Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Global PTM Mapping for Lysine 2-hydroxyisobutyrylation in one Oryza Sativa Japonica sample

ABSTRACT: By the combination of affinity enrichment and high-resolution LC-MS/MS analysis, large-scale lysine 2-hydroxyisobutyrlome analysis was performed in Oryza Sativa. Altogether, 9916 lysine 2-hydroxyisobutyrylation sites in 2512 protein groups were identified. Intensive bioinformatic analysis was then carried out to annotate those lysine 2-hydroxyisobutyrylated targets, including protein annotation, functional classification, functional enrichment, functional enrichment-based cluster analysis, etc. Based on the results, further studies following the large-scale lysine 2-hydroxyisobutyrylome analysis were suggested.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Oryza Sativa (rice)

TISSUE(S): Plant Cell, Whole Body

SUBMITTER: Jones Macke

LAB HEAD: Xiaojun Peng

PROVIDER: PXD005986 | Pride | 2018-10-26

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	1.raw	Raw
	2.raw	Raw
	3.raw	Raw
	4.raw	Raw
	5.raw	Raw

Items per page:

1 - 5 of 9

Publications

Proteome-wide Analysis of Lysine 2-hydroxyisobutyrylation in Developing Rice (Oryza sativa) Seeds.

Meng Xiaoxi X Xing Shihai S Perez Loida M LM Peng Xiaojun X Zhao Qingyong Q Redoña Edilberto D ED Wang Cailin C Peng Zhaohua Z

Scientific reports 20171213 1

Lysine 2-hydroxyisobutyrylation is a recently identified protein post-translational modification that is known to affect the association between histone and DNA. However, non-histone protein lysine 2-hydroxyisobutyrylation remains largely unexplored. Utilizing antibody-based affinity enrichment and nano-HPLC/MS/MS analyses of 2-hydroxyisobutyrylation peptides, we efficaciously identified 9,916 2-hydroxyisobutyryl lysine sites on 2,512 proteins in developing rice seeds, representing the first lys ...[more]

PMID: 29235492

Similar Datasets

Oryza sativa Lysine Acetylation LC-MS/MS

Project description:By the combination of affinity enrichment and high-resolution LC-MS/MS analysis, large-scale lysine acetylome analysis was performed in oryza sativa. Altogether, 1,003 lysine acetylation sites in 692 proteins were identified.

2018-10-24 | PXD002773 | Pride

Systematic analysis of the lysine acetylome in Beauveria bassiana

Project description:Lysine acetylation emerging as a ubiquitous and conserved posttranslational modification plays an important regulatory role in almost every aspect of eukaryotes and prokaryotes. To gain insight into the nature, extent and biological function of lysine acetylation in Beauveria bassiana, a filamentous entomopathogenic fungus, we used immunoaffinity-based acetyl-lysine peptide enrichment integrated with high resolution mass spectrometry to comprehensively characterize lysine acetylated proteins in this fungus. Here we identified a total of 283 proteins with 464 acetylated sites, representing the first acetylproteome reported to date in filamentous fungi. Bioinformatics analysis of this acetylome showed that the acetylated proteins are involved in a wide range of cellular functions, such as metabolism, transcription, and exhibit diverse subcellular localizations. Enrichment of molecular function, biological process, and KEGG pathway implied that identified acetylated proteins of B. bassiana were very important in chromatin organization, ribosome, nucleosome assembly, carbon metabolism, and biosynthesis of secondary metabolites. Moreover, we matched five conserved lysine acetylated motifs containing of KacY, KacH, KacF, FxKac, KacxxxxK and one specific motif KacW in B. bassiana. Taken together, our acetylome analysis revealed a surprising breadth of cellular processes affected by lysine acetylation and also furnishes some fresh intervention nodes for the rational improvement of the friednly entomopathogenic fungus.

2017-11-02 | PXD003682 | Pride

Lysine 2-hydroxyisobutyrylation contributes to aflatoxin production in Aspergillus flavus

Project description:Aspergillus flavus contaminates crops during preharvest and post-harvest periods and produce carcinogenic mycotoxin aflatoxins posing severe threat to food safety and human health. Lysine 2-hydroxyisobutyrylation is one of the most important reversible post-translational modifications and plays a vital regulatory role in various cellular processes. In order to explore the potential roles of lysine 2-hydroxyisobutyrylation in aflatoxin biosynthesis, protein 2-hydroxyisobutyrylation analysis of A. flavus was performed, and a total of 7156 2-hydroxyisobutyrylation sites in 1473 proteins were identified.

2022-06-06 | PXD030912 | 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

Proteome-wide analysis of Lysine 2-Hydroxyisobutyrylation in Candida albicans

Project description:Candida albicans is the most common human fungal pathogen, causing diseases ranging from mucosal to systemic infections for both immunocompetent and immunocompromised individuals. Lysine 2-hydroxyisobutyrylation is a highly conserved posttranslational modification found in a wide variety of organisms. In this study, we survey the biological impact of 2-hydroxyisobutyrylation on lysine residuals (Khib) in C. albicans. Using an antibody-enrichment approach along with the traditional LC-MS/MS method, the pattern of Khib-modified proteins and sites were analyzed in one wild type strain of C. albicans. We identified 1438 Khib-modified proteins with 6659 modified sites in this strain, and a more detailed bioinformatics analysis indicated that the Khib-modified proteins are involved in a wide range of cellular functions with diverse subcellular locations. Functional enrichment analysis featured several prominent functional pathways, including ribosome, biosynthesis of antibiotics, biosynthesis of secondary metabolites, biosynthesis of amino acids and carbon metabolism – of which the ribosome pathway is the most affected pathway. Even when compared with the reported lysine acetylation (Kac) and succinylation (Ksuc), the Khib-modified sites on ribosomal proteins remained the highest for C. albicans. These bioinformatic results suggest that 2-hydroxyisobutyrylation may play an indispensable role in the regulation of the ribosomal biogenesis and protein translation. Confirmation at the biochemical level would enable us to resolve physiological and pathogenic roles of PTM in C. albicans.

2021-01-15 | PXD023013 | Pride

Acetylome analysis of Botrytis cinerea

Project description:Lysine acetylation of proteins is a dynamic and reversible post-translational modification that plays an important role in diverse cellular processes. Botrytis cinerea is the most thoroughly studied necrotrophic species due to its broad host range and huge economic impact. However, to date, little is known about the functions of lysine acetylation in this plant pathogen. In this study, we determined the lysine acetylome of B. cinerea through the combination of affinity enrichment and high-resolution LC-MS/MS analysis. Overall, 1582 lysine acetylation sites in 954 proteins were identified.

2017-11-02 | PXD004031 | 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

Global involvement of lysine crotonylation in protein modification and transcription regulation in rice

Project description:Lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammals. A global crotonylome analysis was undertaken in rice (Oryza sativa L. japonica) using high accuracy nano-LC-MS/MS in combination with crotonylated peptide enrichment. A total of 1,265 lysine crotonylation sites were identified on 690 proteins in rice seedlings. Subcellular localization analysis revealed that 51% of the crotonylated proteins identified were localized in chloroplasts. The photosynthesis-associated proteins were also mostly enriched in total crotonylated proteins. In addition, a genomic localization analysis of histone Kcr by ChIP-seq was performed to assess the relevance between histone Kcr and the genome. Of the 10,923 identified peak regions, the majority (86.7%) of the enriched peaks were located in gene body, especially exons. Furthermore, the degree of histone Kcr modification was positively correlated with gene expression in genic regions. Compared with other published histone modification data, the Kcr was co-located with the active histone modifications. Interestingly, histone Kcr facilitated expression of genes with existing active histone modifications. In addition, 77% of histone Kcr modifications overlapped with DNase hypersensitive sites (DHSs) in intergenic regions of the rice genome, and might mark other cis-regulatory DNA elements which are different from IPA1, a transcription activator in rice seedlings. Overall, our results provide a comprehensive understanding of the biological functions of the crotonylome and new active histone modification in transcriptional regulation in plants.

2018-09-20 | PXD010376 | Pride

Global Proteomic Analysis of lysine 2-hydroxyisobutyrylation in The Plant Pathogen Fusarium oxysporum

Project description:Lysine 2-hydroxyisobutyrylation, a recently discovered post-translational modification, plays a key role in the regulation of diverse cellular processes. Fusarium oxysporum is a destructive necrotrophic fungal pathogen distributed worldwide with broad ranging hosts.

2020-10-15 | PXD022000 | Pride

Proteomic Analysis of Lysine Acetylation and succinylation in pogostemon cablin

Project description:By the combination of affinity enrichment and high-resolution LC-MS/MS analysis, large-scale lysine acetylome analysis was performed. Altogether, 6,925 lysine acetylation sites in 2,526 protein groups were identified. Intensive bioinformatic analysis was then carried out to annotate those identified lysine acetylated 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 acetylome analysis were suggested

2019-12-11 | PXD015567 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data