Dataset Information

Identification of desuccinylase ScCobB2 and its desuccinylation substrates in Streptomyces coelicolor

ABSTRACT: As a recently discovered protein posttranslational modification in eukaryotes, lysine succinylation has attracted increasing interest due to its ability to regulate several critical cellular processes including catabolism, β-oxidation, and ketogenesis. Nevertheless, understanding of the regulation mechanism is still at an early stage due to the lack of identified specific desuccinylases in most microorganisms.Here, in the model soil bacteria Streptomyces coelicolor, we biochemically characterized a sirtuin-like protein ScCobB2 as a divergent desuccinylase. Based on it, we identified a total of 673 unique succinylated sites, of which 470 sites in 317 proteins were quantified by combining tandem mass tag labeling, antibody affinity enrichment, and LC−MS/MS analysis. Furtheranalyses of the quantitative succinylome revealed that at least 114 proteins representing two major pathways, carbon metabolism and protein biosynthesis, are obviously hypersuccinylated in ∆ScCobB2 cells. We experimentally examined the regulatory roles of ScCobB2 on 13 hypersuccinylated proteins, including glyceraldehyde-3-phosphate dehydrogenase, aconitate hydratase, and several ribosomal proteins, the results of which suggested a high confidence in our quantitative data. This work provided the first discovery of a specificdesuccinylase in bacteria, and demonstrated it has pivotal regulatory role in multiple biological processes for S. coelicolor, laid the foundation for future research of succinylation regulation in other microorganisms.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Streptomyces Coelicolor

TISSUE(S): Whole Body

SUBMITTER: Wei Zhao

LAB HEAD: Wei Zhao

PROVIDER: PXD014202 | Pride | 2019-06-11

REPOSITORIES: Pride

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Publications

ScCobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in Streptomyces coelicolor.

Zhang Hong H Li Peng P Ren Shuangxi S Cheng Zhongyi Z Zhao Guoping G Zhao Wei W

Molecular & cellular proteomics : MCP 20190723 10

As a recently discovered protein posttranslational modification in eukaryotes, lysine succinylation has attracted increasing interest due to its ability to regulate several critical cellular processes, including catabolism, β-oxidation, and ketogenesis. Nevertheless, understanding of the regulatory mechanisms is still at an early stage due to the lack of identified specific desuccinylases in microorganisms. Here, in the model soil bacterium Streptomyces coelicolor, we biochemically charac ...[more]

PMID: 31337674

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Project description:Background: Lysine succinylation is a newly identified 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 proteins of Staphylococcus epidermidis has not been investigated. Materials and methods: Using antibody affinity enrichment followed by LC-MS/MS analysis, we examined the succinylome of Staphylococcus epidermidis (ATCC®12228™). Then, bioinformatics analysis was performed, including Gene Ontology, KEGG enrichment, motif characterization, secondary structure, protein-protein interaction, and BLAST analysis. Results: A total of 1557 succinylated lysine sites in 649 proteins were identified in Staphylococcus epidermidis (ATCC 12228). Among these succinylation proteins, GO annotation showed that proteins related to metabolic processes and binding activity accounted for the most based on the analysis of biological process and molecular function, respectively. 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. Conclusions: We performed the first comprehensive profile of succinylation in Staphylococcus 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.

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Dataset Information

Identification of desuccinylase ScCobB2 and its desuccinylation substrates in Streptomyces coelicolor

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Publications

<i>Sc</i>CobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in <i>Streptomyces coelicolor</i>.

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