Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
Nat Methods. 2013 Jul;10(7):676-82. doi: 10.1038/nmeth.2519. Epub 2013 Jun 9.
Cross-talk between different types of post-translational modifications on the same protein molecule adds specificity and combinatorial logic to signal processing, but it has not been characterized on a large-scale basis. We developed two methods to identify protein isoforms that are both phosphorylated and ubiquitylated in the yeast Saccharomyces cerevisiae, identifying 466 proteins with 2,100 phosphorylation sites co-occurring with 2,189 ubiquitylation sites. We applied these methods quantitatively to identify phosphorylation sites that regulate protein degradation via the ubiquitin-proteasome system. Our results demonstrate that distinct phosphorylation sites are often used in conjunction with ubiquitylation and that these sites are more highly conserved than the entire set of phosphorylation sites. Finally, we investigated how the phosphorylation machinery can be regulated by ubiquitylation. We found evidence for novel regulatory mechanisms of kinases and 14-3-3 scaffold proteins via proteasome-independent ubiquitylation.
不同类型的翻译后修饰在同一蛋白质分子上的相互作用为信号处理增加了特异性和组合逻辑，但这种作用还没有在大规模的基础上得到描述。我们开发了两种方法来鉴定酵母酿酒酵母中同时发生磷酸化和泛素化的蛋白质同工型，鉴定出 466 种蛋白质，其 2100 个磷酸化位点与 2189 个泛素化位点同时存在。我们定量应用这些方法来鉴定通过泛素-蛋白酶体系统调节蛋白降解的磷酸化位点。我们的结果表明，不同的磷酸化位点通常与泛素化一起使用，并且这些位点比整个磷酸化位点更保守。最后，我们研究了泛素化如何调节磷酸化机制。我们通过非蛋白酶体依赖的泛素化发现了激酶和 14-3-3 支架蛋白的新的调控机制的证据。
