蛋白质翻译后修饰调控有丝分裂和细胞自噬的生物信息学研究

发布时间：2018-09-12 14:42

【摘要】：蛋白质翻译后修饰是发生在蛋白质翻译完成后,将各类化学小分子基团或者小蛋白质共价结合到底物特定氨基酸残基上的过程,也被称为共价修饰。翻译后修饰可调控蛋白质的构象、活性以及功能从而参与多种生物学过程,如转录调控、信号转导、细胞周期和细胞死亡等。有丝分裂和细胞自噬是细胞中重要的两个生物学过程,虽然在细胞中具有不同的生物学功能,但两者在过程和功能上具有很多相似性和相关性。有丝分裂和细胞自噬过程中都涉及到很多蛋白质,且研究表明蛋白质翻译后修饰在其中发挥着重要的调控作用。近年来,大量的蛋白质已被鉴定参与有丝分裂和细胞自噬过程；并且高通量蛋白质组学的迅速发展促进了蛋白质翻译后修饰的研究,产生了大量的蛋白质翻译后修饰数据。如何收集、整理和分析这些数据,从中提取有用的信息为进一步实验研究提供参考是该领域急需解决的问题。因此,本文对有丝分裂和细胞自噬过程中的蛋白质及其翻译后修饰情况进行了系统的生物信息学研究。细胞有丝分裂是细胞增殖、维持个体正常生长、发育和遗传物质传递的基础。真核生物细胞中,许多蛋白质定位到细胞的不同位置上并形成各种特定复合物,从而精确调控有丝分裂过程中染色体的分离。本文中,首先通过文献阅读收集了八个模式生物中1,872个经实验验证的位于中体、中心体、着丝粒、纺锤体和端粒上的蛋白质。此外,本文中还鉴定了其他144个真核物种中的直系同源蛋白质,并整合了参考文献、蛋白质翻译后修饰等信息,最终构建了一个包含87,983个细胞有丝分裂相关蛋白质信息的综合数据库MiCroKiTS 4.0。细胞自噬是真核生物中进化保守的一种将细胞内物质进行降解的重要生物学过程,在决定细胞存活或死亡、调节细胞内稳态中具有重要作用。除了核心的ATG蛋白质,许多其他的调控蛋白及其翻译后修饰也可参与并调控细胞自噬过程。考虑到细胞自噬是细胞死亡的主要途径之一,本工作从文献中同时收集了参与细胞自噬、细胞凋亡和细胞坏死的蛋白质,得到了4,241个实验验证的蛋白质。富集分析结果表明细胞自噬更倾向于与人类疾病相关,且癌症基因和药物靶标蛋白在人类细胞自噬和细胞死亡途径蛋白质中显著富集。然后,本文构建了人类细胞自噬和细胞死亡途径蛋白质的激酶-底物磷酸化网络,并鉴定了其中重要的蛋白激酶和底物蛋白,结果和之前的相关研究一致。通过整合蛋白质翻译后修饰数据,本工作中得到了11种蛋白质翻译后修饰的54,469个修饰位点,并发现多种翻译后修饰底物蛋白在细胞自噬和细胞凋亡过程中富集。另外,蛋白激酶、蛋白磷酸酶和泛素化相关酶,如泛素连接酶,在细胞自噬和细胞死亡途径蛋白质中富集。由此可知,蛋白质翻译后修饰在调控细胞自噬和细胞死亡途径中发挥了重要作用。在以上研究结果基础上,本文构建了一个细胞自噬和细胞死亡相关蛋白质的综合数据库THANATOS 1.0。基于收集的经实验验证的细胞自噬、细胞凋亡和细胞坏死蛋白质,鉴定了118个真核物种中的直系同源蛋白质,包括47个动物、23个植物和48个真菌,并对斑马鱼的三个蛋白Atg3、Keap1b和Skp2在斑马鱼早期胚胎细胞自噬中的作用进行了实验验证。最终,该数据库包含144,531个细胞自噬和细胞死亡途径的蛋白质,并对已知的蛋白质翻译后修饰、蛋白质-蛋白质相互作用及参考文献等相关信息进行了整合。本工作系统研究了有丝分裂和细胞自噬这两个非常重要又相互联系的生物学过程中的蛋白质及其翻译后修饰情况,为今后深入研究有丝分裂和细胞自噬的分子机制及蛋白质翻译后修饰在其中的调控作用提供了新的思路和数据资源。
[Abstract]:Post-translational modification of proteins occurs when small chemical groups or small proteins are covalently bound to specific amino acid residues after the translation of proteins. It is also called covalent modification. Mitosis and autophagy are two important biological processes in cells. Although they have different biological functions in cells, they have many similarities and correlations in process and function. In recent years, a large number of proteins have been identified to be involved in mitosis and autophagy, and the rapid development of high-throughput proteomics has promoted the study of protein post-translational modification, resulting in a large number of post-translational modification data. Collecting, sorting out and analyzing these data to extract useful information for further experimental research is an urgent problem in this field. Therefore, this paper presents a systematic bioinformatics study of proteins in mitosis and autophagy and their post-translational modifications. In eukaryotic cells, many proteins are located at different locations and form specific complexes that precisely regulate chromosome segregation during mitosis. In this paper, 1,872 of the eight model organisms were first collected through literature review. Proteins located in the centrosome, centrosome, centromere, spindle and telomere were identified. In addition, the direct homologous proteins in 144 other eukaryotic species were identified. References and post-translational modifications of proteins were integrated to construct a comprehensive set of 87,983 cell mitosis-related proteins. MiCroKiTS 4.0. Autophagy is an evolutionarily conserved and important biological process in eukaryotes that degrades intracellular substances. It plays an important role in determining cell survival or death and regulating intracellular homeostasis. In view of the fact that autophagy is one of the main pathways of cell death, we collected 4,241 proteins involved in autophagy, apoptosis and cell necrosis from the literature and obtained 4,241 validated proteins. Genes and drug target proteins were significantly enriched in human autophagy and cell death pathway proteins. Then, we constructed a kinase-substrate phosphorylation network of human autophagy and cell death pathway proteins, and identified the important protein kinases and substrate proteins. The results were consistent with previous studies. In addition, protein kinase, protein phosphatase and ubiquitination-related enzymes, such as ubiquitin ligase, are found in autophagy and cell apoptosis. It is concluded that post-translational modification plays an important role in regulating autophagy and cell death pathway. Based on the above results, a comprehensive database of autophagy and cell death-related proteins, THANATOS 1.0, is constructed. Autophagy, apoptosis and cell necrosis proteins were identified in 118 eukaryotic species, including 47 animals, 23 plants and 48 fungi. The roles of three zebrafish proteins Atg3, Keap1b and SKp2 in zebrafish autophagy in early embryonic cells were tested. Finally, the database contained 144,531 fine particles. The proteins involved in autophagy and cell death pathways are integrated with known post-translational modifications of proteins, protein-protein interactions, and references. Two very important and interrelated biological processes, mitosis and autophagy, and their post-translational modifications are systematically studied. The results provide new ideas and data resources for further study on the molecular mechanism of mitosis and autophagy and the regulation of post-translational modification of proteins.
【学位授予单位】：华中科技大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：Q811.4

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