Comprehensive Profiling of Protein Lysine Acetylation in Escherichia coli
Comprehensive Profiling of Protein Lysine Acetylation in Escherichia coli
复制标题
大肠杆菌中蛋白质赖氨酸乙酰化的综合分析
DOI：
10.1021/pr300912q
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发表时间：
2013-02-01
影响因子：
4.4
通讯作者：
Cheng, Zhongyi
中科院分区：
文献类型：
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作者：
Zhang, Kai;Zheng, Shuzhen;Cheng, Zhongyi
蛋白质赖氨酸乙酰化在真核生物染色质动力学、基因表达和代谢途径的调控中起着关键作用，因此对转录、细胞周期调控和细胞凋亡等多种细胞过程起着重要作用。尽管最近的证据表明，乙酰化蛋白广泛影响原核生物的细胞功能，但由于分析方法的限制，这种修饰的底物和定位仍然广泛未知。由于蛋白质乙酰化的动态特性和较低的丰度，对其进行全面鉴定是目前的主要瓶颈。一个完整的乙酰酶图谱将极大地促进我们对这种修饰在原核生物中的作用的理解。为了实现这一目标，我们开发了一种综合方法来鉴定赖氨酸乙酰化。结合免疫亲和富集和高灵敏度质谱技术，我们在大肠杆菌中鉴定了349个乙酰化蛋白，并定位了1070个乙酰化位点。据我们所知，与之前的报道相比，乙酰化的蛋白和乙酰化的位点分别增加了3倍和8倍。为了进一步表征这种修饰，我们根据细胞成分、分子功能和生物学过程将乙酰化蛋白分为几组。此外，在生物信息学工具的帮助下，研究了乙酰化蛋白的相互作用网络和高自信域结构。最后，根据蛋白质组学调查鉴定的乙酰化蛋白，对大肠杆菌的乙酰化代谢酶进行分析。我们的研究表明，这种组合方法对于大规模地鉴定和表征蛋白质赖氨酸乙酰化是强有力的。这些结果不仅大大扩展了乙酰化蛋白的数量，而且提供了一系列重要的信息，包括乙酰化的定位、网络和表征。
Protein lysine acetylation plays a key role in regulating chromatin dynamics, gene expression and metabolic pathways in eukaryotes, and, thus, contributes to diverse cellular processes like transcription, cell cycle regulation, and apoptosis. Although recent evidence suggests that acetylated proteins impact broadly cellular functions in prokaryotes, the substrates and localization of this modification remain widely unknown due to the limitations of analytical methods. Comprehensive identification of protein acetylation is a major bottleneck due to its dynamic property and pretty low abundance. A complete atlas of acetylome will significantly advance our understanding of this modification functions in prokaryotes. To achieve this goal, we have developed an intergraded approach to identifying lysine acetylation. Combining immunoaffinity enrichment with high sensitive mass spectrometry, we identified 349 acetylated proteins and addressed 1070 acetylation sites in Escherichia coli. To our knowledge, the acetylated proteins and acetylated sites were increased to 3 times and 8 times, respectively, compared to that in previous report. To further characterize this modification, we classified acetylated proteins into several groups according to cell components, molecular functions and biological process. Additionally, interaction networks and high confident domains architectures of acetylated proteins were investigated with the aid of bioinformatics tools. Finally, the acetylated metabolic enzymes were analyzed on the basis of acetylated proteins identified by proteomic survey in E. coli. Our study has demonstrated that the combined approach is powerful for identification and characterization of protein lysine acetylation on a large scale. These results not only greatly expand the number of acetylated proteins, but also provide a series of important information including localization, networks and characterization of acetylome.