Abstract
Post-translational modification of proteins through lysine succinylation plays important regulatory roles in living cells. Lysine succinylation was recently identified as a novel post-translational modification in Escherichia coli, yeast, Toxoplasma gondii, HeLa cells, and mouse liver. Interestingly, only a few sites of lysine succinylation have been detected in plants to date. In this study, we identified 347 sites of lysine succinylation in 202 proteins in tomato by using high-resolution mass spectrometry. Succinylated proteins are implicated in the regulation of diverse metabolic processes, including chloroplast and mitochondrial metabolism. Bioinformatic analysis showed that succinylated proteins are evolutionarily conserved and involved in various cellular functions such as metabolism and epigenetic regulation. Moreover, succinylated proteins exhibit diverse subcellular localizations. We also defined six types of definitively conserved succinylation motifs. These results provide the first in-depth analysis of the lysine succinylome and novel insights into the role of succinylation in tomato, thereby elucidating lysine succinylation in the context of cellular physiology and metabolite biosynthesis in plants.
Highlights
Chromatin has a dynamic multi-level organization starting from the nucleosomal basic unit to the formation of a 30 nm fiber followed by high-order folding, which forms chromosomes [1]
The reagents, namely trichloroacetic acid (TCA), dithiothreitol (DTT), iodoacetamide (IAA), trifluoroacetic acid (TFA), ammonium bicarbonate (NH4HCO3) and ammonium formate, were all purchased from Sigma-Aldrich
In order to obtain a detailed view of lysine succinylation sites in plants, proteins were isolated from a mixed tomato sample with equal roots, leaves, and stems
Summary
Chromatin has a dynamic multi-level organization starting from the nucleosomal basic unit to the formation of a 30 nm fiber followed by high-order folding, which forms chromosomes [1]. Nucleosome remodeling, histone post-translational modifications (HPTMs), DNA methylation, and other factors define various chromatin states that drive transcription and other chromatin-based nuclear processes [2,3,4]. HPTMs largely regulate transcription and participate in DNA replication, histone deposition, and DNA repair and recombination. HPTMs occurring in core histone tails involve various covalent modifications, including acetylation, methylation, phosphorylation, ubiquitination [2], and succinylation [5, 6]. Lysine succinylation is a post-translational modification where a succinyl group is added to a lysine residue of a protein molecule. Lysine is a frequent modification target because it defines the spatial structure of proteins, which in turn regulates protein functions.
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