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Open Access Research article

The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification

Monika Zulawski1, Gunnar Schulze1, Rostyslav Braginets1, Stefanie Hartmann2 and Waltraud X Schulze3*

Author Affiliations

1 Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Golm 14476, Germany

2 Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Golm 14476, Germany

3 Department of Plant Systems Biology, University of Hohenheim, Garbenstraße 30, Stuttgart 70599, Germany

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BMC Genomics 2014, 15:548  doi:10.1186/1471-2164-15-548

Published: 1 July 2014

Abstract

Background

Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase domains and mapped their origin by gene duplication.

Results

The phylogeny showed two major clades of receptor kinases and soluble kinases, each of which was divided into functional subclades. Based on this phylogeny, association of yet uncharacterized kinases to families was possible which extended functional annotation of unknowns. Classification of gene duplications within these protein kinases revealed that representatives of cytosolic subfamilies showed a tendency to maintain segmentally duplicated genes, while some subfamilies of the receptor kinases were enriched for tandem duplicates. Although functional diversification is observed throughout most subfamilies, some instances of functional conservation among genes transposed from the same ancestor were observed. In general, a significant enrichment of essential genes was found among genes encoding for protein kinases.

Conclusions

The inferred phylogeny allowed classification and annotation of yet uncharacterized kinases. The prediction and analysis of syntenic blocks and duplication events within gene families of interest can be used to link functional biology to insights from an evolutionary viewpoint. The approach undertaken here can be applied to any gene family in any organism with an annotated genome.