Research

Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes

Jos Boekhorst¹ , Bas van Breukelen² , Albert JR Heck² and Berend Snel^1,3

¹  Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan, 3584 CH, The Netherlands

²  Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan, 3584 CA Utrecht, The Netherlands

³  Academic Biomedical Centre, Utrecht University, Yalelaan, 3584 CL Utrecht, The Netherlands

author email corresponding author email

Genome Biology 2008, 9:R144doi:10.1186/gb-2008-9-10-r144

Published:	1 October 2008

Subject areas: Biochemistry and structural biology, Evolution

Abstract

Background

Reversible phosphorylation of proteins is involved in a wide range of processes, ranging from signaling cascades to regulation of protein complex assembly. Little is known about the structure and evolution of phosphorylation networks. Recent high-throughput phosphoproteomics studies have resulted in the rapid accumulation of phosphopeptide datasets for many model organisms. Here, we exploit these novel data for the comparative analysis of phosphorylation events between different species of eukaryotes.

Results

Comparison of phosphoproteomics datasets of six eukaryotes yields an overlap ranging from approximately 700 sites for human and mouse (two large datasets of closely related species) to a single site for fish and yeast (distantly related as well as two of the smallest datasets). Some conserved events appear surprisingly old; those shared by plant and animals suggest conservation over the time scale of a billion years. In spite of the hypothesized incomprehensive nature of phosphoproteomics datasets and differences in experimental procedures, we show that the overlap between phosphoproteomes is greater than expected by chance and indicates increased functional relevance. Despite the dynamic nature of the evolution of phosphorylation, the relative overlap between the different datasets is identical to the phylogeny of the species studied.

Conclusion

This analysis provides a framework for the generation of biological insights by comparative analysis of high-throughput phosphoproteomics datasets. We expect the rapidly growing body of data from high-throughput mass spectrometry analysis to make comparative phosphoproteomics a powerful tool for elucidating the evolutionary and functional dynamics of reversible phosphorylation.