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Tomato (Solanum lycopersicum) lysine succinylation LC-MS/MS

ABSTRACT: Post-translational modification of proteins through lysine succinylation plays important regulatory roles in living cells. Lysine succinylation was recently identified as a novel post-translational modification in several organisms, including Escherichia coli, yeast, Toxoplasma gondii, and HeLa cells, as well as mouse liver. Interestingly, few sites of lysine succinylation were detected in plants. In this study, we identified 347 sites of lysine succinylation in 202 proteins of tomato by using high-resolution mass spectrometry.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Alternaria Tomato

TISSUE(S): Whole Body

SUBMITTER: Jun Zhu

LAB HEAD: Weibo Jin

PROVIDER: PXD002380 | Pride | 2018-10-24

REPOSITORIES: Pride

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Publications

Proteome-Wide Identification of Lysine Succinylation in the Proteins of Tomato (Solanum lycopersicum).

Jin Weibo W Wu Fangli F

PloS one 20160201 2

Post-translational modification of proteins through lysine succinylation plays important regulatory roles in living cells. Lysine succinylation was recently identified as a novel post-translational modification in Escherichia coli, yeast, Toxoplasma gondii, HeLa cells, and mouse liver. Interestingly, only a few sites of lysine succinylation have been detected in plants to date. In this study, we identified 347 sites of lysine succinylation in 202 proteins in tomato by using high-resolution mass ...[more]

PMID: 26828863

Similar Datasets

Proteome-wide lysine succinylome profiling and comprehensive analysis of protein lysine co-modification in developing rice seeds

Project description: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 due to bulkier structural changes and greater charge differences on the modified lysine residue. Currently, however, the quantity of identified succinylated proteins and their corresponding functions in cereal plants remain largely unknown. In this study, 854 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 discovered 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 key enzymes involved in central carbon metabolism and starch biosynthetic pathways for rice seed development. Conserved succinylated proteins were identified amongst varying organisms. Rice proteins with co-modifications of succinylation, acetylation, malonylation, crotonylation, and 2-hydroxyisobutyrylation were identified through a comprehensive comparison analysis. A striking number of highly conserved succinyl-proteins and multi-modified proteins were shown to be involved in vital metabolic events. Our study delivers a platform for expansive investigation of molecular networks administrating cereal seed development via PTMs.

2019-09-09 | PXD013664 | Pride

A Qualitative Proteome-wide Lysine Succinylation Profiling of Tea Revealed Its Involvement in Primary Metabolism

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

Phytoplasma induced changes in acetylatome and succinylatome provide evidence for involvement of acetylated proteins in Paulownia witches’ broom

Project description:Lysine acetylation and succinylation are post-translational modifications of proteins, and have been shown to play roles in plant response to pathogen infection. Phytoplasma infection can directly alter multiple metabolic processes in Paulownia and lead to Paulownia witches’ broom (PaWB), the major cause of Paulownia mortality worldwide. To explore the extent and function of lysine acylations during phytoplasma infection, we investigated global proteome, acetylome, and succinylome of phytoplasma-infected Paulownia tomentosa seedlings. In total, we globally yield 8963 proteins, 2893 acetylated, and 1271 succinylated proteins. Among them, 425 substrates were simultaneously acetylated and succinylated. Comparative analysis revealed that 276 proteins, 546 acetylated proteins and 5 succinylated proteins were associated with PaWB. Our results suggested that acetylation may be more important than succinylation in response to phytoplasma infection. Enzymatic assays showed that acetylation modified the activities of protochlorophyllide reductase and RuBisCO in phytoplasma-infected seedlings. On the basis of these results, a model to elucidate the molecular mechanism responses to PaWB was proposed and this research offer a resource for functional studies on the effects of acetylation on protein function.

2019-04-04 | PXD012701 | Pride

Bacillus subtilis acetylome and succinylome

Project description:The two major acyl-modifications on lysine residues, acetylation and succinylation, were analyzed in the gram-positive model bacterium Bacillus subtilis. To identify and quantify the changes in acetylation and succinylation in response to the carbon source, a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomic analysis of cells grown on glucose or citrate was performed.

2015-07-02 | PXD001615 | Pride

Succinylation proteome analysis of seedling leaves of Bd21

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

Systematic analysis of the lysine succinylome in the model medicinal mushroom Ganoderma lucidum

Project description:Ganoderma lucidum, one of the best-known medicinal mushrooms in the world, produces more than 400 different bioactive compounds. 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. Bioinformatics analysis revealed that the modified proteins were involved in multiple cellular functions and participated in a wide variety of biological processes such as carbon metabolism and biosynthesis of secondary metabolites.

2019-07-25 | PXD013954 | Pride

Proteomic Analysis of Lysine Succinylation in oryza sativa

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

Succinylome analysis reveals the involvement of lysine succinylation in extreme resistance of Deinococcus radiodurans

Project description:Increasing evidences showing that succinylation of lysine residue mainly regulates enzymes involved in the carbon metabolism pathway, both in prokaryotic and eukaryotic cells. Deinococcus radiodurans is one of the most radioresistant organisms on earth, which is famous for its robust resistance. A major goal in the current study of protein succinylation is to explore its function in D. radiodurans. We used high-resolution liquid chromatography-mass spectrometry (LC-MS/MS) for qualitative proteomics to perform a global succinylation analysis of D. radiodurans and identified 492 succinylation sites on 270 proteins. These identified proteins are involved in a variety of biological process and pathways.

2021-04-26 | PXD012149 | Pride

Succinlylome profiling of bermudagrass stolons

Project description:Bermudagrass (Cynodon dactylon L.) is an important warm-season turfgrass species with well-developed stolons, which lay the foundation for fast propagation of bermudagrass plants through asexually clonal growth. However, the growth and development of bermudagrass stolons are still poorly understood at the molecular level. In this study, we comprehensively analyzed the succinylation modifications of proteins in fast growing stolons of bermudagrass cultivar Yangjiang. A total of 226 lysine succinylation sites on 128 proteins were successfully identified using liquid chromatography coupled to tandem mass spectrometry.

2022-08-20 | PXD034808 | Pride

Identification of desuccinylase ScCobB2 and its desuccinylation substrates in Streptomyces coelicolor

Project description: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.

2019-06-11 | PXD014202 | Pride

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