The reversible phosphorylation, as one of the most pivotal post-translational modification (PTM) of proteins, regulates multiple physiological processes, such as cell cycle progression, signal transduction, neuronal development and plasticity, metabolism pathway (Cohen, P. et al., 2002; Nguyen, A. et al., 2004). Furthermore, tremendous advances over the past years have greatly promoted our understanding that as a crucial PTM-based regulatory mechanism, much of phosphorylation-mediated signal transduction are achieved through a specific recognition process in which 'phosphoprotein-binding domains' (PPBDs) bind to short motifs containing phosphoserine/threonine/tyrosine (pS/pT/pY) (Yaffe, M. B. and A. E. Elia et al., 2001; Pawson, T. and P. Nash et al., 2003). This feature offers a dynamic means to meditate protein-protein interactions both spatially and temporally (Pawson, T. et al., 2004). Previous considerable works have identified 10 PPBDs—SH2, 14-3-3, FHA, MH2, WD-40, WW, PTB, BRCT, C2, PBD—in the human proteome (Gong, W. et al., 2008). In this work, PBD is the research focus in this work. Since the direct relationship between mutant alleles of the Drosophila melanogaster locus polo with the abnormal spindle poles was first described over 20 years ago (Sunkel, C. E. and D. M. Glover, 1988), more and more attention drawn on these highly conserved kinases, Plks, play crucial roles in orchestrating the cell cycle progression via phosphorylation-dependent molecular recognition and phosphorylation. The most striking character of Plks is the presence of polo-box domain (PBD) in the C-terminal non-catalytic region, which is indispensable and sufficient for proper sub-cellular localization of Plks during multiple stages of mitosis (van Vugt, M.A. and Medema, R.H. , 2005). In addition, clinical evidence suggests that aberrant expression of Plk1 are closely associated with tumorigenesis (Lu, L.Y. and Yu, X. , 2009). Moreover, both the kinase domain and PBD are regarded as attractive targets for design of anticancer chemothrapeutics (Lee, K. S. and J. R. Idle, 2008; Wasch, R. et al., 2010). Accordingly, identification of substrates with exact sites is fundamental for understanding the molecular mechanisms of Plks.

In this work, we manually collected experimentally verified 56 phospho-binding sites in 47 distinct substrates and 275 phosphoylation sites in 124 unique proteins from scientific literatures. A previously self-developed GPS (Group-based Prediction System) algorithm of version 2.1 was employed for its satisfying performance. We calculated the leave-one-out validation and 4-, 6-, 8-, 10-fold cross-validations to evaluate the prediction performance and system robustness. The leave-one-out validation result for phospho-binding prediction is accuracy (Ac) of 95.27%, sensitivity (Sn) of 82.14%, and specificity (Sp) of 95.41%, while for phosphoylation prediction is accuracy (Ac) of 84.55%, sensitivity (Sn) of 53.62%, and specificity (Sp) of 85.03%. The online service and stand-alone packages of GPS-Polo 1.0 were implemented in JAVA 1.4.2 and freely available at: http://polo.biocuckoo.org/.

 

GPS-Polo 1.0 User Interface

For publication of results please cite the following article: 　Systematic analysis of PLK-mediated phosphoproteome in eukaryotes. 　Zexian Liu, Jian Ren, Jun Cao, Jiang He, Xuebiao Yao, Changjiang Jin and Yu Xue. 　Briefings in Bioinformatics, 2012, (In press) 　[Abstract] [Full Text] [PDF]