Lysine acetylation and methylation were among the first epigenetic modifications reported on histones. Over the past 50 years, genetic and biochemical studies have demonstrated key functions of acetylation in gene transcription and other cellular processes; however, the precise mapping of acetylation sites in proteins remained a challenge. Using advanced proteomic technologies, we showed that lysine acetylation targets thousands of histone and non-histone proteins (Choudhary et al., Science, 2009). Surprisingly, large-scale proteomic studies detected a large number of acetylation sites in mitochondria and in bacteria, where other PTMs, such as phosphorylation, are relatively sparse. By combining genetic and proteomic approaches, we showed that acetylation in bacteria occurred through a novel mechanism involving the metabolite acetyl-phosphate (AcP) that can acetylate proteins non-enzymatically (Weinert et al., Mol Cell, 2013). We further showed that acetylation in eukaryotic cells is controlled distinctly in a sub-cellular compartment-dependent manner; and that acetylation of most mitochondrial proteins likely occurs through a non-enzymatic mechanism involving exposure to high concentration of acetyl-CoA in this compartment (Weinert et al., Mol Syst Biol, 2014). We measured the stoichiometry of acetylation using a novel method and showed that most acetylation occurs at a low level, mitochondrial acetylation correlates with the fluctuations in acetyl-CoA levels, and that SIRT3 suppress non-enzymatic acetylation in mitochondria (Weinert et al., EMBO J, 2015). We also investigated the substrates of lysine deacetylases using chemical and genetic approaches (Scholz et al, Nat Biotech, 2015). This work revealed unexpected specificities of several widely used KDAC inhibitors and a possible mechanism by which recently revoked drug bufexamac caused pro-inflammatory adverse effects in patients. Current research in the laboratory is focused on investigating the dynamics and regulatory mechanisms of acetylation.
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