Lysine succinylation in Saccharopolyspora erythraea
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharopolyspora Erythraea
SUBMITTER: 
Ju Chu
PROVIDER: PXD042164 | iProX | Fri May 12 00:00:00 BST 2023
REPOSITORIES: iProX
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Project description:The present data set provides the first description of lysine succinylation and lysine acetylation in P. aeruginosa grown in 4 carbon sources using a two-dimensional immunoaffinity approach coupled with nanoliquid chromatography tandem mass spectrometry. A total of 1522 succinylated sites (612 proteins) and 1103 acetylated sites (522 proteins) were characterized.
2018-05-21 | PXD008662 | Pride
Project description:Background: Lysine succinylation of proteins has potential impacts on protein structure and function, which occurred on post-translation level. However, the information about the lysine succinylation of proteins in tea plants is limited. In the present study, the significant signal of succinylation in tea plants was found by western blot. Subsequently, we performed qualitative analyses to globally identify lysine succinylation substrates by using high accuracy nano LC-MS/MS combined with affinity purification. Results: As a result, a total of 142 lysine succinylation sites were identified in 86 proteins. The identified succinylated proteins are involved in various biological processes and a large proportion of the succinylation sites are present on proteins in the primary metabolism pathway, including glyoxylate and dicarboxylate metabolism, the tricarboxylic acid (TCA) cycle and glycine, serine and threonine metabolism. Moreover, 10 new succinylated sites on histones were detected in tea plants either. Conclusions: These results suggested that succinylated proteins in tea plants might play critical regulatory roles in biological processes, especially in the primary metabolism. This study not only globally analysed the functional annotation of lysine succinylation in tea plants, but also provided valuable information for further investigating the functions of lysine succinylation in tea plants.
2022-02-23 | PXD011717 | Pride
Project description:Protein lysine succinylation, an emerging protein post-translational modification widespread among microbiology, animals and plants, represents an important regulator of cellular processes. In our study, we took the first succinylation proteome analysis in the seedling leaves of Bd21 to draw a schematic map. With high accuracy nano LC-MS/MS combined with affinity purification, a total of 605 succinylated peptides in 323 proteins were identified and were implicated in various molecular functions and cellular biological processes. More than half (53.4%) of the proteins only have one lysine succinylated site. These identified proteins are involved in a variety of cellular functions such as amino acids transport/metabolism, post-translational modification, translation/ribosomal structure and lipid metabolism, especially energy and carbohydrate metabolism via GO, conservation analysis, protein interaction network and other bioinformatics analysis. Motif-X analysis of the succinylation sites identified fourteen significantly enriched succinylation motifs (-Ksucc-----K-, -Ksucc------G- etc) for the first time in plants and will provide possible succinylation binding locus for future studies. Secondary structure analysis showed that the succinylation sites occurred predominantly in alpha helix and coil structures which similar with acetylation. 155 (59.2%) of the homologous succinylated proteins were also identified in other three species (E. coli, S. cerevisiae and H. sapiens). 119 (45.4%) succinylated proteins and 115 (19%) sites were also to be acetylated at the same time. Our succinylated protein data set provides a promising starting point for further functional analysis of succinylation in B. distachyon, which could facilitate the elucidation of the entire metabolic network in the model monocot plant.
2018-10-26 | PXD003428 | Pride
Project description:Physalis angulata is a medicinal plant with a high pharmaceutical value that is widely cultivated in East Asia. Lysine succinylation, a newly identified post-translational modification, is associated with various cellular processes. However, the regulatory mechanism underlying the metabolism of P. angulata is largely unknown. Here, liquid chromatography tandem-mass spectrometry combined with a high-efficiency succinyl-lysine antibody was used to identify the succinylated peptides in P. angulata. In total, 422 lysine succinylation sites in 242 proteins were identified.
2019-11-08 | PXD006778 | Pride
Project description:By the combination of affinity enrichment and high-resolution LC-MS/MS analysis, large-scale lysine succinylome analysis was performed. Altogether, 742 lysine succinylation sites in 382 protein groups were identified. Intensive bioinformatic analyses were then carried out to annotate those identified lysine succinylated targets in response to drug treatment, including GO annotation, domain annotation, subcellular localization, KEGG pathway annotation, functional cluster analysis, etc. Based on the results, further studies following the lysine succinylome analysis were suggested
2018-10-26 | PXD005582 | Pride
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.
2021-02-25 | PXD022866 | Pride
Project description:a quantification method was performed based on tandem mass tag (TMT) labeling and antibody based affinity enrichment of succinylated peptides using high accuracy nano-LC-MS/MS, to explore the portential mechanism of succinylation in affecting the pathogenicity of naturally isolated A. flavus strains with different toxin production. Altogether, 1,240 lysine succinylation sites in 768 proteins were identified with 1,103 lysine succinylation sites in 685 proteins quantified. Comparing the levels of succinylated proteins between high and low aflatoxin-producing A. flavus strains, bioinformatics analysis indicated that almost all succinylated proteins located in the aflatoxin biosynthetic pathway were down-regulated, and these succinylations directly affected the synthesis of aflatoxins.
2022-11-25 | PXD038357 | iProX
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| S-EPMC3418837 | biostudies-literature
Project description:Oxybenzone (OBZ), one of a broad spectrum of ultraviolet (UV) absorbents, has been proven to be harmful to both plants and animals, while omics analysis of big data at the molecular level is still lacking. Lysine succinylation (Ksuc) is an important posttranslational modification of proteins that plays a crucial role in regulating the metabolic network in organisms under stress. Here, we report the changes in intracellular Ksuc modification in plants under oxybenzone stress. A total of 1276 succinylated sites on 507 proteins were identified. Among these sites, 181 modified proteins were hypersulfinylated/succinylated in OBZ-stressed pakchoi leaves. Differentially succinylated proteins (DSPs) are distributed mainly in the chloroplast, cytoplasm, and mitochondria and are distributed mainly in primary metabolic pathways, such as reactive oxygen species (ROS) scavenging, stress resistance, energy generation and transfer, photosynthetic carbon fixation, glycolysis, and the tricarboxylic acid cycle.
2022-08-27 | PXD036378 | iProX
Project description:Protein posttranslational modifications (PTMs) has been shown to regulate biological processes of human diseases via expanding the genetic code and for regulating cellular pathophysiology, however, the system-wide changes at the PTMs levels in ICH brain remains little known. Given that succinylation is one of the important PTMs in regulating many biological processes. Therefore, in this study, we used a high-resolution mass spectrometry-based, quantitative succinyllysine proteomics approach to firstly investigated the ICH-associated brain protein succinyllysine modifications. We totally identified the concentration of approximately 6000 succinylation events and quantified approximately 3500 sites. Among them, 25 succinyllysine sites on 23 proteins were increased, while 13 succinyllysine sites on 12 proteins were downregulated after ICH. Additionally, the subcellular localization analysis of these significantly changed succinylproteins showed that 58.3% hyposuccinylated proteins were located in the mitochondria, while the percentage of succinylproteins located in mitochondria was decreased to about 35% in ICH brains with concomitant increasing in the percentage of cytoplasm to 30.4%. Further bioinformatic analysis showed that the succinylated proteins were mostly located in mitochondria and synapse-related subcellular spaces, and participate in many pathophysiological processes, such as metabolism, cytoskeleton organization, synapse working and ferroptosis, etc.. Moreover, we performed a combination analysis of our succinylproteomics data with previously published transcriptome data and found that most of the differentially succinylated proteins were distributed into neurons, endothelial cells and astrocytes. In conclusion, our analyses uncover a number of succinylation-affected processes and pathways in ICH brains and provide new insights for understanding ICH pathophysiological processes.
2021-10-29 | PXD025621 | Pride