To better understand the role of phosphorylation in maintenance of functional distinctions among subcellular compartments, we provide a compartment-wide map of phosphorylation sites from eight human subcellular compartments analyzed by proteomic characterizations. We collect 10265 phosphorylation proteins for different subcellular compartments and provide the data set as a web-based database ( SubPhosDB ). Our data set reveals that the subcellular phosphorylation distribution is compartment-type dependent and that phosphorylation displays site-specific sequence motifs that diverge between subcellular compartments. Additionally, we demonstrate that phosphorylation targets compartment-specific pathways involved in fundamental physiological processes.
SubPhosPred is a web server that could predict phosphosrylation sites in different subcellular compartments (SCs) of homo sapiens, which combines a novel discrete wavelet transform (DWT) strategy with support vector machine (SVM) approach to identify phosphorylation sites for different SCs in human. We have trained compartment-specific phosphorylation prediction models for eight SCs (Cell membrane, Nucleus, Cytoplasm, Mitochondrion, Golgi apparatus, Endoplasmic reticulum, Secreted, Lysosome) in SubPhos platform. Cross-validation tests show that DWT strategy can boost predictive performance and obtain encouraging prediction results for each SC.
Taken together, this is to our knowledge that the first report of the predictions of phosphorylation sites in SCs, and the prediction results can be helpful as a foundation for system analysis to further investigate the phosphorylation mechanisms of the SCs in relation to the metabolic diseases.
Protein phosphorylation is the most common post-translational modification (PTM) regulating major cellular processes such as cell division, growth, and differentiation through highly dynamic and complex signaling pathways. However, the dynamic interplay of protein phosphorylation is not occurring randomly within the cell but is rather finely orchestrated by specific kinases and phosphatases that are unevenly distributed across subcellular compartments. This spatial separation not only regulates protein phosphorylation but can also control the activity of other enzymes and the transfer of other post-translational modifications.
Xiang Chen, JianDing. Qiu, et al. (2015). Proteomic Analysis and Prediction of Human Phosphorylation Sites in Subcellular Level Reveals Subcellular Specificity, Bioinformatics (2015) 31 (2): 194-200.