolerated than was expected. Howard, Hanson-Smith et al. suggest that this unexpected robustness of cellular circuits enabled the evolution of the wide variety of protein kinases seen today.

DOI:http://dx.doi.org/10.7554/eLife.04126.002