Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Title（Project name）Proteomic Investigation of the Molecular Mechanisms in Response to the PEG-Induced Drought Stress in Soybean Roots

ABSTRACT: Roots are generally the critical drought sensors, but little is known about their molecular response to drought stress. We used the drought-tolerant soybean variety ‘Jiyu 47’ to investigate the differentially expressed proteins (DEPs) in soybean roots during the seedling stage based on the TMT proteomics analysis. Results of enrichment analyses based on a total of 468 DEPs revealed a coordinated expression pattern of proteins involved in various cellular metabolisms responding to drought stress in soybean roots. Our results showed that drought stress caused significant alterations in the expression of proteins involved in several metabolic pathways in soybean roots, including the carbohydrate metabolism, the metabolism of the osmotic regulation substances, and the antioxidant defense system (i.e., the glutathione metabolism). Increased production of reduced glutathione (GSH) enhanced the prevention of the damage caused by reactive oxygen species and the tolerance of the abiotic stress. The glutathione metabolism played a key role in modifying the antioxidant defense system in response to drought stress in soybean roots. Our proteomic study demonstrated that the soybean plants responded to drought stress by coordinating their protein expression during the vegetative stage, providing novel insights into the molecular mechanisms regulating the response to abiotic stress in plants.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Glycine Max

TISSUE(S): Root

SUBMITTER: Ying Zhou

LAB HEAD: Ying Zhou

PROVIDER: PXD033092 | Pride | 2022-05-08

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Plasma membrane proteomics

Project description:Aluminum (Al) toxicity in acid soil is a worldwide agricultural problem that inhibits crop growth and productivity. However, the signal pathways associated with Al tolerance in plants still remain largely unclear. In this study, tandem mass tag (TMT)-based quantitative proteomic methods was used to identify the expression changes of plasma membrane (PM) proteins in Tamba black soybean (TBS) root tips under Al stress. The results showed that a total of 907 PM proteins were identified, and 90 differentially expressed proteins (DEPs) were disclosed between Al-treated and untreated plants, with 46 up-regulated and 44 down-regulated (fold change > 1.3 or < 0.77, P < 0.05). Functional enrichment based on GO, KEGG and protein domain revealed that the DEPs were associated with membrane trafficking and transporters, modifying cell wall composition, defense response and signal transduction.

2020-06-25 | PXD017160 | Pride

Quantitative phosphoproteomic analysis provides insights into the aluminum-responsive in Tamba black soybean

Project description:Aluminum (Al) toxicity is one of the most important limitations to agricultural production worldwide. The overall response of plants to Al stress has been documented, but the contribution of protein phosphorylation to Al detoxicity and tolerance in plants is unclear. Using a combination of tandem mass tag (TMT) labelling, immobilized metal affinity chromatography (IMAC) enrichment and liquid chromatography-mass spectrometry /mass spectrometry (LC-MS/MS), Al-induced phosphoproteomic changes in roots of Tamba black soybean (TBS) was investigated in this study. After AlCl3 treatment, 314 proteins harbouring 420 phosphosites, were significantly changed (fold change > 1.2 or < 0.83, p < 0.05) with 151 up-regulated, 157 down-regulated and 6 up/down-regulated. Enrichment and protein interaction analyses revealed that differentially phosphorylated proteins (DPPs) under Al treatment was mainly related to G-mediated signaling, Ca2+, transcription, translation, transporters and carbohydrate metabolism, roughly clustered for one of associated with inhibition to root growth, and another of citric acid production for resistance to Al detoxicity, which was facilitated by Al3+ through modifying phosphorylation of proteins responsible for carbohydrate metabolism. The results provide novel insights into the molecular mechanisms of TBS post-translational modifications in response to Al stress.

2020-08-27 | PXD019807 | Pride

Effect of soybean agglutinin on biological function of gut

Project description:This study aims to investigate the effects of SBA on the cell cycle, apoptosis, and to verify the mechanism of SBA anti-nutritional characters based on proteomic-based analysis. The IPEC-J2 cell line was cultured with medium containing 0.0, 0.5 or 2.0 mg/mL SBA. With increasing SBA levels, the percentage of the cells at G0/G1 phase, cell apoptosis rates, expressions of Bax and p21, and the activities of Casp-3 and Casp-9 were increased, while cyclin D1 and Bcl-2 expressions were declined (p<0.05). The proteomic analysis showed that the numbers of differentially expressed proteins, induced by SBA, were mainly enriched in different pathways including DNA replication, base excision repair, nucleus excision repair, mismatch repair, amide and peptide biosynthesis, ubiquitin-mediated proteolysis, as well as structures and functions of mitochondria and ribosome. In conclusion, the anti-nutritional mechanism of SBA is a complex cellular process. Such process including DNA related activities; protein synthesis and metabolism; signal-conducting relation; as well as subcellular structure and function. This study provides comprehensive information to understand the toxic mechanism of SBA in monogastrics.

2021-05-04 | PXD025751 | Pride

Comparative expression analysis of roots of two soybean cultivars with contrasting drought-tolerant phenotype under well-watered and dehydration conditions.

Project description:To understand the responses of plants to environmental stresses will help mitigate the problems via creating stress-tolerant crop cultivars. We have carried out comparative expression analysis of roots of two soybean varieties Williams 82 and DT2008 that have constrasting drought-responsive phenotype under dehydration and well-watered (control) conditions. Affymetrix’s whole Soybean Gene Expression Microarray (66K) was used.

2015-07-02 | GSE65553 | GEO

Transcriptome analysis reveals GmZF351-affected gene expression in leaf and root.

Project description:GmZF351 has previously been characterized as a seed preferred gene participating mainly in oil accumulation. Here we report that over-expression of GmZF351 confers drought and salt tolerance in transgenic soybean seedlings. When soybean seedlings grew to V1 stage, leaves and roots were cut for RNA sequencing. Transcriptome analysis shows that GmZF351 regulates expression of downstream genes related to abiotic stress process.

2023-06-24 | GSE201762 | GEO

Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice

Project description:Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. The transcriptome from leaf, root, and young panicle at three developmental stages was comparatively analyzed combined with bioinformatics exploring drought stress related cis-elements. In this study, the gene expression patterns across six tissues including leaves and roots at tillering stage and panicle elongation stage, leaves and young panicle at booting stage ( TL: leaves at tillering stage; TR: roots at tillering stage; PL: leaves at panicle elongation stage; PR: roots at panicle elongation stage; BP: young panicle at booting stage; BL: leaves at booting stage) were characterized by using the Affymetrix rice microarray platform based on a drought tolerant rice line derived from IR64.

2010-12-23 | E-GEOD-26280 | biostudies-arrayexpress

The distinct transcription patterns correlate with the differential growth responses to salt stress in maize roots

Project description:We found that primary root (PR) is more resistant to salt stress compared with crown roots (CR) and seminal roots (SR). To understand better salt stress responses in maize roots, six RNA libraries were generated and sequenced from primary root (PR), primary roots under salt stress (PR-salt) , seminal roots (SR), seminal roots under salt stress (SR-salt), crown roots (CR), and crown roots under salt stress (CR-salt). Through integrative analysis, we identified 444 genes regulated by salt stress in maize roots, and found that the expression patterns of some genes and enzymes involved in important pathway under salt stress, such as reactive oxygen species scavenging, plant hormone signal perception and transduction, and compatible solutes synthesis differed dramatically in different maize roots. 16 of differentially expressed genes were selected for further validation with quantitative real time RT-PCR (qRT-PCR).We demonstrate that the expression patterns of differentially expressed genes are highly diversified in different maize roots. The differentially expressed genes are correlated with the differential growth responses to salt stress in maize roots. Our studies provide deeper insight into the molecular mechanisms about the differential growth responses of different root types in response to environmental stimuli in planta. Examination of three root types of maize under salt treatment for understanding the different responding mechenism to salt stress.

2014-03-01 | E-GEOD-53995 | biostudies-arrayexpress

Molecular dissection of drought tolerance mechanisms in rice by comparative deep transcriptome sequencing

Project description:To dissect the molecular mechanisms underlying drought tolerance (DT) in rice, transcriptome differences of a DT introgression line H471, the DT donor P28 and the drought sensitive recurrent parent HHZ under drought stress were investigated using deep transcriptome sequencing. Results revealed a differential constitutive gene expression prior to stress and distinct global transcriptome reprogramming among three genotypes under time-series drought stress, consistent with their differential genotypes and DT phenotypes. DT introgression line H471, the DT donor P28 and the drought sensitive recurrent parent HHZ under drought stress were investigated using deep transcriptome sequencing.The drought stress treatment was started by withholding water at the tillering stage. The days were counted after the AWC in the soil reached 20% to allow drought measurements at precisely determined intervals, and the soil water content reached 15%, 10% and 7.5% after 1d, 3d and 4d drought treatment, respectively.Three top leaves for each sample were harvested for each genotype under 1d and 3d drought stress and control conditions. All samples were immediately frozen in liquid nitrogen and stored at -80C and then for transcriptome sequencing.

2014-12-30 | E-GEOD-57950 | biostudies-arrayexpress

Proteome analysis of the soybean nodule phosphorus response mechanism and characterisation of stress-induced ribosome structural and protein expression changes

Project description:In agroecosystems, a plant-usable form of nitrogen is mainly generated by legume-based biological nitrogen fixation, a process that requires phosphorus (P) as an essential nutrient. To investigate the physiological mechanism whereby phosphorus influences soybean nodule nitrogen fixation, soybean root nodules were exposed to four phosphate levels: 1 mg/L (P stress), 11 mg/L (P stress), 31 mg/L (Normal P), 61 mg/L (High P) then proteome analysis of nodules was conducted to identify phosphorus-associated proteome changes. We found that phosphorus stress-induced ribosomal protein structural changes were associated with altered key root nodule protein synthesis profiles. Importantly, up-regulated expression of peroxidase was observed as an important phosphorus stress-induced nitrogen fixation-associated adaptation that supported two nodule-associated activities: scavenging of reactive oxygen species (ROS) and cell wall growth. In addition, phosphorus transporter (PT) and purple acid phosphatase (PAPs) were up-regulated that regulated phosphorus transport and utilisation to maintain phosphorus balance and nitrogen fixation function in phosphorus-stressed root nodules.

2022-08-11 | PXD033875 | Pride

Proteomics Study Reveals Involvement of Lysine Acetylation in Metabolic Disorder in Human Hepatocellular Carcinoma

Project description:Protein lysine acetylation is a vital post-translational modification (PTM) that plays important roles in biological processes and human diseases. However, its potential roles in hepatocellular carcinoma (HCC) development remain largely unknown. Here we performed a quantitative acetylome analysis of tumor and normal liver tissues from HCC patients. Overall, we identified 792 lysine acetylation sites in 415 proteins, and almost half of their acetylation levels were significantly changed in HCC tumor tissues. The acetylated proteins mainly consisted of metabolic enzymes, which was consistent with the subcellular location analysis that they were primarily located in mitochondria and cytoplasm. Consistently, Bioinformatics analysis showed that differently acetylated proteins were mainly involved in metabolic pathways, such as glycolysis, the tricarboxylic acid (TCA) cycle, fatty acid oxidation, and glutamine metabolism. Then we selected two down-regulated enzymes and verified their acetylation levels in HCC liver tissues. In addition, transcription factors and proteins associated with oxidative stress were identified with aberrant acetylation levels in HCC tumor tissues. Our findings illustrate abundant lysine acetylation sites in HCC liver tissues, which provides insight into the role of lysine acetylation in HCC development, and further contributes to possible implications for its use in diagnose and therapy in the future.

2021-06-14 | PXD014915 | 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