Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Birch acetylome profiling reveals lysine acetylation dynamics in drought stress

ABSTRACT: Acetylation modifies protein subcellular localization, stability, enzymatic activity, and protein-protein and protein-DNA interactions, playing a crucial role in mediating protein function. However, research on non-histone acetylation remains limited. This study investigates changes in lysine acetylation (Kac) in proteins in response to drought using 4D label-free quantitative lys-acetylproteome analysis. We identified a total of 15,064 acetylated peptides across 4,393 proteins, with 2,486 Kac sites exhibiting significant changes: 246 proteins showed increased Kac levels, while 1,406 displayed reductions. Notably, proteins associated with metabolic pathways, such as nucleotide sugar biosynthesis, proteasome, glutamate decarboxylase and the tricarboxylic acid (TCA) cycle, were significantly impacted. The alterations in Kac levels correlated with various KEGG pathways, suggesting that acetylation plays a regulatory role in drought response mechanisms. Furthermore, we identified specific acetylation sites in transcription factors (TFs), highlighting their involvement in this process. Functional validation demonstrated that mutations in Kac sites of five randomly selected TFs resulted in significant changes in drought tolerance, emphasizing the critical role of lysine acetylation in modulating stress responses. Overall, our findings indicate that Kac modification serves as a key regulatory mechanism in birch adaptation to drought stress, influencing both metabolic processes and transcriptional regulation.

ORGANISM(S): Betula Platyphylla

SUBMITTER: Yucheng Wang

PROVIDER: PXD056992 | iProX | Sat Oct 19 00:00:00 BST 2024

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

Proteomic analysis of lysine acetylation provides strong evidence for involvement of acetylated histone and chloroplast proteins in CWMV infected plant

Project description:Protein lysine acetylation (Kac) is an important post-translational modification (PTM) mechanism in both eukaryotes and prokaryotes, with key roles in cellular regulation. To investigate the role of Kac in plants infected with virus, we characterized the lysine acetylome of Nicotiana benthamiana plants with or without a Chinese Wheat Mosaic Virus (CWMV) infection by using TMT labeling-based protein modification differential analysis, high-resolution liquid chromatography mass spectrometry analysis, and integrated bioinformatics analysis. Here, we identified 4803 acetylated lysine sites on 1964 proteins. A comparison of the acetylation levels of the CWMV-infected group with those of the uninfected group revealed that 747 sites were up-regulated on 422 proteins, including chloroplast localization proteins and histone H3, and 150 sites were down-regulated on 102 proteins when using a change threshold of at least 1.2 times and a t-test p-value of <0.05. Nineteen conserved motifs were extracted; 51% of the identified proteins were localized to the chloroplast. Among the acetylated proteins, 19 Kac sites were combined in core histones, including 10 Kac sites on histone 3. Bioinformatics analysis revealed that Kac occurs on a diverse range of proteins involved in a wide variety of biological processes, especially photosynthesis. Furthermore, we demonstrate that the acetylation level of chloroplast localization proteins and histone H3 are significantly increased. In summary, our results reveal the regulatory roles of Kac in response to CWMV infection.

2021-05-07 | PXD012537 | Pride

Rice (Oryza sativa) lysine-acetylation LC-MS/MS

Project description:Lysine acetylation is a dynamic and reversible post-translational modification that plays an imporant role in the gene transcription regulation. Here, we report high quality proteome-scale data for lysine-acetylation sites and proteins in rice (Oryza sativa). A total of 1337 Kac sites in 716 Kac proteins with diverse biological functions and subcellular localizations were identified in rice seedlings.

2016-02-24 | PXD002291 | Pride

Acetyl-proteome profiling of Staphylococcus aureus revealed lysine acetylation in bacterial antibiotic resistance

Project description:Protein post-translational modifications (PTMs) play crucial roles in various biological processes across prokaryotes and eukaryotes. Lysine acetylation (Kac), which is observed in different bacteria species and is known to be a dynamic and reversible PTM involved in numerous physiological functions. However, limited research has been conducted to explore the connection between Kac and bacterial antibiotic resistance. In this investigation, we employed advanced 4D label-free quantitative proteomics technology to examine the differential expression of Kac-modified proteins in Staphylococcus aureus strains: one susceptible to erythromycin (Ery-S) and another induced to be resistant (Ery-R). Our systematic analysis identified a total of 1808 acetylated proteins with 6791 specific Kac sites. Notably, we quantified 1907 of these sites across 483 proteins. A total of 548 Kac sites were affected by erythromycin pressure on 316 acetylated proteins. Functional analyses uncovered a notable presence of differentially acetylated proteins (DAPs) within pathways associated with ribosome assembly, glycolysis, and lysine biosynthesis. Moreover, our findings indicate a significant acetylation of ribosomal proteins in antibiotic-resistant strains, implying a potential regulatory role of this modification in translation processes. Further investigations using polysome profiling experiments revealed that Kac modification of ribosomal and ribosome-associated proteins can maintain translation in response to antibiotic stress. Our data provides support for the link between protein lysine acetylation and bacterial antibiotic resistance, highlighting the potential involvement of ribosome translation. These findings collectively unveil a novel mechanism that enhances our understanding of bacterial antibiotic resistance and offer valuable insights for the development of antibiotic treatment strategies.

2024-10-17 | PXD043277 | 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

Protein acetylation landscape of developing rice anthers

Project description:Protein lysine acetylation (KAC) is a dynamic and reversible post-translational modification, playing important biological roles in many organisms.Here, we reported results from a proteomic investigation to detect KAC status of the developing rice anthers near the time of meiosis (RAM), providing strong biochemical evidence for roles of many KAC-affected proteins during rice anther development and meiosis. We identified a total of 1,354 KAC sites in 676 proteins.

2019-03-06 | PXD007986 | Pride

First proteomic analysis of lysine acetylation on extensive functions in Solenopsis invicta Buren

Project description:Lysine acetylation (Kac) plays a critical role in the regulation of a great deal of important cellular processes. However, little is known about Kac in Solenopsis invicta, which is one of the 100 most dangerous invasive species in the world. Lysine acetylome in S. invicta was evaluated for the first time in this study. Altogether, 2387 Kac sites were tested in 992 proteins. The prediction of subcellular localization indicated that most identified proteins were located in cytoplasm, mitochondria and nucleus. The enriched Kac site motifs included Kac H, Kac Y, Kac G, Kac F, Kac T, and Kac W. H, Y, F, and W were of frequent occurrence at the +1 position, whereas G, Y and T were of frequent occurrence at the –1 position. Based on cellular component, acetylated proteins were enriched in cytoplasmic part, mitochondrial matrix, and cytosolic ribosome. Furthermore, 25 pathways were detected to be significantly enriched. Interestingly, arginine and proline metabolism as well asphagosome, which were related to immunity, contained several Kac proteins. Acetylation or deacetylation of the proline and phagosome proteins may adjust the protein function, which may be why S. invicta was highly immune. As for interaction network investigation, diverse interactions were adjusted by Kac. Our study of lysine acetylome supplies abundant information for function analysis of reversible Kac in the growth and development of S. invicta and other Hymenoptera insects. Confirming the functions of Kac target proteins may be useful to design specific and effective drugs to prevent and control this dangerous invasive species.

2020-12-02 | PXD019033 | Pride

Potential Role of Lysine Acetylation in the Stepwise Adaptation of Candida albicans to Fluconazole

Project description:Candida albicans is an opportunistic fungal pathogen capable of causing superficial mucosal and systemic infections, sometimes leading to life-threatening conditions. The increasing resistance of C. albicans to azole antifungals has become a significant challenge in clinical treatment. Lysine acetylation (Kac) is a well-studied post-translational modification that plays crucial roles in various biological processes. However, its impact on antifungal resistance in C. albicans remains poorly understood. Five strains of C. albicans isolated from the same patient, representing different stages of acquired fluconazole resistance in vivo, were used in this study to investigate the potential regulatory mechanism of Kac on the development of azole resistance in C. albicans. Quantitative proteomic analysis using tandem mass tag (TMT) labeling, acetylation enrichment, and liquid chromatography-mass spectrometry (LC-MS) was conducted on these five strains. We divided all strains into four comparison groups and identified a total of 1796 lysine acetylation sites across 938 proteins, with quantitative data available for 1314 acetylation sites in 712 proteins. Analysis of 155 significantly differentially modified sites revealed that the acetylation levels of key proteins involved in the conversion of pyruvate to acetyl-CoA for entry into the tricarboxylic acid (TCA) cycle for energy production were initially downregulated and then upregulated during the acquisition of fluconazole resistance. Additionally, the acetylation levels of proteins involved in ribosome synthesis, translation processes, and amino acid synthesis were found to increase. Therefore, lysine acetylation in C. albicans may contribute to azole resistance by regulating energy metabolism and protein synthesis.

2025-03-25 | PXD057826 | 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

Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification

Project description:We report the identification of 67 previously undescribed histone modifications, increasing the current number of known histone marks by about 70%. We further investigated one of the marks, lysine crotonylation (Kcr), confirming that it represents an evolutionarily-conserved histone posttranslational modification. The unique structure and genomic localization of histone Kcr suggest that it is mechanistically and functionally different from histone lysine acetylation (Kac). Specifically, in both human somatic and mouse male germ cell genomes, histone Kcr marks either active promoters or potential enhancers. In male germinal cells immediately following meiosis, Kcr is enriched on sex chromosomes and specifically marks testis-specific genes, including a significant proportion of X-linked genes that escape sex chromosome inactivation in haploid cells. These results therefore dramatically extend the repertoire of histone PTM sites and designate Kcr as a specific mark of active sex chromosome-linked genes in postmeiotic male germ cells. 2 histone marks (pan-lysine acetylation and pan-lysine crotonylation) were studied in 1 human cell type and 2 mouse cell types using ChIP-Seq. Input was sequenced for each cell type as a control. Pan-anti_Kac and pan-anti_Kcr antibodies were custom developed with PTM BioLab, Co., Ltd (Chicago, IL).

2011-10-06 | E-GEOD-32663 | biostudies-arrayexpress

Crosstalk of Protein Expression and Lysine Acetylation in Response to TMV Infection in Nicotiana benthamiana

Project description:Kac, a reversible PTM, plays essential roles in various biological processes, including those involving metabolic pathways, pathogen resistance and transcription, in both prokaryotes and eukaryotes. TMV, the major factor that causes poor quality of Solanaceae crops worldwide, directly alters many metabolic processes in tobacco. However, the extent and function of Kac during TMV infection have not been determined. Here, using LC−MS/MS in conjunction with highly sensitive immune-affinity purification, we comprehensively analyzed the changes in the proteome and acetylome of TMV-infected tobacco (Nicotiana benthamiana) seedlings. In total, 2082 lysine-acetylated sites on 1319 proteins differentially expressed in response to TMV infection were identified. Extensive bioinformatic studies disclosed changes in acetylation of proteins engaged in cellular metabolism and biological processes. The vital influence of Kac in fatty acid degradation and alpha-linolenic acid metabolism was also revealed in TMV-infected seedlings. This study first revealed Kac information in N. benthamiana under TMV infection and expands upon the existing landscape of acetylation in pathogen infection.

2022-10-15 | PXD035737 | 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