Bioinformatics Analysis Of The In Situ Crosstalk Of Tyrosine Modifications

Post-translational modifications (PTMs) play important roles in protein maturation and processing. By altering protein physicochemical property,3D Structure, subcelluar localization and stability, PTMs dynamically regulate their biological activity and function. From simple life forms like bacteria, archaea, cyanobacteria to multicellular nematode, fruit fly, from plant and animal to human, PTMs widely distribute in various prokaryotes and eukaryotes. The number of currently known PTMs has exceeded350, and their functional significance has long been widely recognized.Recent studies have confirmed that different PTMs prefer to synergistically orchestrate specific biological processes and functions by crosstalks, thus identification of crosstalks among PTMs is fundamental for elucidating the complexity and diversity of their regulatory mechanisms.In this work, we proposed that sulfation, nitration and phosphorylation can in situ crosstalk by competitively modifying specific tyrosine residues at the same site. Currently known sites by experimental identification of sulfation and nitration are limited, restricting the analysis of in situ crosstalk among these three PTMs at proteomic level. On the other hand, traditional experimental methods are manpower, material and time consuming, while applying calculating methods to predict PTM sites receive more and more attention for its advantages in unparalleled simplicity, high speed and low cost.At present, however, the only two available sulfation sites predicting tools, whose training sites are extremely limited, can’t meet the requirements of predicting protein sulfation sites. Thus at first, we collected all known protein tyrosine sulfation sites; subsequently, based on GPS2.2algorithm and JAVA programming language, we developed a new sulfation sites predicting tool named GPS-TSP1.0with much better performance.The preference of in situ crosstalk among these three PTMs was systematically analyzed, while statistical results suggested that in situ crosstalk between sulfation and nitration is significantly under-represented, however, we observed that both sulfation and nitration prefer to in situ crosstalk with phosphorylation at known phosphorylation sites rather than non-phosphorylatable tyrosines, and up to24.4%of known phosphorylation tyrosines might also be modified by sulfation or nitration through computational prediction. Further statistical analysis of GO annotations and KEGG pathways suggested that sulfation and nitration preferentially crosstalk with phosphorylation in distinct biological processes and functions. In order to interpret the mechanism of crosstalk among these three PTMs, we analyzed the interaction network of proteins with phosphorylated tyrosines. According to our results, crosstalk is significantly distributed in closely related sub-network. Hence, crosstalk may play important roles in regulating phosphorylation network. To understand its functional significance, we explored the loss of tyrosine in situ crosstalk caused by SNP mutation, and concluded that in situ crosstalk may have potential effects in cancer and disease.Taken together, we proposed that in situ crosstalk among sulfation, nitration and phosphorylation at tyrosines is a ubiquitous regulatory mechanism. By affecting the state of protein modifications and thus altering its biological activities and functions, crosstalk can regulate various biological processes. In this research, our high-performance sulfation sites predicting tool GPS-TSP1.0and the systematical analysis of in situ crosstalk among these three PTMs, are valuable and reliable data resources to experimenters. Apparently, close combinations of our computational prediction and analysis with experimental validation, will effectively promote crosstalk research of PTMs.