Protein deacetylation affects acetate metabolism, motility and acid stress response in Escherichia coli

Although protein acetylation is widely observed, it has been associated with few specific regulatory functions making it poorly understood. To interrogate its functionality, we analyzed the acetylome in Escherichia coli knockout mutants of cobB, the only known sirtuin-like deacetylase, and patZ, the best-known protein acetyltransferase. For four growth conditions, more than 2,000 unique acetylated peptides, belonging to 809 proteins, were identified and differentially quantified. Nearly 65% of these proteins are related to metabolism. The global activity of CobB contributes to the deacetylation of a large number of substrates and has a major impact on physiology. Apart from the regulation of acetyl-CoA synthetase, we found that CobB-controlled acetylation of isocitrate lyase contributes to the fine-tuning of the glyoxylate shunt. Acetylation of the transcription factor RcsB prevents DNA binding, activating flagella biosynthesis and motility, and increases acid stress susceptibility. Surprisingly, deletion of patZ increased acetylation in acetate cultures, which suggests that it regulates the levels of acetylating agents. The results presented offer new insights into functional roles of protein acetylation in metabolic fitness and global cell regulation.

尽管蛋白质乙酰化现象已被广泛报道，但目前仅与少量特定调控功能存在关联，因此其具体作用机制仍未得到充分阐明。为解析其功能，我们针对大肠杆菌（Escherichia coli）中cobB（已知唯一的类沉默信息调节因子（sirtuin）去乙酰化酶）与patZ（目前研究最为广泛的蛋白质乙酰转移酶）的敲除突变株，开展了乙酰化蛋白质组（acetylome）分析。在四种生长条件下，我们共鉴定出隶属于809种蛋白质的2000余种独特乙酰化肽段，并完成了差异定量检测。其中近65%的蛋白质参与代谢过程。CobB的全局调控活性可介导大量底物的去乙酰化修饰，并对细胞生理状态产生显著影响。除调控乙酰辅酶A合成酶（acetyl-CoA synthetase）外，我们还发现CobB介导的异柠檬酸裂解酶（isocitrate lyase）乙酰化修饰，可对乙醛酸分流途径（glyoxylate shunt）实现精细调控。转录因子RcsB的乙酰化修饰会阻碍其与DNA的结合，进而激活鞭毛生物合成与细胞运动能力，并提升细胞对酸性胁迫的敏感性。令人意外的是，在乙酸盐培养体系中，patZ的敲除反而提升了蛋白质乙酰化水平，这提示patZ可调控乙酰化剂的含量水平。本研究结果为解析蛋白质乙酰化在代谢适应性与全局细胞调控中的功能角色提供了全新视角。