Bioinformatics Analyses Of Protein Ubiquitination Sites

Post-translational modification of proteins by ubiquitination at lysine residues mediates 80% to 85% of the protein degradation in eukaryotic cells, and this process is dependent on ATP, efficient and highly selective. Ubiquitination not only regulates protein degradation, but also directly participates in a broad spectrum of cellular processes including cell cycle progression, apoptosis, transcriptional regulation, DNA damage response and immune response. Disorder of ubiquitination is found to be related with various human diseases, such as cancer and neuronal disorders. The specificity of ubiquitination sites extends the functions of ubiquitination, making it possible to regulate various biological processes with accuracy and specificity. Exploring the properties of ubiquitination sites would be helpful to understand the underlying mechanism and function of ubiquitination. In recent years, with the development of large scale proteomic technology, more and more protein ubiquitination sites data are generated, effective management, organization, presentation and analysis of these data is of great importance. This paper explores the properties of ubiquitination sites, constructs an efficient ubiquitination sites predictor and a comprehensive human ubiquitination sites database, develops of a proteome-wide human ubiquitination sites presentation system and performs the evolutionary study of ubiquitination sites. We hope that these bioinformatics resources would benefit the ubiquitination research community and contribute to uncovering the underlying mechanism of ubiquitination.First of all, identification of ubiquitination sites is a basic step to understand their molecular mechanism in biological systems. However, it is often time consuming and expensive to screen the protein ubiquitination sites by experiment. The computational approaches are promising to map the proteome-wide ubiquitination profile, however, none of the existing computational models offer satisfying performance(fast speed, high specificity and sensitivity). To construct an efficient human ubiquitinated sites predictor, we first identified and examined two categories of biological evidences: protein sequence similarity and protein sequence properties including protein physicochemical property, protein disorder score, protein secondary structure, position specific scoring matrix(PSSM) and composition of k-spaced amino acid pairs(CKSAAP), finding that ubiquitination sites tend to be located at more structured regions, with bigger size and average accessible surface area, and with higher hydrophobicity and average flexibility indices; then a ubiquitination site prediction model was developed based on these biological features. This prediction model shows high sensitivity and specificity against both cross validation and independent test. Combining our prediction results and known human ubiquitinated sites in literature, we built the largest human ubiquitinated sites database. Both the prediction model and human ubiquitinated sites database have been developed into an online ubiquitinated sites exploration system named Ubi Site Xplorer(a proteome-wide ubiquitination sites explorer for human proteins). Users may submit their query proteins, and the matched/predicted ubiquitination sites together with the detailed supporting evidences will be returned. This system also supports the function of user customization of training datasets for better target ubiquitinated sites prediction performance, for example that of certain type of ubiquitin chain. The web interface of Ubi Site Xplorer is available at http://prodigy.bprc.ac.cn/ubisitexplorer.Exploring evolutionary events of ubiquitination sites is another way of uncovering the mechanism of ubiquitination. However, it is still unclear whether there are functional constraints on the evolution of protein ubiquitination sites, because most previous studies regarded all protein ubiquitination sites as a whole or only focused on limited structural properties. With the deposition of more and more protein ubiquitination sites from mass spectrometry, we tried to clarify the relation between functional constraints and ubiquitination sites evolution. We investigated the evolutionary conservation of human ubiquitination sites in a broad evolutionary scale by aligning them with their orthologs from G.gorilla to E.coli, and we found that in organisms originated after the divergence of vertebrate, ubiquitination sites are more conserved than their flanking regions, while the opposite tendency is observed before this divergence time. We conjecture that this improved conservation of ubiquitination sites might be linked with functional constraints. By grouping the ubiquitination proteins into different functional categories, we confirms that many functional constraints like certain molecular functions, protein tissue expression specificity and protein connectivity in protein-protein interaction network enhance the evolutionary conservation of ubiquitination sites. Furthermore, by analyzing the gains of ubiquitination sites at different divergence time and their functional characters, we validates that the emergence of ubiquitination sites at different evolutionary time were also up against the uncovered functional constraints. The above results suggest that functional constraints on the adaptive evolution of ubiquitination sites increase the opportunity for ubiquitination to synthetically regulate various cellular and developmental processes during evolution.