Department of Biochemistry & Molecular Biology and Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
Mol Cell Proteomics. 2013 Sep;12(9):2456-67. doi: 10.1074/mcp.M112.023416. Epub 2013 May 28.
Damaged and misfolded proteins that are no longer functional in the cell need to be eliminated. Failure to do so might lead to their accumulation and aggregation, a hallmark of many neurodegenerative diseases. Protein quality control pathways play a major role in the degradation of these proteins, which is mediated mainly by the ubiquitin proteasome system. Despite significant focus on identifying ubiquitin ligases involved in these pathways, along with their substrates, a systems-level understanding of these pathways has been lacking. For instance, as misfolded proteins are rapidly ubiquitylated, unconjugated ubiquitin is rapidly depleted from the cell upon misfolding stress; yet it is unknown whether certain targets compete more efficiently to be ubiquitylated. Using a system-wide approach, we applied statistical and computational methods to identify characteristics enriched among proteins that are further ubiquitylated after heat shock. We discovered that distinct populations of structured and, surprisingly, intrinsically disordered proteins are prone to ubiquitylation. Proteomic analysis revealed that abundant and highly structured proteins constitute the bulk of proteins in the low-solubility fraction after heat shock, but only a portion is ubiquitylated. In contrast, ubiquitylated, intrinsically disordered proteins are enriched in the low-solubility fraction after heat shock. These proteins have a very low abundance in the cell, are rarely encoded by essential genes, and are enriched in binding motifs. In additional experiments, we confirmed that several of the identified intrinsically disordered proteins were ubiquitylated after heat shock and demonstrated for two of them that their disordered regions are important for ubiquitylation after heat shock. We propose that intrinsically disordered regions may be recognized by the protein quality control machinery and thereby facilitate the ubiquitylation of proteins after heat shock.
细胞内不再具有功能的损伤或错误折叠的蛋白质需要被清除。如果不能做到这一点，可能会导致它们的积累和聚集，这是许多神经退行性疾病的一个标志。蛋白质质量控制途径在这些蛋白质的降解中起着主要作用，主要由泛素蛋白酶体系统介导。尽管人们非常关注鉴定参与这些途径的泛素连接酶及其底物，但对这些途径的系统水平理解仍存在不足。例如，由于错误折叠的蛋白质会迅速被泛素化，因此在折叠应激下，未共轭的泛素会迅速从细胞中耗尽；然而，目前尚不清楚某些靶标是否更有效地竞争被泛素化。我们采用了一种系统范围的方法，应用统计和计算方法来识别在热休克后进一步被泛素化的蛋白质中富集的特征。我们发现，结构不同的蛋白质和令人惊讶的固有无序蛋白质群体更容易被泛素化。蛋白质组学分析显示，在热休克后，大量和高度结构化的蛋白质构成了低可溶性部分中蛋白质的大部分，但只有一部分被泛素化。相比之下，在热休克后，泛素化的固有无序蛋白质在低可溶性部分中富集。这些蛋白质在细胞中的丰度非常低，很少由必需基因编码，并且富含结合基序。在额外的实验中，我们证实了几种鉴定出的固有无序蛋白质在热休克后被泛素化，并证明其中两种蛋白质的无序区域对于热休克后泛素化是重要的。我们提出，固有无序区域可能被蛋白质质量控制机制识别，从而促进热休克后蛋白质的泛素化。
