Browse
Submit Data
Databases
API
Help

Dataset Information

447 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Arabidopsis col and rglg iron deficiency response

ABSTRACT: To dissect the mechanisms that control and mediate cellular iron homeostasis, we conducted quantitative high-resolution iTRAQ proteomics and microarray-based transcriptomic profiling of iron-deficient Arabidopsis thaliana plants. Proteomic and transcriptomic profiling of Arabidopsis Col and RING DOMAIN LIGASE1 (RGLG1) and RING DOMAIN LIGASE2 (RGLG2) double mutation in response to iron deficiency were conducted. This integrative analysis provides a detailed catalog of post-transcriptionally regulated proteins and allows the concept of a chiefly transcriptionally regulated iron deficiency response to be revisited.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Root, Leaf

SUBMITTER: I-Chun Pan

LAB HEAD: Wolfgang Schmidt

PROVIDER: PXD002126 | Pride | 2015-08-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Post-Transcriptional Coordination of the Arabidopsis Iron Deficiency Response is Partially Dependent on the E3 Ligases RING DOMAIN LIGASE1 (RGLG1) and RING DOMAIN LIGASE2 (RGLG2).

Pan I-Chun IC Tsai Huei-Hsuan HH Cheng Ya-Tan YT Wen Tuan-Nan TN Buckhout Thomas J TJ Schmidt Wolfgang W

Molecular & cellular proteomics : MCP 20150807 10

Acclimation to changing environmental conditions is mediated by proteins, the abundance of which is carefully tuned by an elaborate interplay of DNA-templated and post-transcriptional processes. To dissect the mechanisms that control and mediate cellular iron homeostasis, we conducted quantitative high-resolution iTRAQ proteomics and microarray-based transcriptomic profiling of iron-deficient Arabidopsis thaliana plants. A total of 13,706 and 12,124 proteins was identified with a quadrupole-Orbi ...[more]

PMID: 26253232

Similar Datasets

Systems-wide analysis of manganese deficiency-induced changes in gene activity of Arabidopsis roots

Project description:In this study, we undertook a comprehensive quantitative proteomic profiling of Arabidopsis roots from plants grown on Mn-deplete media, aiming at dissecting and cataloging the responses of Arabidopsis roots to Mn deficiency. We used LC-Q Exactive Orbitrap mass spectrometer to compile a near complete inventory of the Arabidopsis root proteome. We identified several novel components of cellular Mn homeostasis and show that many putatively important changes in response to Mn deficiency are only evident at one of the omics levels under investigation.

2018-10-26 | PXD003309 | Pride

iTRAQ-Facilitated Proteomic Profiling of Cotton Anthers

Project description:Cotton (Gossypium hirsutum L.) is an important economic crop, used mainly for the production of textile fiber. Using a space mutation breeding technique, a novel photosensitive genetic male sterile mutant CCRI9106 was isolated from the wild-type upland cotton cultivar CCRI040029. To use CCRI9106 in cotton hybrid breeding, it is of great importance to study the molecular mechanisms of its male sterility. Here, histological and iTRAQ-facilitated proteomic analyses of anthers were performed to explore male sterility mechanisms of the mutant. Scanning and transmission electron microscopy of the anthers showed that the development of pollen wall in CCRI9106 was severely defective with a lack of exine formation. At the protein level, 6,121 high-confidence proteins were identified and 365 of them showed differential expression patterns between mutant and wild-type anthers. The proteins up- or down-regulated in MT anthers were mainly involved in exine formation, protein degradation, calcium ion binding and etc. These findings provide valuable information on the proteins involved in anther and pollen development, and contribute to elucidate the mechanism of male sterility in upland cotton.

2015-06-11 | PXD002209 | Pride

Gel-free/label-free proteomic analysis of wheat root in stress tolerant varieties under iron nanoparticles exposure

Project description:Iron nanoparticles (Fe NPs) have stimulatory effects on the germination ratio and plant growth of wheat. To elucidate the effects of Fe NPs on shoot of drought tolerant Pakistan-13 and salt tolerant NARC-11, a gel-free/label-free proteomic technique was used.

2016-08-19 | PXD004277 | Pride

SOX4 supports cancer stemness by enhancing HDAC1 transcription revealed by comparative proteomics

Project description:We have investigated the proteome changes induced by SOX4 overexpression in HCT-116 cells using iTRAQ-based quantitative proteomics. Bioinformatics analysis revealed that HDAC1 could be one of the important regulators in cancer stem cells (CSCs) maintenance. We found that SOX4 transcriptionally regulates HDAC1 to support the stemness of cancer stem cells (CSCs). This work revealed a novel underlying mechanism, SOX4-HDAC1 axis, for stemness maintenance of human cancer.

2021-09-09 | PXD019694 | Pride

Quantitative phosphoproteomics of drought-stressed Arabidopsis thaliana Col-0 wild type as well as mutants of Clade E and Clade A (Highly ABA-Induced 1) protein phosphatase 2Cs.

Project description:I-Traq based quantitative phosphoproteomics was used to examine changes in phosphopeptide abundance over longer term drought (low water potential) treatments. Samples were analyzed from unstressed seedlings grown on agar plates and from seedlings of the same age that had been transferred to low water potential (-1.2 MPa) for 96 h on PEG-infused agar plates. The genotypes analyzed were wild type Col-0 and two phosphatases mutants. One was a double mutant of two Clade E protein phosphatase 2Cs (Salk_011589 which lacks activity of AT3G05640 and Salk_048861 which lacks activity of AT5G27930). The other was a mutant (hai1-2) of the Clade A protein phosphatase 2C Highly ABA-Induced 1 (HAI1): Salk_108282 which lacks activity of AT5G59220). Our characterization of hai1-2 as well as detailed description of growth conditions and stress treatments has been reported in Bhaskara et al. (Plant Physiology 160:379-395, 2012). Characterization of the Clade E protein phosphatase 2Cs have not been previously reported and we have designated these as Clade E Growth Regulating PP2Cs (EGRs) based on characterization in our laboratory. The double mutant used for phosphoproteomic analysis has been designated egr1-1egr2-1. Three biological replicates were performed and microarray analysis of gene expression was performed on samples collected from the same experiments. The gene expression data sets have been deposited in Gene Expression Onmibus (GEO) under accession numbers GSE35258 (hai1-2 data) and GSE71237 (egr1-1egr2-1 data).

2017-01-17 | PXD004869 | Pride

Salinity effects on guard cell proteome in Chenopodium quinoa

Project description:Quinoa plants were treated with 300 mM NaCl or under control conditions (n=4) for three weeks

2023-04-27 | PXD022693 | Pride

Proteomic interrogation of the cell envelope of Neisseria gonorrhoeae exposed to physiologically relevant environmental cues.

Project description:Gonorrhea occurs at high incidence worldwide and has a major impact on reproductive and neonatal health worldwide. Alarmingly, with each new antibiotic introduced for gonorrhea, resistance has emerged, including resistance to penicillin, tetracycline, fluoroquinolones, and recently the third-generation cephalosporins. Treatment options are currently seriously limited and the development of a gonorrhea vaccine is a critical, longterm solution to this problem. Progress on gonorrhea vaccines has been slow, however, in part due to the high number of surface molecules in Neisseria gonorrhoeae (GC) that undergo phase or antigenic variation and a lack of understanding of protective responses. Gonorrhea vaccine development can therefore benefit from a comprehensive, unbiased approach for antigen discovery. Here we identified cell envelop proteins from Neisseria gonorrhoeae exposed to physiology relevant conditions: presence of human serum, iron limitation and anaerobic growth.

2016-05-09 | PXD001944 | Pride

Identification of Cypermethrin Induced Proteins Changes in Green Algae by iTRAQ Quantitative Proteomics

Project description:Cypermethrin (CYP) is one of the most widely used pesticides in large scale for agricultural and domestic purpose and the residue often seriously affects aquatic system. Environmental pollutants induced protein changes in organisms could be detected by proteomics, leading to discovery of potential biomarkers and understanding of mode of action. While proteomics investigations of CYP stress in some animal models have been well studied, few reports about the effects of exposure to CYP on algae proteome were published. To determine CYP effect in algae, the impact of various dosages (0.001 µg/L, 0.01 µg/L and 1 µg/L) of CYP on green algae Chlorella Vulgaris for 24h and 96h were investigated by using iTRAQ quantitative proteomics technique. A total of 162 and 198 proteins were significantly altered after CYP exposure for 24h and 96h, respectively. Overview of iTRAQ results indicated that the influence of CYP on algae protein might be dosage-dependent. Functional analysis of differentially expressed proteins showed that CYP could induce protein alterations related to photosynthesis, stress responses and carbohydrates metabolism. This study provides a comprehensive view of complex mode of action of algae under CYP stress and highlights several potential biomarkers for further investigation of pesticides exposed plant and algae.

2016-03-14 | PXD003521 | Pride

The hierarchy of transition metal homeostasis: Iron controls manganese accumulation in a unicellular cyanobacterium.

Project description:Iron and manganese are part of a small group of transition metals required for photosynthetic electron transport. Here, we present evidence for a functional link between iron and manganese homeostasis. In the unicellular cyanobacterium, Synechocystis sp. PCC 6803 Fe and Mn deprivation resulted in distinct modifications of the function of the photosynthetic apparatus. For example, iron limitation modifies the rate of QA re-oxidation in photosystem II, a complex that contains more Mn than Fe. The intracellular elemental quotas of Fe and Mn are also linked. Fe limitation reduces the intracellular Mn quota. Mn limitation did not exert a reciprocal effect on Fe quotas. Microarray analysis comparing Mn and Fe limitation revealed a stark difference in the extent of the transcriptional response to the two limiting conditions, reflective of the physiological data. The effects of Fe limitation on the transcriptional network are widespread while the effects on Mn limitation are highly specific. Our analysis also revealed an overlap in the transcriptional response of specific Fe and Mn transporters. This overlap provides a framework for explaining Fe limitation induced changes in Mn quotas. Fe transporters can serve as a low affinity Mn transport system. Under iron limitation the specificity of the Fe transport system changes, making it a less efficient Mn transport system. We monitored the gene expression of Synechocystis PCC6083 at standard conditions and after 2 days of iron limitation (0Fe), manganese limitation (0Mn) and combined iron and manganese limitation (0Fe0Mn). Each timepoint and condition was sampled in triplicates. Due to strong deviations in one of the three repeats for the 0Mn and 0Fe0Mn conditions, the corresponding replicates were excluded from further analysis.

2013-06-29 | E-GEOD-48416 | biostudies-arrayexpress

Analysis of the proteomic response of Arabidopsis seedlings exposed to priming and heat shock

Project description:We evaluated the effect of a 2h pre-treatment at 38°C on the response of Arabidopsis thaliana 6d-old seedlings to a 2h heat shock at 43°C applied 24 h later. A shotgun proteomics approach using total protein extracts was used to compare the proteome of seedlings from four type of samples, using 4 replicates: C=Control (just before heat shock on day 7) P= Primed (on day 7, 22 h after priming performed on day 6) H= Heat shock (on day 7, 2h after heat shock) PH= Priming + heat shock (on day 7, for primed seedlings, 2h after heat shock).

2024-04-02 | PXD045392 | 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