PlantPhos
A Plant Phosphorylation Prediction Tool

Introduction to PlantPhos


Background

Protein phosphorylation is the most widespread and well-studied post-translational modification in eukaryotic cells. It is one of the most prevalent intracellular protein modifications that influence numerous cellular processes (Steen, Jebanathirajah et al. 2006). It has been estimated that one-third to one-half of all proteins in a eukaryotic cell are phosphorylated (Hubbard and Cohen 1993). Furthermore, protein phosphorylation, catalyzed by specific kinases, plays crucial regulatory roles in intracellular signal transduction. The networks of proteins and small molecules that transmit information from the cell surface to the nucleus, where they ultimately affect transcriptional changes (Steffen, Petti et al. 2002). An estimated 1 to 3% of functional eukaryotic genes encode protein kinases, suggesting that they are involved in many aspects of cellular regulation and metabolism (Stone and Walker 1995). However, a full understanding of the mechanism of intracellular signal transduction remains a major challenge in cellular biology.

Protein phosphorylation is an important post-translational modification that regulates various cellular processes not only in humans but also in plants. It is reported that the regulation of carbon and nitrogen metabolism in plants is driven by phosphorylation (Diolez, Kesseler et al. 1993). Phosphorylation is involved in modulating a sucrose phosphate synthase enzyme which controls the signaling pathway for the process of sucrose synthesis from carbon in plants (Huber 2007). Phosphorylation is also involved in modulating the plant process of synthesizing Ammonia, an organic compound which is required to give energy to certain organs which are not able to photosynthesize (Huber 2007). Furthermore, although not yet fully studied, it appears that phosphorylation is also involved in the process of plant growth and plant response to stress (Luan 2002; Huber 2007) . Stone et al. have identified part of the plant kinases; however, the precise functional roles of specific protein kinases were elucidated for only a few (Stone and Walker 1995).

Motivation of the Study

Information regarding protein kinases that phosphorylate substrates in plants is very limited. According to the collection of experimentally verified plant phosphorylation sites from TAIR9 and UniProtKB/Swiss-Prot, no phosphorylation site is annotated with its catalytic kinase. Due to this limitation, majority of the published methods for computationally identifying kinase-specific phosphorylation sites are trained mainly by using data from non-plant organisms. This study aims to analyze plant phosphorylation sites, investigate motifs of catalytic kinases in plants, and most importantly, present a novel method for identifying potential phosphorylation sites in plant proteins using potential catalytic kinase information. Due to the inconvenience of detecting the conserved motifs for all data with larger size, this work applies MDD to cluster all sequences of phosphorylation site into subgroups which has statistically significant motifs.

 

 
Dept. of Computer Science & Engineering, Yuan Ze University, Chungli 320, Taiwan.