The CX-MS-based quantifitative proteomic analysis of interactome of plant nucleus
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Glycine Max
SUBMITTER: 
Shuaijian DAI
LAB HEAD: Ning Li
PROVIDER: PXD034796 | Pride | 2023-05-10
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| MS181452_F10_CID.raw | Raw | |||
| MS181452_F10_HCD.raw | Raw | |||
| MS181452_F11_CID.raw | Raw | |||
| MS181452_F11_HCD.raw | Raw | |||
| MS181452_F12_CID.raw | Raw |
Items per page: 5 1 - 5 of 503 |
Similar Datasets
Project description:Cesium (Cs+) is a potentially toxic mineral element that is released into the environment and taken up by plants. Although Cs+ is chemically similar to potassium (K+), and much is known about K+ transport mechanisms, it is not clear through which K+ transport mechanisms Cs+ is taken up by plant roots. In this study, the role of AtHAK5 in high affinity K+ and Cs+ uptake was characterized. It is demonstrated that AtHAK5 is localized to the plasma membrane under conditions of K+ deprivation, when it is expressed. 9 samples were used in this experiment.
2010-04-28 | E-GEOD-20222 | biostudies-arrayexpress
Project description:Homodimerization of Mpl can also be accomplished in the absence of Tpo, by binding of a synthetic ligand (Chemical inducer of dimerization, CID) to a constitutively expressed fusion protein F36VMpl consisting of a ligand binding domain (F36V) and the intracellular signaling domain of Mpl. In contrast to Tpo stimulation, F36VMpl dimerization in human CD34+ progenitor cells generates robust erythropoiesis. Microarray gene expression profiling of progenitors demonstrated that F36VMpl dimerization, but not Tpo, results in upregulation of critical erythroid genes. CD34+ cord blood cells were transduced with F36VMpl-GFP (GFP reporter gene) and cultured on MS-5 stroma for 7 days in the presence of CID, Tpo, Epo or no factors (no CID, negative control). CD34+GFP+ cells were sorted on day 7 and subjected to microarray (n=3 independent experiments).
2011-08-31 | E-GEOD-30585 | biostudies-arrayexpress
Project description:Microarray experiments were performed on the roots and leaves samples seperately using custom based Nimblegen platform (12plex). This is a time-course study. The plants were grown in controlled growth chamber condiditons. The seeds were sown in sterile petri plates with modified half-strength MS agar medium. The seedlings were then aseptically transferred into sterile polycarbonate container with half-strength MS liquid medium. Seedlings were grown for 2 weeks in an incubator set at 25 oC with constant light and subjected to dehydration for 20min, 40min, 1hr, 2hrs, and 4hrs. We used a hydrophonics system for the trancriptome profiling of tobacco (cv Burley 21) root and leaves samples to study plant reponses during water- deficit or drought. Plants were grown in controlled growth chamber conditions and subjected to water deficit condition after 2 weeks.The plants were transferred to empty containers without touching to nullify any possibility of wounding and harvested subsequently. For 0mins, plants were taken out of the well-watered conditions and transfered to empty boxes and immediately harvested for both tissues and hence called 0-min dehydrated tissue. Similarly other time-points were processed( for instance, 20 min of dehydration, plants were dehydrated for 20 min after being taken out from the container and then harvested). Tissues for three biological replicates and 20 plants per biological replicates were collected for each time-point. RNA was isolated from both tissues using RNeasy Kit from Qiagen and quality was accessed with Nano-drop as well as with Agilent-Bioanalyzer using RNA-600 kit. 20ug of sample was processed at Micro Array Facility.
2015-03-31 | E-GEOD-67434 | biostudies-arrayexpress
Project description:O-GlcNAcylation occurs on thousands of proteins involved in various cellular events. O-GlcNAc transferase (OGT), one of the enzymes responsible for protein O-GlcNAcylation, is known to be auto-O-GlcNAcylated at multiple sites. However, the role of O-GlcNAcylation on OGT is still unknown. Here, we report the role of O-GlcNAcylation on short form OGT (sOGT). By LC-ETD-MS analysis and western blot, we show that sOGT was mainly O-GlcNAcylated in the tetratricopeptide repeat (TPR) motifs with T12 and S56 being two “key” sites. T12 was a predominant O-GlcNAcylation site and the absence of S56 O-GlcNAcylation enhanced sOGT O-GlcNAcylation level. We found that O-GlcNAcylation of sOGT did not affect the enzyme activity but increased its binding to substrate proteins. S56A bound to and hence glycosylated more proteins, while T12A associated with fewer substrates. Proteomic studies combined with cell proliferation/cell cycle analyses indicated that S56A substantially enhanced cell proliferation, while T12A reduced it, and T12A led to a G2/M cell cycle arrest, due to O-GlcNAcylation of diverse proteins. These findings demonstrate that the O-GlcNAc pattern on sOGT modulates its function in cells by targeting different proteins.
2019-09-16 | PXD010173 | Pride
Project description:Glycosylation, the posttranslational linking of sugar molecules to proteins, is notoriously altered during tumor transformation. More specifically in carcinomas, GalNAc-type O-glycosylation, is characterized by biosynthetically immature truncated glycans present on the cancer cell surface which profoundly impacts anti-tumor immune recognition. The tumor associated glycan pattern may thus be regarded as a biomarker of immune modulation. In Epithelial Ovarian Cancer (EOC) there is a particular lack of specific biomarkers and molecular targets to aid early diagnose and develop novel therapeutic interventions, respectively. The aim of this study was therefore to interrogate the ovarian cancer O-glycoproteome and identify tumor associated glycoproteins relevant in tumor-Dendritic Cell (DC) interactions, mediated by the MGL C-type lectin, recognizing the tumor associated Tn O-glycan. Here we present a strategy, employing a recombinant human MGL protein, to probe the ovarian cancer O-glycoproteome. This was achieved by a MGL Lectin Weak Affinity Chromatography (LWAC) approach using glycoengineered ovarian cancer cells and ovarian cancer tissues as input material. Biochemical and bioinformatics analysis allowed us to identify the glycan structure/arrangement identified by MGL and furthermore to recognize potential MGL binders located at cell membrane, as expected, but also within the intracellular compartment and the matrisome, strongly suggesting that MGL in vivo could act as sensor of cellular distress/damage and modulator of DC motility. The tumor glycoproteins binders for MGL may become relevant as potential “onco-immune” biomarkers for EOC progression and prognosis. Furthermore, these results contribute to the design of glyco-immunogens for DC-based cancer immunotherapy.
2020-10-19 | PXD017510 | Pride
Project description:Sirtuins (SIRTs) form a critical family of nicotinamide adenine dinucleotide (NAD)-dependent enzymes that govern genome regulation, metabolism, and aging. Despite conserved deacetylase domains, SIRTs4-7 have little to no deacetylase activity, and a robust catalytic activity for mitochondrial SIRT4 has remained elusive. Moreover, in vitro characterization of SIRT4 has been hampered by difficulty in maintaining soluble and active recombinant protein. Therefore, to investigate potential cellular substrates of SIRT4, we used proteomics to define its mitochondrial protein interactions in human fibroblasts.
2015-01-05 | PXD001447 | Pride
Project description:A multibillion dollar pharmaceutical industry targets purinergic signaling pathways in humans. However, in contrast, little is known about purinergic signaling in plants. Extracellular adenosine-5’-triphosphate (eATP) acts as a damage-associated molecular pattern (DAMP) in both animals and plants. The first plant eATP receptor, DORN1, was identified in Arabidopsis, defining a new kinase family (P2K) of purinoceptors. Stomates are leaf pores that control gas exchange and, therefore, impact critical functions such as photosynthesis and drought tolerance. Stomates are also the prefer entry point for leaf pathogens. The addition of ATP led to the rapid closure of Arabidopsis leaf stomates resulting in enhanced resistance to the bacterial pathogen Psuedomonas syringae. The data indicate that this response is mediated by eATP recognition by DORN1 followed by direct phosphorylation of the NADPH oxidase RBOHD, resulting in elevated production of reactive oxygen species and stomatal closure. Mutation of the DORN1 phosphorylation sites on RBOHD eliminated the ability of eATP to induce stomatal closure. To date, in contrast to work in animals, purinergic signaling in plants has been viewed as a curiosity without any direct, mechanistic connection to key plant processes. The data presented clearly demonstrates eATP as an important signal controlling stomatal aperture with important implications for the control of plant photosynthesis, water homeostasis, pathogen resistance and ultimately yield.
2018-10-24 | PXD006678 | Pride
Project description:Chemical-Crosslinking Mass Spectrometry (XLMS) using MS-cleavable crosslinkers is fast becoming an established technique in the study of protein-protein interactions for both small and large scale samples. With the increased uptake of XLMS as a technique, different combinations of crosslinker types, fragmentation strategies and analysis programs are being applied to a diverse array of biological samples. This study is focused on understanding how the three variables of an XLMS experiment – crosslinker type, fragmentation and program – could generate differences in identifications, leading to increased biological coverage of a sample. Here we probe for the first time, the known enzyme:substrate interaction between yeast arginine methyltransferase Hmt1p and its substrate, heterologous nucleolar protein Npl3p. We use this known interaction as a platform to compare two analysis programs, MeroX and XlinkX2.0, using two crosslinker types, DSSO and DSBU, and two mass-spectrometry fragmentation strategies, CID/ETD and SteppedHCD. Through these we also compare different algorithm strategies, Precursor and Reporter-Ion, as well as assess the impact of restricting data searches to lysine only crosslinks versus the inclusion of serine, threonine and tyrosine as reactive residues. From this analysis we show direct evidence of Hmt1p in contact with its known methylation sites on Npl3p, the intrinsically disordered “SRGG” region. We also show through our multi-crosslinker, multi-fragmentation and multi-software approach that two approaches leads to greater understanding and depth of a crosslinked sample, and this is due to some combinations of experimental variables creating greater coverage of crosslinks than others.
2018-07-20 | PXD008348 | Pride
Project description:Microarray experiments were performed on the roots and leaves samples seperately using custom based Nimblgen platform (12plex). This is a time-course study. The plants were grown in controlled growth chamber condiditons ambiient to soybean growth and development using a hydrophonics system. The tissues were harvested after 30days of growth in six time points- 0min, 30mins, 1hour, 2hours, 3hours and 5hours of dehydration. We used a hydrophonics system for the trancriptomics analysis of the soybean(William -82) root and leaves samples to study the reponse during water- deficit or drought. Plants were grown in controlled growth chamber conditions and harvested after 30days in six time-points. The plants were transferred to empty pots without touching to nullify any possibility of wounding and harvested subsequently. For 0mins, plants were taken out of the well-watered conditions and transfered to empty boxes and immediately harvested for both tisses and hence called 0-min dehydrated tissue. Similarly other time-points were processed (for instance, 2hrs of dehydration, plants were dehydrated for 2hours after being taken out from well-waterted pots and then harvested). Tissues for three biological replicates and three plants per biological replicates were collected for each time-point (n=9). RNA was islolated from both tissues using RNeasy Kit from Qiagen and quality was accessed with Nano-drop as well as with Agilent-Bioanalyzer using RNA-600 kit. 20ug of sample was processed at Micro Array Facility.
2015-04-26 | E-GEOD-49537 | biostudies-arrayexpress
Project description:In Arabidopsis, mitogen-activated protein kinases MPK3, MPK4 and MPK6 constitute essential relays for a variety of functions including cell division, development and innate immunity. While some substrates of MPK3, MPK4 and MPK6 have been identified, the picture is still far from complete. To identify substrates of these MAPKs in cell division, growth and development we compared the phosphoproteomes of wild-type and mpk3, mpk4 and mpk6. To study the function of these MAPKs in innate immunity, we analyzed their phosphoproteomes following activation by a microbe-associated molecular pattern (MAMP). Partially overlapping substrates were retrieved for all three MAPKs, showing target specificity to one, two or all three MAPKs in different biological processes. More precisely, our results illustrate the fact that the entity to be defined as a specific or a shared substrate for MAPKs is not a phosphoprotein but a particular (S/T)P phosphorylation site in a given protein. As a whole, 152 peptides were identified to be differentially phosphorylated in response to MAMP treatment and/or when compared between genotypes and 70 of them could be classified as putative MAPK targets. Biochemical analysis of a number of putative MAPK substrates by phosphorylation and interaction assays confirmed the global phosphoproteome approach. Our study finally expands the set of MAPK substrates to involve other protein kinases, including calcium-dependent (CDPK) and sugar non-fermenting (SnRK) protein kinases.
2017-12-06 | PXD006807 | Pride