Quantitative analysis of the Arabidopsis thaliana leaf acetylome after treatment with deacetylase inhibitors trichostatin A and apicidin

Lysine acetylation is a common post-translational modification in eukaryotes and prokaryotes which is known to be involved in the regulation of various cellular processes, such as transcriptional activation, metabolic signaling, and energy homeostasis. Nevertheless, its role in plant primary metabolism, and photosynthesis in particular, is not well understood. Lysine acetylation is catalyzed by acetyltransferases (KATs) and removed by corresponding deacetylases (KDACs). The Arabidopsis thaliana genome encodes for at least 16 KATs and 18 KDACs, belonging to seven different gene families. The cellular functions of these enzymes have been explored only partially, describing effects of single enzymes and their interaction with specific targets. In this dataset we investigated the effect of two distinct lysine deacetylase inhibitors on protein lysine acetylation in Arabidopsis thaliana leaves on a proteome-wide scale. Trichostatin A (TSA), an inhibitor of class I and II KDACs, and apicidin, an inhibitor of class I KDACs, were applied in solution to leaf strips to induce KDAC inhibition. Proteins were extracted and digested using an adapted FASP procedure, peptides were dimethyl-labeled, ZIC-HILIC fractionated and lysine-acetylated peptides were antibody-enriched. Peptide identification and quantitative data analysis was carried out using MaxQuant.