Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of potential interactors of NKS1 and QUA1

ABSTRACT: Adjacent plant cells are connected by specialized cell wall regions, called middle lamellae, which influence critical agricultural characteristics, including fruit ripening and organ abscission. Middle lamellae are enriched in pectin polysaccharides, specifically homogalacturonan (HG). Pectins are made in the Golgi apparatus by the coordinated action of transporters and enzymes. Here, in this project, we identify a plant-specific Arabidopsis DUF1068 protein, called NKS1/ELMO4, that is required for middle lamellae integrity and cell adhesion. We did an immunoprecipitation-mass spectrometry (IP-MS) analysis to identify potential interactors of NKS1. And we also performed an IP-MS analysis of QUA1, which is one of the interactors of NKS1.

INSTRUMENT(S): Bruker Daltonics timsTOF series

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

TISSUE(S): Leaf

SUBMITTER: Staffan Persson

LAB HEAD: Staffan Persson

PROVIDER: PXD047727 | Pride | 2024-03-20

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Col0_RFPTrap_Rep1.d.zip	Other
	Col0_RFPTrap_Rep2.d.zip	Other
	Col0_RFPTrap_Rep3.d.zip	Other
	Col_0_GFPTrap_Rep1.d.zip	Other
	Col_0_GFPTrap_Rep2.d.zip	Other

Items per page:

1 - 5 of 17

Similar Datasets

Protein interactions with HA-tagged cytoplasmic dynein-2 DATASET2

Project description:To identify those proteins interacting with the cytoplasmic dynein-2 using mammalian cell lines stably expressing HA-tagged intermediate chain subunits, WDR34 (DYNC2I2) or WDR60 (DYNC2I1).

2023-01-24 | PXD031152 | Pride

GRO analysis of rap1-sil, tpk1 & tpk2.

Project description:GRO (Genomic run-on) experiments with different mutants that affect to the accumulation of non active RNA pol II along the yeast genome. Keywords: Genomic run-on GRO There are 4 different strains: rap1-sil (without the silencing domain), RAP1(both from Graham I.R. et al 1999) and tpk1 & tpk2 mutants (Euroscarf). For each experiment there are GRO data (Transcription Rate) and gDNA data used for normalizing the GRO signals. The last number of the GRO filters correspond to the number of gDNA filters.There are 3 independent biological replicates of Rap1 and rap1-sil experiments and 2 for the tpk1 & tpk2 experiments.

2010-06-24 | E-GEOD-14080 | biostudies-arrayexpress

Analysis of Spt16 depletion

Project description:Transcription rate analysis in Yeast by means of GRO, mRNA amount and ChIP-on-chip during the depletion of Spt16p. Keywords: Genomic run-on GRO ChIP-chip Transcription rate analysis by means of GRO and mRNA amount (RA) of three independent replicates during the depletion of Spt16p (Control and 5 & 7 hours after the depletion). Each time point replicate has been hybridized on a different macroarray (F14-F16). ChIP-on-chip analysis of Spt16 were done during exponential grow in YPD.

2010-06-24 | E-GEOD-14082 | biostudies-arrayexpress

Mechanism of chaperone coordination during cotranslational protein folding in bacteria

Project description:Protein folding is assisted by molecular chaperones that bind nascent polypeptides during mRNA translation. Several structurally-distinct classes of chaperones promote de novo folding, suggesting that their activity is coordinated at the ribosome. Here we use biochemical reconstitution and structural proteomics to explore the molecular basis for cotranslational chaperone action in bacteria. We find that chaperone binding is disfavoured close to the ribosome, allowing folding to precede chaperone recruitment. Trigger factor subsequently recognises compact folding intermediates exposing extensive non-native surface and dictates DnaJ access to nascent chains. DnaJ uses a large surface to bind structurally diverse intermediates, and recruits DnaK to solvent-accessible sites in a sequence non-specific manner. Neither Trigger factor, DnaJ nor DnaK destabilize cotranslational folding intermediates. Instead, the chaperones collaborate to create a protected space for protein maturation that extends well beyond the ribosome exit tunnel. Our findings show how the chaperone network selects and modulates cotranslational folding intermediates.

2024-07-03 | PXD048638 | Pride

GRO analysis of topoisomerase mutants

Project description:Genomic Run-on analysis of topoisomerase mutants (top1-delta/top2ts or top2ts) has been conducted at reference temperature for wt strain and at non-permissive temperature for wt and mutant strains. Keywords: Genomic Run On The analysis includes 3 repeats of the wild type strain (JCW25) at 30ÂºC and 3 more at 37ÂºC, 3 repeats of the top2ts mutant (JCW26) at 37ÂºC and 3 repeats of the double top1 (delta) top2ts mutant at 37ÂºC. A single genomic DNA hybridization on one of the filters can be used for normalization between gene probes if needed.

2010-06-24 | E-GEOD-16673 | biostudies-arrayexpress

Comparison of gene expression from surviving and dying Pacific oysters reveals a motality signature

Project description:This experiment was designed to enable the identification of field mortality sensitive Pacific oysters while also permitting the repetitive, non-lethal sampling of tissue from identifiable individual oysters. These samples have been difficult to obtain because pre-mortality phenotypes are obscured by the presence of an outer shell which occludes all views of body tissues. Additionally, mortality triggers have not been identified and there is need to better characterize the pathophysiology preceding mortality. 300 three year old oysters were sampled on 6 dates from May to October, 2008 from their grow out site at Totten Inlet, WA, USA. 100-200ul of hemolymph was withdrawn from the adductor muscle and preserved for possible mRNA analysis by microarray. At the end of the summer, mortality phenotypes were assigned to individuals (alive vs. dead/mortality). Gene expression profiles from screened mortality individuals showed up-regulation of a set of 124/11904 ESTs within one month of death that were not usually found in the alive individuals. This indicates that the path to death in oysters occurs over several days and maybe weeks, and is a molecularly coordinated response in which the hemolymph is involved. Gene expression predictors of survival fate could be developed from this data set.

2011-03-16 | E-MTAB-548 | biostudies-arrayexpress

Species-specific metabolic reprogramming in human and mouse microglia during inflammatory pathway induction

Project description:Metabolic reprogramming is a hallmark of the immune cells in response to inflammatory stimuli. This metabolic process involves a switch from oxidative phosphorylation (OXPHOS)to glycolysis, or alterations in other metabolic pathways. However, most of the experimental findings have been acquired in murine immune cells and little is known about the metabolic reprogramming of human microglia. In this study, we investigated the transcriptomic and metabolic profiles of mouse and iPSC-derived human microglia challenged with the TLR4 agonist LPS. We found that both species displayed a metabolic shift and an overall increased glycolytic gene signature in response to LPS treatment. The metabolic reprogramming was characterized by the upregulation of hexokinases in mouse microglia and phosphofructokinases in human microglia. This study provides the first direct comparison of energy metabolism between mouse and human microglia, highlighting the species-specific pathways involved in immunometabolism and the importance of considering these differences in translational research.

2023-09-02 | PXD043836 | Pride

Proteome of C. elegans upon NCL-1 or TIF-IA KD during aging

Project description:Anabolic activities such as ribosome biogenesis and protein synthesis are linked to aging. Ribosomal RNA (rRNA) synthesis is the limiting step of ribosome biogenesis, thus dictating the number of ribosomes in cells and, consequently, the capacity for mRNA translation. Knockdown of the rRNA synthesis repressor, NCL-1, accelerated aging, whereas knocking down the transcription initiation factor C36E8.1 promoted longevity. This suggested that rRNA synthesis has a negative correlation with lifespan. To investigate the metabolic changes upon manipulation of rRNA synthesis the proteome of NCL-1 KD and C36E8.1 KD were analyzed at young, middle, and old age (AD2, AD6, AD12).

2024-01-11 | PXD028600 | Pride

Identification of 8-oxoG binding proteins in Deinococcus radiodurans

Project description:8-oxo-7,8-dihydroguanine (8-oxoG) is a common RNA oxidation that has been implicated in carcinogenesis, neurodegeneration, and aging. Some? Many? RNA-binding proteins have shown binding preference for 8-oxoG modified RNA; such binding? can protect cells from oxidative stress. To date, the presence of specific 8-oxoG-recognizing proteins is only known in model organisms, but, how these proteins cooperate is still unclear. Here, we use RNA affinity chromatography and mass spectrometry to search for proteins that specifically bind 8-oxoG-modified RNA in Deinococcus radiodurans, an extremophilic bacterium with extraordinary resistance to oxidative stresses. We identified four proteins that selectively bind to oxidized RNA: polynucleotide phosphorylase (DR_2063/PNPase), ATP-dependent DEAD-box RNA helicase (DR_0335/RhlB), ribosomal protein S1 (DR_1983/RpsA), and transcriptional termination factor (DR_1338/Rho). The knockout of PNPase and RhlB in D. radiodurans caused increased sensitivity to hydrogen peroxide and a significant accumulation of 8-oxoG modified RNA. Importantly, PNPase directly interacts with RhlB in D. radiodurans; however, no additional phenotypic effect was observed for the double deletion of pnp and rhlB compared to the individual single deletions. Overall, our findings suggest a role of the PNPase-RhlB complex in targeting 8-oxoG-modified RNAs for rapid degradation and thereby constitutes an important component of D. radiodurans resistance to oxidative stress.

2022-07-10 | PXD028861 | Pride

metaproteomic analysis of microbiota and metabolic pathways involved in taste formation during Chinese traditional fish sauce

Project description:Complex microbial metabolism is key to taste formation in high-quality fish sauce during fermentation. To guide quality supervising and targeted regulation, we analyzed the function of microbial flora during fermentation based on a previous metagenomic database. Most of the identified genes involved in metabolic functions showed an upward trend in abundance during fermentation. In total, 571 proteins extracted from fish sauce at different fermentation stages were identified. The proteins were mainly derived from Halanaerobium, Psychrobacter, Photobacterium, and Tetragenococcus. Functional annotation showed 15 pathways related to amino acid metabolism, including alanine, aspartate, glutamate, and histidine metabolism; lysine degradation; and arginine biosynthesis.

2022-05-20 | PXD031089 | Pride