Succinyl-proteome profiling of Dendrobium officinale, an important traditional Chinese orchid herb, revealed involvement of succinylation in the glycolysis pathway

Abstract

BackgroundLysine succinylation is a ubiquitous and important protein post-translational modification in various eukaryotic and prokaryotic cells. However, its functions in Dendrobium officinale, an important traditional Chinese orchid herb with high polysaccharide contents, are largely unknown.ResultsIn our study, LC-MS/MS was used to identify the peptides that were enriched by immune-purification with a high-efficiency succinyl-lysine antibody. In total, 314 lysine succinylation sites in 207 proteins were identified. A gene ontology analysis showed that these proteins are associated with a wide range of cellular functions, from metabolic processes to stimuli responses. Moreover, two types of conserved succinylation motifs, ‘***Ksuc******K**’ and ‘****EKsuc***’, were identified. Our data showed that lysine succinylation occurred on five key enzymes in the glycolysis pathway. The numbers of average succinylation sites on these five enzymes in plants were lower than those in bacteria and mammals. Interestingly, two active site amino acids residues, K103 and K225, could be succinylated in fructose-bisphosphate aldolase, indicating a potential function of lysine succinylation in the regulation of glycolytic enzyme activities. Furthermore, the protein–protein interaction network for the succinylated proteins showed that several functional terms, such as glycolysis, TCA cycle, oxidative phosphorylation and ribosome, are consisted.ConclusionsOur results provide the first comprehensive view of the succinylome of D. officinale and may accelerate future biological investigations of succinylation in the synthesis of polysaccharides, which are major active ingredients.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3978-x) contains supplementary material, which is available to authorized users.

SIRT5 impairs aggregation and activation of the signaling adaptor MAVS through catalyzing lysine desuccinylation

“…Dysregulation of succinate metabolism can cause accumulation of succinyl-CoA, which may induce lysine succinylation (Peyssonnaux et al, 2007;Zhang et al, 2011;Xie et al, 2012;Park et al, 2013;Weinert et al, 2013). The enzyme responsible for succinylation has yet to be identified, and indeed, it is possible that this reaction occurs non-enzymatically by direct reaction between succinyl-CoA and the modified protein (Feng et al, 2017). It is evident that succinylation can modulate macrophage function.…”

A qualitative proteome-wide lysine crotonylation profiling of papaya (Carica papaya L.)

“…Post-translation modification (PTM) of lysine, a covalent modification involved in various biological processes, is an efficient strategy for increasing the structural and functional diversity of proteins 1 , 2 . To date, a large number of PTMs, including phosphorylation, ubiquitination, acetylation, and succinylation, have been identified in both eukaryotic and prokaryotic species 3 – 5 . PTMs alter protein functions by modulating their activity, cellular localisation, and domain structure 6 .…”

Systematic identification and comparative analysis of lysine succinylation between the green and white parts of chimeric leaves of Ananas comosus var. bracteatus

“…But the number of succinylated proteins in Ananas comosus var. bracteatus was much higher than that in strawberry stigmata [23], common wheat [24], rice seeds [25], tomato [26], Taxus×media [27], Brachypodium distachyon [28], Dendrobium officinale [29]. In physiological level, different species and tissues may possess differential profile of succinylation.…”

“…One possibility is that a functional α-KGDH complex exist in outside of mitochondria. Some study indicated that the component and activity of α-KGDH complex can be readily measured in cytosolic fractions [29]. And experiments have shown that α-KGDH complex can be localized in the nucleus [31].…”