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Protein Lysine Acetylation of Seedling Leaf in Brachypodium distachyon L.

ABSTRACT: Using high accuracy nano LC-MS/MS combined with affinity purification, we identified 636 lysine acetylated peptides matched on 353 proteins, and these acetylated proteins were implicated in various molecular functions and basic cellular processes by gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and domain enrichment analyses.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Brachypodium Distachyon (purple False Brome) (trachynia Distachya)

TISSUE(S): Plant Cell, Leaf

SUBMITTER: Shoumin Zhen

LAB HEAD: Yueming Yan

PROVIDER: PXD003161 | Pride | 2018-10-25

REPOSITORIES: Pride

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First Comprehensive Proteome Analyses of Lysine Acetylation and Succinylation in Seedling Leaves of Brachypodium distachyon L.

Zhen Shoumin S Deng Xiong X Wang Jian J Zhu Gengrui G Cao Hui H Yuan Linlin L Yan Yueming Y

Scientific reports 20160812

Protein acetylation and succinylation are the most crucial protein post-translational modifications (PTMs) involved in the regulation of plant growth and development. In this study, we present the first lysine-acetylation and lysine-succinylation proteome analysis of seedling leaves in Brachypodium distachyon L (Bd). Using high accuracy nano LC-MS/MS combined with affinity purification, we identified a total of 636 lysine-acetylated sites in 353 proteins and 605 lysine-succinylated sites in 262 ...[more]

PMID: 27515067

Similar Datasets

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

A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium

Project description:PARE (parallel analysis of RNA ends) was performed to study the change of uncapped mRNAs before and after cold treatment in Brachypodium. Different change patterns were identified. We have provided a complete view of uncapped transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants. The uncapped mRNA profiles of 12-day-old Brachypodium seedlings with and without cold treatment (4 M-BM-0C for 24 h) were generated by deep sequencing using Illumina GAIIx

2013-07-15 | E-GEOD-48234 | biostudies-arrayexpress

A global profiling of gene expression under cold stress in Brachypodium

Project description:RNA-Seq was performed to study the change of gene expression before and after cold treatment in Brachypodium. Different change patterns were identified. We have provided a complete view of transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants. The mRNA profiles of 12-day-old Brachypodium seedlings with and without cold treatment (4 M-BM-0C for 24 h) were generated by deep sequencing using Illumina HiSeqM-bM-^DM-" 2000.

2013-07-15 | E-GEOD-48040 | biostudies-arrayexpress

Large-scale phosphoproteome analysis in seedling leaves of Brachypodium distachyon L

Project description:In this study, we carried out the first large-scale phosphoproteome analysis of seedling leaves in Brachypodium accession Bd21 using TiO2 microcolumns combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) and MaxQuant software. A total, 1,470 phosphorylation sites in 950 phosphoproteins were identified. Of the 950 phosphoproteins identified, 127 contained 3 to 8 phosphorylation sites. The phosphoproteins and phosphosites identified in our study expanded our knowledge of protein phosphorylation modification in plants, especially in monocot.

2016-07-09 | PXD000868 | Pride

Proteomic Quantification of Lysine Acetylation in mouse hippocampus

Project description:Major depressive disorder (MDD) is a leading cause of disability around the world and contributes greatly to the global burden of disease. Mounting evidence suggests that gut microbiota dysbiosis may be involved in the pathophysiology of MDD through the microbiota–gut–brain axis. Recent research suggests that epigenetic modifications might relate to depression. However, our knowledge of the role of epigenetics in host–microbe interactions remains limited. In the present study, we used a combination of affinity enrichment and high-resolution liquid chromatography tandem mass spectrometry analysis to identify hippocampal acetylated proteins in germ-free(GF) and specific pathogen-free(SPF) mice. In total, 986 lysine acetylation sites in 543 proteins were identified, of which 747 sites in 427 proteins were quantified. Motif analysis identified several conserved sequences surrounding the acetylation sites, including D*Kac, DKac, KacY, KacD, and D**Kac. Gene ontology annotations revealed that these differentially expressed acetylated proteins were involved in multiple biological functions and mainly located in mitochondria. In addition, pathway enrichment analysis showed that oxidative phosphorylation and the tricarboxylic acid (TCA) cycle II (eukaryotic), both of which are exclusively localized to the mitochondria, were the primarily disturbed functions. Taken together, this study indicates that lysine acetylation changes may play a pivotal role in the mitochondrial dysfunction by which gut microbiota regulate brain function and behavioral phenotypes.

2021-03-09 | PXD022577 | Pride

Comprehensive Profiling of Lysine Acetylome in Baculovirus Infected Silkworm (Bombyx mori) Cells

Project description:Bombyx mori is one of the key lepidopteran model species, and is economically important for silk production and proteinaceous drug expression. Baculovirus and insect host are important natural biological models for studying host-pathogen interactions. The impact of Bombyx mori nucleopolyhedrovirus (BmNPV) infection on the proteome and acetylome of Bombyx mori ovarian (BmN) cells were explored to facilitate a better understanding of infection-driven interactions between BmNPV and host in vitro. The proteome and acetylome were profiled through 6-plex Tandem mass tag (TMT) labelling-based quantitative proteomics. Totally, 4,194 host proteins were quantified, of which 33 were up-regulated and 47 were down-regulated in BmN cells at 36 h post-infection. Based on the proteome, quantifiable differential Kac proteins were identified and functionally annotated to gene expression regulation, energy metabolism, substance synthesis and metabolism after BmNPV infection. Altogether, 644 Kac sites in 431 host proteins and 39 Kac sites in 22 viral proteins were identified and quantified in infected BmN cells. Our study demonstrated that BmNPV infection globally impacts the proteome and acetylome of BmN cells. The viral proteins are also acetylated by the host acetyltransferase. Protein acetylation is essential for cellular self-regulation and response to virus infection. This study provides new insights for understanding the host-virus interaction mechanisms, and the role of acetylation in BmN cellular response to viral infection.

2017-11-27 | PXD008054 | Pride

Quantitative acetylome analysis reveals histone modifications that may predict prognosis in hepatitis B-related hepatocellular carcinoma

Project description:The post-translational modification of lysine acetylation is related to hepatocellular carcinoma (HCC), and understanding this relationship requires detailed knowledge about the acetylated proteome in HCC tissue and about differences in protein acetylation between cirrhosis and liver cancer. Here we characterized the acetylome in three paired sets of cirrhotic tissue and hepatitis B-related HCC tissue. Combining affinity-based enrichment of acetylated peptides with highly sensitive mass spectrometry, we identified 1493 acetylation sites in 777 proteins and quantified 1040 acetylation sites in 587 proteins. We discovered that the histone acetyltransferases p300 and CBP were hyperacetylated in HCC and cirrhosis but not in normal liver tissue. We also identified several proteins acetylated at more than 10 lysines in HCC and cirrhosis. In addition, our results revealed that HCC was associated with up-regulation of acetylation at 353 sites in 237 proteins and down-regulation of acetylation at 209 sites in 122 proteins. We validated our results using western blotting and immunohistochemistry. Validation with an independent set of clinical samples confirmed our initial screening result that acetylation of lysine 120 in histone H2B type 1-C/E/F/G/I and lysine 18 in histone H3.3 was significantly associated with survival of HCC patients. Acetylation of lysine 77 in histone H4 was associated with survival as well as recurrence. Our study provides numerous new leads to examine the role of acetylation in HCC and its potential as a prognostic marker as well as therapeutic target.

2021-09-08 | PXD014994 | Pride

Genome- and proteome-wide analysis of lysine acetylation in Vibrio vulnificus Vv180806 reveals its regulatory roles in virulence and antibiotic resistance

Project description:V. vulnificus is an emergent pathogen and causes deadly septicemia in human. Protein acetylation regulates many important biological processes in bacteria. In this study, we identified the first lysine acetylome of V. vulnificus based on the whole-genome sequence of a cefoxitin-resistant strain isolated from a mortality case in China. A total of 6,626 acetylation sites at 1,924 acetylated proteins were uncovered, which to our knowledge represented the largest acetylated protein number that has been identified in bacteria. The presence of acetylation sites in virulence- and antibiotic resistance-related proteins further indicated the important role of acetylated modification on bacterial virulence and antibiotic resistance. Further investigation on the regulatory mechanisms will provide a better understanding of pathogen-host interactions in this increasingly pathogen.

2020-12-01 | PXD020376 | Pride

The acetylome analysis of lysine acetylation in the plant pathogenic bacterium Brenneria nigrifluens

Project description:Protein lysine acetylation, a dynamic and reversible posttranslational modification, plays a crucial role in several cellular processes including cell cycle regulation, metabolic pathways, enzymatic activities and protein interactions. Brenneria nigrifluens is the pathogen of shallow bark canker of walnut trees and can cause serious disease on walnut trees. Up to now, it is little known about the roles of lysine acetylation in the plant pathogenic bacteria. In the present study, the lysine acetylome of B. nigrifluens was determined by high-resolution LC-MS/MS analysis. In total, we identified 1,866 lysine acetylation sites distributed in 737 acetylated proteins. Bioinformatics results indicate that acetylated proteins participate in many different biological functions in B. nigrifluens. Four conserved motifs, namely, LKac, Kac*F, I*Kac and L*Kac, were identified in this bacterium. Protein interaction network analysis indicates that all kinds of interactions are modulated by protein lysine acetylation. Overall, 14 acetylated proteins are related to the virulence of B. nigrifluens.

2019-09-30 | PXD014046 | Pride

Crotonylation versus acetylation in PaACL-silenced corollas in petunia

Project description:Protein acetylation and crotonylation are important post-translational modifications (PTMs) of lysine. In animal cells, histone lysines are crotonylated or acetylated depends on the relative intracellular concentrations of crotonyl-CoA and acetyl-CoA, and adding crotonate to cell cultures, or reducing the intracellular levels of acetyl-CoA, leads to an increase in histone crotonylation through the direct production of crotonyl-CoA. However, in plant the relationship of acetylation and crotonylation and the effect of the concentration of acetyl-CoA on protein crotonylation were not well known. Our previous study showed that PhACL silencing changed the content of acetyl CoA in petunia corollas. In this study, we performed a global crotonylation proteome analysis of petunia (Petunia hybrida) and found that protein crotonylation have close relationship with protein acetylation and the protein with more crotonylation sites often had more acetylation sites. Crotonylated proteins and acetylated proteins enriched in many common KEGG pathway. However, PhACL silencing resulted in different KEGG pathway enrichment of proteins with different level of crotonylated sites and acetylated sites. Cytoplasm non-histone lysine crotonylation may not depend on the concentrations of acetyl-CoA in petunia corollas. There was a positive correlation between crotonylome and acetylome expression levels in corollas of PhACL-silenced plants and control.

2022-10-12 | PXD023270 | Pride

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