Ultradeep Lysine Crotonylome Reveals the Crotonylation Enhancement on Both Histones and Nonhistone Proteins by SAHA Treatment
Ultradeep Lysine Crotonylome Reveals the Crotonylation Enhancement on Both Histones and Nonhistone Proteins by SAHA Treatment
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超深赖氨酸巴豆酰化组揭示 SAHA 处理对组蛋白和非组蛋白蛋白的巴豆酰化增强
DOI：
10.1021/acs.jproteome.7b00380
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发表时间：
2017-10-01
影响因子：
4.4
通讯作者：
Wang, Fengsong
中科院分区：
文献类型：
--
作者：
Wu, Quan;Li, Wenting;Wang, Fengsong
赖氨酸巴豆酰化是一种新发现的蛋白质翻译后修饰，据报道与赖氨酸乙酰化共享转移酶和脱酰酶。据报道，乙酰转移酶 p300 也含有巴豆酰转移酶活性，并且 I 类组蛋白脱乙酰酶被证明是主要的组蛋白去巴豆酰化酶。然而，非组蛋白蛋白的去巴豆酰化酶尚不清楚。此外，由于缺乏高质量的泛抗体，巴豆组的大规模分析仍然是一个挑战。在这项工作中，我们全面研究了 SAHA 处理后组蛋白和非组蛋白上的赖氨酸巴豆酰化位点，并显着鉴定了 A549 细胞中的 10 163 个赖氨酸巴豆酰化位点。这是首次鉴定数万个赖氨酸巴豆酰化位点，也是迄今为止最大的赖氨酸巴豆酰化位点数据集。此外，还进行了基于平行反应监测的实验进行验证，其结果与SILAC实验高度一致。通过深入的生物信息分析，发现赖氨酸巴豆酰化参与广泛的生物功能和过程。更重要的是，经SAHA处理后，大多数核心组蛋白位点和许多非组蛋白以及Ha类和lib类HDAC的一些已知底物的巴豆酰化和乙酰化水平均上调。这些结果表明，SAHA 可能通过抑制 HDAC 对组蛋白和非组蛋白具有去巴豆酰化抑制活性。
Lysine crotonylation is a newly discovered protein post-translational modification and was reported to share transferases and deacylases with lysine acetylation. The acetyltransferase p300 was reported to also contain crotonyltransferase activity, and class I histone deacetylases were demonstrated to be the major histone decrotonylases. However, the decrotonylases for nonhistone proteins are unclear. Moreover, because of the lack of high-quality pan-antibodies, large-scale analysis of crotonylome still remains a challenge. In this work, we comprehensively studied lysine crotonylome on both histones and nonhistone proteins upon SAHA treatment and dramatically identified 10 163 lysine crotonylation sites in A549 cells. This is the first identification of tens of thousands of lysine crotonylation sites and also the largest lysine crotonylome data set up to now. Moreover, a parallel-reaction-monitoring-based experiment was performed for validation, which presented highly consistent results with the SILAC experiments. By intensive bioinformatic analysis, it was found that lysine crotonylation participates in a wide range of biological functions and processes. More importantly, it was revealed that both the crotonylation and acetylation levels of most core histones sites and a number of nonhistone proteins as well as some known substrates of class Ha and lib HDACs were up-regulated after SAHA treatment. These results suggest that SAHA may have decrotonylation inhibitory activities on both histones and nonhistone proteins by inhibiting HDACs.