Walton Alan, Stes Elisabeth, Cybulski Nicolas, Van Bel Michiel, Iñigo Sabrina, Durand Astrid Nagels, Timmerman Evy, Heyman Jefri, Pauwels Laurens, De Veylder Lieven, Goossens Alain, De Smet Ive, Coppens Frederik, Goormachtig Sofie, Gevaert Kris
Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium.
Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
Plant Cell. 2016 Jan;28(1):6-16. doi: 10.1105/tpc.15.00878. Epub 2016 Jan 7.
Ubiquitination, the covalent binding of the small protein modifier ubiquitin to a target protein, is an important and frequently studied posttranslational protein modification. Multiple reports provide useful insights into the plant ubiquitinome, but mostly at the protein level without comprehensive site identification. Here, we implemented ubiquitin combined fractional diagonal chromatography (COFRADIC) for proteome-wide ubiquitination site mapping on Arabidopsis thaliana cell cultures. We identified 3009 sites on 1607 proteins, thereby greatly increasing the number of known ubiquitination sites in this model plant. Finally, The Ubiquitination Site tool (http://bioinformatics.psb.ugent.be/webtools/ubiquitin_viewer/) gives access to the obtained ubiquitination sites, not only to consult the ubiquitination status of a given protein, but also to conduct intricate experiments aiming to study the roles of specific ubiquitination events. Together with the antibodies recognizing the ubiquitin remnant motif, ubiquitin COFRADIC represents a powerful tool to resolve the ubiquitination maps of numerous cellular processes in plants.
泛素化是小蛋白修饰物泛素与靶蛋白的共价结合，是一种重要且经常被研究的蛋白质翻译后修饰。多篇报道为植物泛素组提供了有用的见解，但大多是在蛋白质水平上，没有进行全面的位点鉴定。在此，我们采用泛素组合分数对角线色谱法（COFRADIC）对拟南芥细胞培养物进行全蛋白质组泛素化位点图谱绘制。我们在1607个蛋白质上鉴定出3009个位点，从而大大增加了这种模式植物中已知泛素化位点的数量。最后，泛素化位点工具（http://bioinformatics.psb.ugent.be/webtools/ubiquitin_viewer/）提供了所获得的泛素化位点，不仅可以查询给定蛋白质的泛素化状态，还可以进行复杂的实验以研究特定泛素化事件的作用。与识别泛素残余基序的抗体一起，泛素COFRADIC是解析植物众多细胞过程泛素化图谱的有力工具。
