泛素化特异性及其调控细胞自噬的生物信息学研究

As one of the most important protein post-translational modifications, ubiquitination was specifically catalyzed by the ubiquitin E3 ligases through transferring the ubiquitin to the specific lysine residues of the substrates. Ubiquitination regulates various biological processes mainly by mediating the degradation of the targets, while deubiquitinating enzymes (DUBs) specifically regulate the deubiquitination. The understanding of regulatory specificity was critical for studying the molecular mechanisms and functional roles of ubiquitination, and dissecting the involvement of ubiquitination in disease and cancer. Currently, a large number of ubiquitination related studies were accumulated, and proteomic techniques enable the high-throughput identification of ubiquitination substrates and sites. However, the molecular and regulatory details were unclear and it is difficult to transform data into knowledge, while developing bioinformatic platform for computational analyses of ubiquitination regulations could advance the studies of ubiquitination. In this proposal, we will collect the experimentally identified E3-specific ubiquitination sites and DUB-specific deubiquitination sites, study the features of substrate recognition, and develop the predictors. Based on the computational predictions, the previous identified ubiquitination proteome could be analyzed to reveal the regulatory details and experiments could be carried out to verify the predictions. Then the ubiquitination regulatory network could be constructed with the predicted regulatory relations and protein-protein interaction data, and employed to study the ubiquitination regulation in autophagy processes to explore the key E3 and DUB and related important ubiquitination events.

作为最重要的蛋白质翻译后修饰之一，泛素化主要通过介导底物的降解来调控细胞内的生命活动。泛素化和去泛素化的特异性分别由泛素连接酶 (E3) 和去泛素化酶 (DUB) 决定。研究泛素化调控的特异性对了解泛素化在生命活动中的功能和分子机制以及与疾病和癌症的关系有着重要的意义。目前，蛋白质组学的发展极大地推动了泛素化底物位点的鉴定，但是具体的调控机制并不清楚，且缺乏相关的分析方法与工具。建立计算分析泛素化调控的生物信息学平台将推动对泛素化的研究。本项目拟收集实验证实的E3和DUB特异性的泛素化底物位点并研究其特征，构建E3和DUB特异性调控泛素化的预测工具。利用该工具系统分析已知的泛素化底物位点数据并结合实验进行验证与探索。整合计算预测的泛素化调控关系与蛋白质相互作用数据构建泛素化调控网络，结合网络分析方法研究自噬过程中的泛素化调控，探索其中重要的E3、DUB及泛素化事件并进行实验验证与探索。

作为最广泛和最重要的蛋白质翻译后修饰之一，泛素化通过介导底物蛋白质的降解从而调控细胞内各项生命活动的过程。泛素化的可逆调控由级联的泛素活化酶 (E1) 、泛素结合酶 (E2) 和泛素连接酶 (E3) 介导，而泛素化的精确调控则主要由E3的特异性决定。因此，开发分析和预测E3特异性泛素化调控的计算方法和工具将极大地助力探索泛素化在各种生命活动中的功能与分子机制。本项目的主要研究内容在于建立计算分析泛素化调控的生物信息学方法和软件工具，并基于这些方法和软件工具对泛素化底物位点数据进行分析和研究，探索泛素化这一分子调控机制在各种生物学过程中的作用与功能。项目实施过程中，在基于分组的预测系统 (GPS) 算法基础上进行改进和完善，构建出了预测E3特异性泛素化位点的计算模型，开发出了软件工具GPS-PLUB，取得了良好的预测性能，预测准确度较高。在此基础上，利用GPS-PLUB软件对大规模的泛素化组数据进行了注释。此外，通过结合蛋白质相互作用数据，构建了泛素化调控网络，并将其应用到细胞自噬相关蛋白质的泛素化调控网络分析、水稻幼穗泛素化组数据分析的研究中。通过该项目的实施，开发了E3特异性的泛素化位点预测分析方法与软件工具，并成功应用到相关生物学过程的泛素化调控机制研究中。