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

ABSTRACT: 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.

INSTRUMENT(S): QSTAR

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

TISSUE(S): Seed

SUBMITTER: Subhra Chakraborty

LAB HEAD: Subhra Chakraborty

PROVIDER: PXD017515 | Pride | 2020-03-11

REPOSITORIES: Pride

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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

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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

Project description: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.

2020-03-11 | PXD017514 | Pride

Serum amyloid A correlates with the osteonecrosis of femoral head

Project description:We observed 21 prominent protein spots that differed between the two groups. Three of these proteins were upregulated and the rest 18 proteins were downregulated in patients with steroid-induced ONFH. The spots determined in the steroid-induced ONFH and health control groups were replicable.The spot no. 21 corresponding to an upregulated protein in patients with steroid-induced ONFH was identified as SAA.

2022-02-15 | PXD028318 | Pride

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

In-depth assembly of organ and development dissected Picrorhiza kurroa proteome map using mass spectrometry

Project description:Background Picrorhiza kurroa, being a rich source of phytochemicals, is a promising higher altitude medicinal herb of Himalaya. The medicinal potential is attributed to picrosides i.e. iridoid glycosides, which synthesized in organ-specific manner through highly complex pathways. Here, we present a large-scale proteome reference map of P. kurroa, consisting of four morphologically differentiated organs and two developmental stages. Results We were able to identify 5186 protein accessions (FDR<1%) providing a deep coverage of protein abundance array, spanning around six orders of magnitude. Most of the identified proteins are associated with metabolic processes, response to abiotic stimuli and cellular processes. Organ specific sub-proteomes highlights organ specialized functions that would offer insights to explore tissue profile for specific protein classes. With reference to P. kurroa development, vegetative phase is enriched with growth related processes, however generative phase harvests more energy in secondary metabolic pathways. Furthermore, stress-responsive proteins, RBPs and PTMs, particularly phosphorylation and ADP-ribosylation play an important role in P. kurroa adaptation to alpine environment. The proteins involved in the synthesis of secondary metabolites are well represented in P. kurroa proteome. The phytochemical analysis revealed that marker compounds were highly accumulated in rhizome and overall, during the late stage of development. Conclusions This report represents first extensive proteomic description of organ and developmental dissected P. kurroa, providing a platform for future studies related to stress tolerance and medical applications.

2022-02-15 | PXD030263 | Pride

GPR35 promotes glycolysis, proliferation and oncogenic signalling by engaging with the sodium potassium pump

Project description:We used human embryonic kidney HEK293T cells transfected with human GPR35 cDNAs as baits that were engineered to express Strep or hemagglutinin (HA) tags at the C terminus to perform an unbiased proteomics survey for GPR35 interaction partners.

2019-11-12 | PXD011269 | Pride

Identification of proteins from the secretory / excretory products (SEPs) of the branchiuran ectoparasite Argulus foliaceus

Project description:A. foliaceus secretory / excretory products (SEPs) were collected from 560 active adult parasites and identified and characterised using LC-ESI-MS/MS analysis.

2020-02-28 | PXD016226 | Pride

Comparison of phosphorylation status of Wnt proteins in control and Fto deficient cells upon Wnt 3a stimulation

Project description:Wnt Phospho protein profiling comparing control and Fto deficient cell after Wnt3a stimulation Control vs Fto deficient MEFs treated with Wnt 3a condioned medium for 40 minutes. 6 replicates per array

2013-11-21 | E-GEOD-52572 | biostudies-arrayexpress

Identification of proteins interacting with cytoplasmic high-mobility group box 1 (HMGB1) during the hepatocellular response to ischemia reperfusion injury

Project description:Ischemia/reperfusion injury (IRI) occurs in liver transplantations and major resections and can lead to liver dysfunction. HMGB1 locates in nucleus of normal hepatocytes, but translocates to cytoplasm and the extracellular space during IRI. Although the functions of nuclear and extracellular HMGB1 are well explored, the role cytoplasmic HMGB1 plays in hepatic IRI is still unknown. We hypothesize cytoplasmic HMGB1 interacts with binding proteins involved in the hepatocellular response to IRI. In this study binding proteins of cytoplasmic HMGB1 during hepatic IRI were identified. Normal and warm ischemia reperfusion (WI/R) liver tissues were used for cytoplasmic protein extraction. The protein extracts were subjected to co-immunoprecipitation to enrich HMGB1-protein complexes. To identify the immunoprecipitated proteins in eluates, 2DE and subsequent MS detection were performed. Three identified proteins were verified using western blotting: betaine--homocysteine S-methyltransferase 1 (BHMT), cystathionine gamma-lyase (CTH) and ATP synthase beta subunit (ATP5B). All three identified proteins have a role in metabolic pathways and autophagy. Our results demonstrate cytoplasmic HMGB1 binds to BHMT, CTH and ATP5B during hepatic WI/R. Since both, cytoplasmic HMGB1 and binding proteins, are involved in autophagy, we speculate this protein complex may be involved in the hepatocellular response to IRI via the autophagy pathway.

2017-03-10 | PXD003538 | Pride

Novel targets of the CbrAB/Crc carbon catabolite control system revealed by transcript abundance in Pseudomonas aeruginosa [BSM]

Project description:The opportunistic human pathogen Pseudomonas aeruginosa can utilize several carbon and nitrogen compounds as energy sources, which allows the bacterium to grow on a variety of different environments. Nevertheless, the uptake and utilization of these compounds is organized in a hierarchical manner, which is guaranteed by a mechanism named catabolite repression. In P. aeruginosa catabolite repression is a post-transcriptional process with the translational repressor protein, Crc, as the main component. Crc recognizes CA-motifs (acronym for catabolite activity) present in the vicinity of the ribosome binfing site of corresponding target mRNAs and therefore compete with ribosome binding. Certain conditions, which are mainly related to changes in the carbon to nitrogen ratio, induce the two component system CbrAB, which activates the transcription of the sRNA CrcZ. The sRNA sequesters Crc and allows the translation of the target mRNAs. The main focus of this study was to identify novel direct targets of the CbrAB/Crc system with the use of a transcriptome analysis in combination with the search for CA-motifs. We were able to identify five novel targets (estA, acsA, dctP, bkdR and aroP2), which were involved in the uptake and utilization of less preferred carbon sources and amino acids. Direct interaction of Crc with these genes and the resulting regulation by CbrB and CrcZ were verified using mutational analysis and in vitro and in vivo experiments. Moreover, these targets were discussed in the light of growth and biofilm development in synthetic CF sputum medium which emphasised the importance of the CbrAB/Crc system as a regulator of chronic infection. keyword(s): genetic modification Comparative transcriptome analysis with the PAO1 wild type strain and PAO6673 (delta crc), PAO66711 (delta cbrB), PAO6679 (delta crcZ) strains grown in BSM-Succinate medium.

2012-03-31 | E-GEOD-33241 | biostudies-arrayexpress

Novel targets of the CbrAB/Crc carbon catabolite control system revealed by transcript abundance in Pseudomonas aeruginosa [LB]

Project description:The opportunistic human pathogen Pseudomonas aeruginosa can utilize several carbon and nitrogen compounds as energy sources, which allows the bacterium to grow on a variety of different environments. Nevertheless, the uptake and utilization of these compounds is organized in a hierarchical manner, which is guaranteed by a mechanism named catabolite repression. In P. aeruginosa catabolite repression is a post-transcriptional process with the translational repressor protein, Crc, as the main component. Crc recognizes CA-motifs (acronym for catabolite activity) present in the vicinity of the ribosome binfing site of corresponding target mRNAs and therefore compete with ribosome binding. Certain conditions, which are mainly related to changes in the carbon to nitrogen ratio, induce the two component system CbrAB, which activates the transcription of the sRNA CrcZ. The sRNA sequesters Crc and allows the translation of the target mRNAs. The main focus of this study was to identify novel direct targets of the CbrAB/Crc system with the use of a transcriptome analysis in combination with the search for CA-motifs. We were able to identify five novel targets (estA, acsA, dctP, bkdR and aroP2), which were involved in the uptake and utilization of less preferred carbon sources and amino acids. Direct interaction of Crc with these genes and the resulting regulation by CbrB and CrcZ were verified using mutational analysis and in vitro and in vivo experiments. Moreover, these targets were discussed in the light of growth and biofilm development in synthetic CF sputum medium which emphasised the importance of the CbrAB/Crc system as a regulator of chronic infection. Comparative transcriptome analysis with the PAO1 wild type strain and PAO6673 (delta crc), PAO66711 (delta cbrB), PAO6679 (delta crcZ) strains grown in LB medium.

2012-03-31 | E-GEOD-33244 | biostudies-arrayexpress

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