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Integrated seed proteome and phosphoproteome analyses reveal interplay of nutrient dynamics, carbon-nitrogen partitioning and oxidative signaling in chickpea, part 1

ABSTRACT: To understand nutrient dynamics during embryonic and cotyledonary photoheterotrophic transition to mature and germinating autotrophic seeds, 2-DE based proteomics study in six sequential seed developmental stages in chickpea was performed.

INSTRUMENT(S): QSTAR

ORGANISM(S): Cicer Arietinum (chickpea) (garbanzo)

TISSUE(S): Seed

SUBMITTER: Subhra Chakraborty

LAB HEAD: Subhra Chakraborty

PROVIDER: PXD017514 | Pride | 2020-03-11

REPOSITORIES: Pride

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			Action	DRS
	1016.mgf	Mgf
	1016.wiff	Wiff
	1016.wiff.scan	Wiff
	1017.mgf	Mgf
	1017.wiff	Wiff

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Publications

Integrated Seed Proteome and Phosphoproteome Analyses Reveal Interplay of Nutrient Dynamics, Carbon-Nitrogen Partitioning, and Oxidative Signaling in Chickpea.

Sinha Arunima A Haider Toshiba T Narula Kanika K Ghosh Sudip S Chakraborty Niranjan N Chakraborty Subhra S

Proteomics 20200406 8

Nutrient dynamics in storage organs is a complex developmental process that requires coordinated interactions of environmental, biochemical, and genetic factors. Although sink organ developmental events have been identified, understanding of translational and post-translational regulation of reserve synthesis, accumulation, and utilization in legumes is limited. To understand nutrient dynamics during embryonic and cotyledonary photoheterotrophic transition to mature and germinating autotrophic s ...[more]

PMID: 32146728

Similar Datasets

Integrated seed proteome and phosphoproteome analyses reveal interplay of nutrient dynamics, carbon-nitrogen partitioning and oxidative signaling in chickpea, part 2

Project description:To understand nutrient dynamics during embryonic and cotyledonary photoheterotrophic transition to mature and germinating autotrophic seeds, 2-DE based phosphoproteomics study in six sequential seed developmental stages in chickpea was performed.

2020-03-11 | PXD017515 | Pride

Integrated seed proteome and phosphoproteome analyses reveal interplay of nutrient dynamics, carbon-nitrogen partitioning and oxidative signaling in chickpea, part 3

Project description:To understand nutrient dynamics during embryonic and cotyledonary photoheterotrophic transition to mature and germinating autotrophic seeds, TiO2-based phosphoproteomics study in three sequential seed developmental phases in chickpea was performed.

2020-03-11 | PXD017516 | Pride

Effect of 1-methylcyclopropene (1-MCP) and ozone (Ο 3 ) post-harvest treatments on the proteomic profiling of Granny Smith apple peel (Malus x domestica Borkh) after cold storage

Project description:Superficial scald is a major physiological disorder in apple fruit that is induced by cold storage and is mainly expressed as brown necrotic patches on peel tissue. However, a global view of the gene-protein-metabolite interactome underlying scald prevention/sensitivity is currently missing. Herein, we have found for the first time that cold storage in an atmosphere enriched with ozone (O3) induced scald symptoms in ‘Granny Smith’ apple fruits during subsequent ripening at room temperature. In contrast, treatment with the ethylene perception inhibitor 1-methylcyclopropene (1-MCP) reversed this O3-induced scald effect. Amino acids, including branched-chain amino acids, were the most strongly induced metabolites in peel tissue of 1-MCP treated fruits. Proteins involved in oxidative stress and protein trafficking were differentially accumulated prior to and during scald development. Genes involved in photosynthesis, flavonoid biosynthesis and ethylene signaling displayed significant alterations in response to 1-MCP and O3. Analysis of regulatory module networks identified putative transcription factors (TFs) that could be involved in scald. Subsequently, a transcriptional network of the genes-proteins-metabolites and the connected TFs was constructed. This approach enabled identification of several genes co-regulated by TFs, notably encoding glutathione S-transferase (GST) protein(s) with distinct signatures following 1-MCP and O3 treatments. Overall, this study is an important contribution to future functional studies and breeding programs for this fruit, aiding to the development of improved apple cultivars to superficial scald.

2020-05-27 | PXD016849 | Pride

Genomewide methylation analysis in Silver Russell syndrome patients

Project description:Genomewide methylation analysis in Silver Russell syndrome patients compared to healthy controls Bisulphite converted DNA from the 24 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

2015-01-12 | E-GEOD-55491 | biostudies-arrayexpress

Differentially expressed genes in cotyledon of ewes fed mycotoxins

Project description:Consumption of ergot alkaloids, specifically ergovaline, found in endophyte-infected tall fescue causes potent vasoconstriction and has been linked to reductions in placental mass and fetal growth and development. The objective of this study was to elucidate differences in the cotyledonary transcriptome of ewes consuming ergovaline during gestation through RNA-sequencing.

2020-09-08 | GSE155975 | GEO

Comparison of the total liver proteomes of postnatal-day-7 mice with liver-specific UBA3 deficiency and their littermate controls

Project description:The total liver proteomes of postnatal-day-7 mice with liver-specific UBA3 deficiency and their littermate controls were compared by two-dimensional (2-D) electrophoresis mapping. 25 protein spots were obviously changed in their expression upon UBA3 deficiency. These 25 protein spots were excised from 2-D gels. After in-gel digestion, the tryptic digests were subjected to mass spectrometric analysis by LC–MS/MS, followed by database searching. Here, we identified ETFA expression in spot 14, which was decreased in UBA3-deficient conditions.

2020-01-07 | PXD016111 | Pride

The resistance of oilseed rape microspore-derived embryos to osmotic stress is associated with the accumulation of proteins in energy metabolism, redox homeostasis and up-regulation of abscisic acid and cytokinin contents

Project description:The aim of the present study was to investigate the response of rapeseed microspore-derived embryos (MDE) to osmotic stress at proteome level. The PEG-induced osmotic stress was studied in cotyledonary MDE of two genotypes: Cadeli (D), and Viking (V), which were previously reported to reveal contrasting leaf proteome responses under drought. 156 representative protein spots – obtained by 2D-DIGE – have been selected for MALDI-TOF/TOF, 63 proteins have been successfully identified and divided into 8 functional groups. Eight selected protein accumulation trends were validated by using qRT-PCR. Biomass accumulation in treated D was significantly higher (3-fold) than in V, so we can claim D as resistant to osmotic stress. Cultivar D displayed resistance strategy thanks to accumulation of proteins in energy metabolism, redox homeostasis, protein destination and signalling functional groups accompanied by high ABA and active cytokinins. In contrast, V protein profile displayed high requirements of energy (ATP) and nutrients with a significant number of stress-related proteins and cell structure changes accompanied by quick down-regulation for active CK content, SA, JA, GA20. MDE proteome profile is discussed together with leaf proteome results from our previous study (Urban et al., 2017, 30:152, J. Proteomics). We propose different mechanisms to cope with osmotic stress in the genotypes studied. This proteomic study is a first step to validate MDE as a suitable model for follow-up research on characterization of new crossings, and can be used for selection of resistant genotypes.

2021-06-14 | PXD024552 | Pride

Perturbed adult sperm methylome after in utero undernutrition is associated with transmission of metabolic disease

Project description:The pre and postnatal environment can affect both an individual’s risk of adult onset metabolic disease and that of subsequent generations. Although animal models and epidemiological data implicate epigenetic inheritance, little is known of the mechanisms involved. In a robust intergenerational model of developmental programming we demonstrate that the nutritional environment experienced in utero by F1 generation embryos alters the DNA methylome of the F1 adult male germ line in a locus-specific manner, without affecting overall methylation levels. Differentially methylated regions are mostly hypomethylated and are enriched in nucleosome retaining regions in adult sperm. A substantial fraction is resistant to early embryo methylation reprogramming, and thus have the potential to alter F2 generation development. Altered expression of transcripts neighbouring differentially methylated regions are evident in tissues of F2 offspring despite lack of persistence of differential methylation. Transmitted methylation variation in the germline at key regulatory loci may therefore contribute to the development of metabolic disease in the subsequent generation. 2 biological replicates of pooled sperm samples for each control (C) or undernutrition (UN) model

2014-07-16 | E-GEOD-58747 | biostudies-arrayexpress

Identify proteins that interact with CDC25B

Project description:Identify proteins that interact with CDC25B in HS578T cells using Mass Spectrometry

2021-09-09 | PXD020368 | Pride

The p-MYH9/USP22/HIF-1α axis promotes lenvatinib resistance and cancer stemness in hepatocellular carcinoma

Project description:To understand the role of HIF1a in lenvatinib resistance, we conducted label-free quantitative proteome analysis in both control and lenvatinib resistance cell lines. This analysis revealed changes in the proteome due to the lenvatinib resistance, providing a valuable reference for further investigations.

2024-08-20 | PXD054805 | Pride

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