Table_3_Comprehensive Succinylome Profiling Reveals the Pivotal Role of Lysine Succinylation in Energy Metabolism and Quorum Sensing of Staphylococcus epidermidis.XLSX

BackgroundLysine succinylation is a newly identified posttranslational modification (PTM), which exists widely from prokaryotes to eukaryotes and participates in various cellular processes, especially in the metabolic processes. Staphylococcus epidermidis is a commensal bacterium in the skin, which attracts more attention as a pathogen, especially in immunocompromised patients and neonates by attaching to medical devices and forming biofilms. However, the significance of lysine succinylation in S. epidermidis proteins has not been investigated.ObjectivesThe purpose of this study was to investigate the physiological and pathological processes of S. epidermidis at the level of PTM. Moreover, by analyzing previous succinylome datasets in various organisms, we tried to provide an in-depth understanding of lysine succinylation.MethodsUsing antibody affinity enrichment followed by LC-MS/MS analysis, we examined the succinylome of S. epidermidis (ATCC 12228). Then, bioinformatics analysis was performed, including Gene Ontology (GO), KEGG enrichment, motif characterization, secondary structure, protein–protein interaction, and BLAST analysis.ResultsA total of 1557 succinylated lysine sites in 649 proteins were identified in S. epidermidis (ATCC 12228). Among these succinylation proteins, GO annotation showed that proteins related to metabolic processes accounted for the most. KEGG pathway characterization indicated that proteins associated with the glycolysis/gluconeogenesis and citrate cycle (TCA cycle) pathway were more likely to be succinylated. Moreover, 13 conserved motifs were identified. The specific motif KsuD was conserved in model prokaryotes and eukaryotes. Succinylated proteins with this motif were highly enriched in the glycolysis/gluconeogenesis pathway. One succinylation site (K144) was identified in S-ribosylhomocysteine lyase, a key enzyme in the quorum sensing system, indicating the regulatory role succinylation may play in bacterial processes. Furthermore, 15 succinyltransferases and 18 desuccinylases (erasers) were predicted in S. epidermidis by BLAST analysis.ConclusionWe performed the first comprehensive profile of succinylation in S. epidermidis and illustrated the significant role succinylation may play in energy metabolism, QS system, and other bacterial behaviors. This study may be a fundamental basis to investigate the underlying mechanisms of colonization, virulence, and infection of S. epidermidis, as well as provide a new insight into regulatory effects succinylation may lay on metabolic processes (Data are available via ProteomeXchange with identifier PXD022866).

背景：赖氨酸琥珀酰化是一种新近发现的翻译后修饰（PTM），其存在于从原核生物到真核生物的广泛生物体中，并参与多种细胞过程，尤其是在代谢过程中。表皮葡萄球菌是一种存在于皮肤上的共生细菌，由于其能够附着于医疗器械并形成生物膜，因此在免疫受损患者和新生儿中作为病原体引起了更多的关注。然而，赖氨酸琥珀酰化在表皮葡萄球菌蛋白质中的意义尚未得到研究。目标：本研究旨在从PTM层面研究表皮葡萄球菌的生理和病理过程。此外，通过分析不同生物的先前琥珀酰化组数据集，我们试图深入理解赖氨酸琥珀酰化。方法：利用抗体亲和富集结合LC-MS/MS分析，我们研究了表皮葡萄球菌（ATCC 12228）的琥珀酰化组。随后，进行了生物信息学分析，包括基因本体（GO）、KEGG富集、基序特征化、二级结构、蛋白质-蛋白质相互作用和BLAST分析。结果：在表皮葡萄球菌（ATCC 12228）中，共鉴定出649种蛋白质中的1557个琥珀酰化赖氨酸位点。在这些琥珀酰化蛋白中，GO注释显示与代谢过程相关的蛋白质所占比例最高。KEGG通路特征化表明，与糖酵解/糖异生和柠檬酸循环（TCA循环）通路相关的蛋白质更可能被琥珀酰化。此外，鉴定出13个保守基序。特定的基序KsuD在模式原核生物和真核生物中保守。具有该基序的琥珀酰化蛋白在糖酵解/糖异生通路中高度富集。在群感应系统中的关键酶S-核糖基同型半胱氨酸裂合酶中，鉴定到一个琥珀酰化位点（K144），这表明琥珀酰化可能在细菌过程中发挥调节作用。此外，通过BLAST分析预测出表皮葡萄球菌中有15种琥珀酰转移酶和18种脱琥珀酰化酶（擦除酶）。结论：我们首次对表皮葡萄球菌的琥珀酰化进行了全面分析，并阐明了琥珀酰化可能在能量代谢、QS系统及其他细菌行为中发挥的重要作用。本研究可能为探究表皮葡萄球菌定植、致病性和感染的基础机制提供了根本的依据，并为进一步揭示琥珀酰化对代谢过程可能产生的调控效应提供了新的视角（数据可通过ProteomeXchange提供，标识符为PXD022866）。