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

Abstract

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. image An integrated analysis of proteomic, transcriptomic and metabolic flux data reveals functional roles of protein acetylation in E. coli . Acetylation regulates protein function directly, by modulating metabolic enzyme activity, or indirectly by affecting transcriptional regulators. Protein acetylation is analyzed under four different growth conditions and is found to be highly context‐dependent. The global activity of the lysine deacetylase CobB contributes to the deacetylation of a large number of substrates and affects physiology and metabolism. Acetylation of the transcription factor RcsB prevents DNA binding, impairs flagella biosynthesis and motility and increases acid stress susceptibility. Deletion of the lysine acetyltransferase patZ increases acetylation in acetate cultures, suggesting that PatZ regulates the levels of acetylating agents.