Turnover of protein phosphorylation evolving under stabilizing selection

Abstract

Most proteins are regulated by posttranslational modifications and changes in these modifications contribute to evolutionary changes as well as to human diseases. Phosphorylation of serines, threonines, and tyrosines are the most common modifications identified to date in eukaryotic proteomes. While the mode of action and the function of most phosphorylation sites remain unknown, functional studies have shown that phosphorylation affects protein stability, localization and ability to interact. Two broad modes of action have been described for protein phosphorylation. The first mode corresponds to the canonical and qualitative view whereby single phosphorylation sites act as molecular switches that either turn on or off specific protein functions through direct or allosteric effects. The second mode is more akin to a rheostat than a switch. In this case, a group of phosphorylation sites in a given protein region contributes collectively to the modification of the protein, irrespective of the precise position of individual sites, through an aggregate property. Here we discuss these two types of regulation and examine how they affect the rate and patterns of protein phosphorylation evolution. We describe how the evolution of clusters of phosphorylation sites can be studied under the framework of complex traits evolution and stabilizing selection.

Keywords: cell signaling; evolutionary turnover; molecular evolution; molecular rheostats; molecular switches; protein evolution; protein phosphorylation.

FIGURE 1

The relationship between site phosphorylation, localization and protein functions determines how much conservation is expected among species under purifying or stabilizing selection. (A) Toy examples of phosphorylation sites (indicated as “P”s) and cluster of sites and how they may affect protein functions individually or collectively. Phosphorylation sites regulate three putative functions A, B, C. The aggregate function of phosphorylation sites affects the fitness function of the protein and thus determines how many possible equivalent genotypes may give rise to equivalent functions or fitness. Only few possible examples are shown to illustrate the complex relationships expected and their impact on the evolution of phosphorylation profiles and many more are possible. (B) Shows a possible fitness landscape for CDK inhibition of Ste5. Ste5 inhibition is proportional to the charge (twice the number of phosphorylated residues) in the disordered region surrounding the PM domain. Evolutionary changes that create CDK consensus sites ([ST]-P) will increase the strength of the inhibition, while changes that destroy consensus sites will reduce the strength of inhibition. The stabilizing selection model suggests that as long as the total strength of inhibition is within an acceptable range, the exact number and location of phosphorylation sites will drift nearly neutrally. A sequence alignment of the disordered regions surrounding the PM domain of Ste5 from S. cerevisiae and related yeasts is shown on the right. During evolution consensus sites are gained and lost (+ [ST]-P or - [ST]-P) on the phylogenetic tree, leading to a large diversity in number and location of phosphorylation sites in this region.