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Comprehensive Analysis of the Lysine Succinylome and Protein Co-modifications in Developing Rice Seeds*

Xiaoxi Meng,Hana Mujahid,Ya-dong Zhang,Xiaojun Peng,E. Redoña,Cailin Wang,Zhaohua Peng

Published 2019 in Molecular & Cellular Proteomics

ABSTRACT

Protein lysine succinylation were investigated together with acetylation, malonylation, crotonylation, and 2-hydroxisobutyrylation in developing rice seeds. The results showed that the modification sites had sequence preferences and the proteins were selected. Some lysine residues of selected proteins were modified by all the five tested modifications in the cell. Given that these moieties are intermediate products of different cellular metabolic pathways, these modifications may mediate the cross-talking among different metabolic pathways via modifying these lysine residues by feedback control. Graphical Abstract Highlights Nonenzymatically Ksu proteins shown different pattern from native cell Ksu proteins. Motif preference of Ksu proteins was associated with different biological processes. Up to 67 developing rice seeds proteins contain PTMs of Kac, Ksu, Kcr, Kmal, and Khib. Some lysine residues of the key pathway enzymes are modified by succinylation. Lysine succinylation has been recognized as a post-translational modification (PTM) in recent years. It is plausible that succinylation may have a vaster functional impact than acetylation because of bulkier structural changes and more significant charge differences on the modified lysine residue. Currently, however, the quantity and identity of succinylated proteins and their corresponding functions in cereal plants remain largely unknown. In this study, we estimated the native succinylation occupancy on lysine was between 2% to 10% in developing rice seeds. Eight hundred fifty-four lysine succinylation sites on 347 proteins have been identified by a thorough investigation in developing rice seeds. Six motifs were revealed as preferred amino acid sequence arrangements for succinylation sites, and a noteworthy motif preference was identified in proteins associated with different biological processes, molecular functions, pathways, and domains. Remarkably, heavy succinylation was detected on major seed storage proteins, in conjunction with critical enzymes involved in central carbon metabolism and starch biosynthetic pathways for rice seed development. Meanwhile, our results showed that the modification pattern of in vitro nonenzymatically succinylated proteins was different from those of the proteins isolated from cells in Western blots, suggesting that succinylation is not generated via nonenzymatic reaction in the cells, at least not completely. Using the acylation data obtained from the same rice tissue, we mapped many sites harboring lysine succinylation, acetylation, malonylation, crotonylation, and 2-hydroxisobutyrylation in rice seed proteins. A striking number of proteins with multiple modifications were shown to be involved in critical metabolic events. Given that these modification moieties are intermediate products of multiple cellular metabolic pathways, these targeted lysine residues may mediate the crosstalk between different metabolic pathways via modifications by different moieties. Our study exhibits a platform for extensive investigation of molecular networks administrating cereal seed development and metabolism via PTMs.

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