Browse
Submit Data
Databases
API
Help

Dataset Information

217 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A phosphoproteomic landscape of rice (Oryza sativa L.) tissues

ABSTRACT: Here, we first reported the construction of a phosphoproteomic landscape of 6 tissues, including callus, leaves, roots, shoot meristem (SM), young panicles (YP) and mature panicles (MP), from Nipponbare (Oryza sativa ssp. japonica). By employing a non-gel, quantitative phosphoproteomic approach, a total of 4792 phosphopeptides from 2657 phosphoproteins were identified, which were found to be differentially phosphorylated among tissues.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Oryza Sativa (rice)

TISSUE(S): Plant Cell, Leaf

SUBMITTER: Jian Zhang

LAB HEAD: Jian Zhang

PROVIDER: PXD005241 | Pride | 2018-04-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

A phosphoproteomic landscape of rice (Oryza sativa) tissues.

Wang Yifeng Y Tong Xiaohong X Qiu Jiehua J Li Zhiyong Z Zhao Juan J Hou Yuxuan Y Tang Liqun L Zhang Jian J

Physiologia plantarum 20170525 4

Protein phosphorylation is an important posttranslational modification that regulates various plant developmental processes. Here, we report a comprehensive, quantitative phosphoproteomic profile of six rice tissues, including callus, leaf, root, shoot meristem, young panicle and mature panicle from Nipponbare by employing a mass spectrometry (MS)-based, label-free approach. A total of 7171 unique phosphorylation sites in 4792 phosphopeptides from 2657 phosphoproteins were identified, of which 4 ...[more]

PMID: 28382632

Similar Datasets

A phosphoproteomic analysis of ABA induced protein phosphorylation revealed that Serine 71 is a major phosphosite for bZIP72 in SAPK10-mediated ABA signaling

Project description:we focused on the profiling of rice young seedling phosphosites, phosphopeptides and phosphorylation intensity dynamics in response to ABA by employing a label-free, MS-based phosphoproteomic approach

2018-10-27 | PXD004705 | Pride

A comprehensive proteomic survey of ABA-induced protein phosphorylation in rice (Oryza sativa L.)

Project description:In this study, we focused on the profiling of rice young seedling phosphosites, phosphopeptides and phosphorylation intensity dynamics in response to ABA by employing a label-free, MS-based phosphoproteomic approach, and aimed to reveal the biological significance of protein phosphorylation in ABA signaling from the phosphoproteomic data.

2017-01-17 | PXD004939 | Pride

Rice-xoo interaction phosphoproteome LC-MSMS

Project description:A comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight at 0h and 24h after xoo infection

2015-06-29 | PXD002222 | Pride

Phospo-proteomic profiling of Castration Resistant Prostate Cancer

Project description:The integration of diverse ‘omic’ datasets will increase our understanding of the key signaling pathways that drive disease. Here, we used clinical tissue cohorts corresponding to lethal metastatic castration resistant prostate cancer (CRPC) obtained at rapid autopsy to integrate mutational, transcriptomic, and phosphoproteomic datasets for pathway analysis. Using Tied Diffusion through Interacting Events (TieDIE), we integrated differentially expressed transcriptional master regulators, functionally mutated genes, and differentially ‘activated’ kinases in CRPC tissues to synthesize a robust signaling network consisting of pathways with known and novel gene interactions. For 6 individual CRPC patients for which we had transcriptomic and phosphoproteomic data we observed distinct pathway activation states for each patient profile. In one patient, the activated pathways were strikingly similar to a prostate cancer cell line, 22Rv1, providing us with a good pre-clinical model to test targeted, combination therapies. In all, synthesis of multiple ‘omic’ datasets revealed a plethora of pathway information suitable for targeted therapies in lethal prostate cancer.

2016-08-19 | PXD002286 | Pride

Simulated phosphopeptide spectral library for confident site localization

Project description:We have developed a new workflow to unambiguously localize phosphorylation sites on proteins. We demonstrate that spectral matching of phosphopeptide datasets against a library of the well-simulated spectra provided higher sensitivity for confident site localization than other tested programs. To computationally simulate tandem mass spectra representing all possible singly phosphorylated forms of a peptide, characteristic fragment ions are predicted from ions of their dephosphorylated form generated by beam-type collision-induced dissociation.

2015-03-17 | PXD000474 | Pride

Rice perception of symbiotic arbuscular mychorrhizal fungi requires the karrikin receptor complex

Project description:In terrestrial ecosystems plants take up phosphate predominantly via association with arbuscular mycorrhizal fungi (AMF). We discovered that the loss of responsiveness to AMF in the rice deletion mutant hebiba is encoded by the alpha/beta fold hydrolase, DWARF 14 LIKE (D14L), which is one of the 26 deleted genes. It is a component of an intracellular receptor complex involved in the detection of the smoke-compound karrikin. On the basis of the early and pronounced hebiba mutant phenotype, we hypothesized that functional D14L is required for the perception of AM fungi prior to contact. Germinated spore exudates of AMF activate pre-contact plant responses. Therefore, we used RNAseq to monitor the transcriptional changes of hebiba and wild type roots in response to germinated spore exudates, and also karrikin, over the first 24 hours post treatment. WT seedlings were treated with GSE, Karrikin or a mock and iho seedlings with GSE or a mock. Root material was collected for sequencing at 0, 3, 6, 9, 12 and 24 hours. This gave a total of 27 samples (WT+Mock: 6, WT+GSE: 5, WT+Karrikin:5, iho+Mock:6, iho+GSE: 5).

2016-03-14 | E-MTAB-4072 | biostudies-arrayexpress

Phosphoproteomic profiling responds to phosphate starvation in rice

Project description:Phosphorus is one of the most important macronutrients required for plant growth and development. The importance of phosphorylation modification in regulating phosphate (Pi) homeostasis in plants is emerging. We performed phosphoproteomic profiling to characterize proteins whose degree of phosphorylation is altered in response to Pi starvation in rice root.

2021-01-13 | PXD012764 | Pride

Natural aging and ovariectomy induces parallel phosphoproteomic alterations in skeletal muscle of female mice

Project description:The loss of skeletal muscle strength mid-life in females is associated with the decline of estrogen. Here, we questioned how estrogen deficiency might impact the overall skeletal muscle phosphoproteome after contraction, as force production induces phosphorylation of several muscle proteins. Phosphoproteomic analyses of the tibialis anterior muscle after contraction in two mouse models of estrogen deficiency, ovariectomy (Ovariectomized [Ovx] vs Sham) and natural aging-induced ovarian senescence (Older Adult [OA] vs Young Adult [YA]), identified a total of 2,593 and 3,507 phosphopeptides in Ovx/Sham and OA/YA datasets, respectively. Further analysis of estrogen deficiency-associated proteins and phosphosites identified 66 proteins and 21 phosphosites from both datasets. Of these, 4 estrogen deficiency-associated proteins and 4 estrogen deficiency-associated phosphosites were significant and differentially phosphorylated or regulated, respectively. Comparative analyses between Ovx/Sham and OA/YA using Ingenuity Pathway Analysis (IPA) found parallel patterns of inhibition and activation across IPA-defined canonical signaling pathways and physiological functional analysis, which were similarly observed in downstream GO, KEGG, and Reactome pathway overrepresentation analysis pertaining to muscle structural integrity and contraction, including AMPK and calcium signaling. IPA Upstream regulator analysis identified MAPK1 and PRKACA as candidate kinases and calcineurin as a candidate phosphatase sensitive to estrogen. Our findings highlight key molecular signatures and pathways in contracted muscle suggesting that the similarities identified across both datasets could elucidate molecular mechanisms that may contribute to skeletal muscle strength loss due to estrogen deficiency.

2023-09-01 | PXD035171 | Pride

General anaesthesia leads to phosphoproteome changes in proteins involved in cytoskeleton remodelling and synaptic processes in the supraoptic nucleus of the hypothalamus

Project description:Despite the widespread use of general anaesthetics, the mechanisms mediating their effects are still not understood. Although suppressed in most parts of the brain, neuronal activity, as measured by FOS activation, is increased in the hypothalamic supraoptic nucleus (SON) by numerous general anaesthetics, and evidence points to this brain region being involved in the induction of general anaesthesia and natural sleep. Posttranslational modifications of proteins, including changes in phosphorylation, enable fast modulation of protein function which could be underlying the rapid effects of general anaesthesia. In order to identify potential phosphorylation events in the brain mediating general anaesthesia effects, we have explored the phosphoproteome responses in the rat SON, and compared these to cingulate cortex (CC) which displays no FOS activation is response to general anaesthetics. We found many changes in the phosphoproteomes of both the CC and SON in response to 15 minutes of isoflurane exposure. Pathway analysis indicated that proteins undergoing phosphorylation adaptations are involved in cytoskeleton remodelling and synaptic signalling events. Importantly, changes in protein phosphorylation appeared to be brain region-specific suggesting that differential phosphorylation adaptations might underlie the different neuronal activity responses to general anaesthesia between the CC and SON. In summary, these data suggest that rapid posttranslational modifications in proteins involved in cytoskeleton remodelling and synaptic signalling events might mediate the central mechanisms mediating general anaesthesia.

2024-01-23 | PXD039391 | Pride

Global phosphoproteomic profiling of skeletal muscle in ovarian-hormone deficient mice

Project description:Phosphorylation is important in skeletal muscle development, growth, regeneration, and contractile function. Alterations in the skeletal muscle phosphoproteome due to aging have been reported in males; however, studies in females are lacking. We have demonstrated that estrogen deficiency decreases muscle force which correlates with decreased myosin regulatory light chain phosphorylation. Thus, we questioned whether the decline of estrogen in females that occurs with aging might alter the skeletal muscle phosphoproteome. C57BL/6J female mice randomly assigned to a sham-operated (Sham) or ovariectomy (Ovx) group to investigate the effects of estrogen deficiency on skeletal muscle protein phosphorylation in a resting, non-contracting condition. After 16 weeks of estrogen deficiency, the tibialis anterior muscle was dissected and prepped for label-free nano-liquid chromatography tandem mass spectrometry phosphoproteomic analysis. We identified 4,780 phosphopeptides in tibialis anterior muscles of ovariectomized (Ovx) and Sham-operated (Sham) control mice. Further analysis revealed 647 differentially regulated phosphopeptides (Benjamini – Hochberg adjusted p-value < 0.05 and 1.5-fold change ratio) that corresponded to 130 proteins with 22 proteins differentially phosphorylated (3 unique to Ovx, two unique to Sham, six upregulated, and 11 downregulated). Differentially phosphorylated proteins associated with the sarcomere, cytoplasm, and metabolic and calcium signaling pathways were identified. Our work provides the first global phosphoproteomic analysis in females and how estrogen deficiency impacts the skeletal muscle phosphoproteome.

2022-09-28 | PXD035107 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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