Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China; Department of Pharmacy, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China.
Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China.
J Proteomics. 2021 Jan 16;231:103996. doi: 10.1016/j.jprot.2020.103996. Epub 2020 Oct 2.
Protein ubiquitylation regulates almost all aspects of the biological processes including gene expression, DNA repair, cell proliferation and apoptosis in eukaryotic cells. Dysregulation of protein ubiquitylation caused by abnormal expression of enzymes in the ubiquitin system results in the onset of many diseases including cancer, neurodegenerative diseases, and metabolic syndromes. Therefore, targeting the ubiquitin system becomes a promising research area in drug discovery. Identification of protein ubiquitylation sites is critical for revealing the key ubiquitylation events associated with diseases and specific signaling pathways and for elucidating the biological functions of the specific ubiquitylation events. Many approaches that enrich for the ubiquitylated proteins and ubiquitylated peptides at the protein and peptide levels have been developed to facilitate their identification by MS. In this paper, we will review the proteomic approaches available for the identification of ubiquitylation events at the proteome scale and discuss their advantages and limitations. We will also brief the application of the profiling of ubiquitylation events in drug target discovery and in target validation for proteolysis-targeting chimera (PROTAC). Possible future research directions in this field will also be discussed. SIGNIFICANCE: Ubiquitylation plays critical roles in regulating many biological processes in eukaryotic cells. Identification of ubiquitylation sites can provide the essential information for the functional study of the specific modified substrates. Since ubiquitylated proteins have much lower abundance than non-ubiquitylated proteins, enrichment of ubiquitylated proteins or peptides is critical for their identification by MS. This review focuses on different enrichment approaches that facilitate their isolation and identification by MS and discusses the advantages and drawbacks of these approaches. The application of the profiling of ubiquitylation events in drug target discovery and future research directions will be beneficial to the research community.
蛋白质泛素化调节真核细胞中几乎所有的生物学过程，包括基因表达、DNA 修复、细胞增殖和细胞凋亡。泛素系统中酶的异常表达导致蛋白质泛素化的失调，从而导致许多疾病的发生，包括癌症、神经退行性疾病和代谢综合征。因此，靶向泛素系统成为药物发现的一个有前途的研究领域。鉴定蛋白质泛素化位点对于揭示与疾病和特定信号通路相关的关键泛素化事件以及阐明特定泛素化事件的生物学功能至关重要。已经开发了许多在蛋白质和肽水平上富集泛素化蛋白质和泛素化肽的方法，以便通过 MS 进行鉴定。在本文中，我们将回顾可用于鉴定蛋白质组范围内泛素化事件的蛋白质组学方法，并讨论它们的优缺点。我们还将简要介绍泛素化事件在药物靶标发现和蛋白水解靶向嵌合体（PROTAC）靶标验证中的应用。还将讨论该领域未来的研究方向。意义：泛素化在调节真核细胞中的许多生物学过程中起着关键作用。鉴定泛素化位点可为特定修饰底物的功能研究提供必要信息。由于泛素化蛋白的丰度远低于非泛素化蛋白，因此富集泛素化蛋白或肽对于通过 MS 进行鉴定至关重要。这篇综述重点介绍了不同的富集方法，这些方法有助于通过 MS 对其进行分离和鉴定，并讨论了这些方法的优缺点。泛素化事件谱在药物靶标发现中的应用和未来的研究方向将有利于研究界。
