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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Analysis of gene expression from fbn5-1 T-DNA insertion mutant of Arabidopsis

ABSTRACT: We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes in fbn5-1 T-DNA insertion Arabidopsis mutant. Fibrillins are lipid-associated proteins in plastids and are ubiquitous in plants. Fibrillins are known to accumulate and sequester carotenoids in chromoplasts during the development of flowers and fruits; however, little is known about the function of fibrillins in leaf tissues. Here we identified a novel protein fibrillin5 (FBN5) that is essential for plastoquinone-9 (PQ-9) biosynthesis in Arabidopsis thaliana. We showed that homozygous fbn5-1 plants were seedling-lethal, and XVE:FBN5-B transgenic plants expressing low levels of FBN5-B showed a lower growth rate and were smaller than wild-type. In chloroplasts, FBN5-B physically interacts with solanesyl-diphosphate synthase (SPS) 1 and 2, which synthesize the solanesyl moiety of PQ-9. Plants containing defective FBN5-B accumulated less PQ-9 and its cyclized product, plastochromanol-8, which is consistent with mutant phenotypes showing lower photosynthetic performance and higher levels of hydrogen peroxide. The role of FBN5-B in the FBN5-B/dimeric SPS complex is discussed with respect to biosynthesis of the solanesyl moiety. 4 replicats of wild-type as control and fbn5-1 T-DNA insertion mutants were analized.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Yeon-Ki Kim

PROVIDER: E-GEOD-68275 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Analysis of gene expression from fbn5-1 T-DNA insertion mutant of Arabidopsis

Project description:We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes in fbn5-1 T-DNA insertion Arabidopsis mutant. Fibrillins are lipid-associated proteins in plastids and are ubiquitous in plants. Fibrillins are known to accumulate and sequester carotenoids in chromoplasts during the development of flowers and fruits; however, little is known about the function of fibrillins in leaf tissues. Here we identified a novel protein fibrillin5 (FBN5) that is essential for plastoquinone-9 (PQ-9) biosynthesis in Arabidopsis thaliana. We showed that homozygous fbn5-1 plants were seedling-lethal, and XVE:FBN5-B transgenic plants expressing low levels of FBN5-B showed a lower growth rate and were smaller than wild-type. In chloroplasts, FBN5-B physically interacts with solanesyl-diphosphate synthase (SPS) 1 and 2, which synthesize the solanesyl moiety of PQ-9. Plants containing defective FBN5-B accumulated less PQ-9 and its cyclized product, plastochromanol-8, which is consistent with mutant phenotypes showing lower photosynthetic performance and higher levels of hydrogen peroxide. The role of FBN5-B in the FBN5-B/dimeric SPS complex is discussed with respect to biosynthesis of the solanesyl moiety.

2017-04-30 | GSE68275 | GEO

XVE AMY3C-EY induction in SAM

Project description:To study the molecular basis for chlorotic and reticulate phenotypes, we took advantage of a time course experiment on XVE AMY3C-EY plants designed for microarray analysis.

2017-03-01 | GSE93084 | GEO

Gene expression-based investigation of a new role for the glyoxylate shunt in contributing to tolerance to oxidative stress.

Project description:Transcriptional profiling in Pseudomonas aeruginosa MPAO1 and its glyoxylate shunt gens transposon insertion mutants (aceA and glcB) was perfomed using microarray analysis with or without 1mM PQ treatment. Based on the gene expression, we investigated role of glyoxylate shunt in P. aeruginosa and found out pathway related with glyoxylate shunt under oxidative stress.

2016-02-24 | GSE78230 | GEO

Genome wide expression analysis of EST-induced EBE-XVE using Affymetrix ATH1 array

Project description:Global transcriptome patterns were determined in XVE-14 and wild-type seedlings induced for 45 min b-estradiol in order to identify the genes early regulated by EBE transcription factor. We used microarrays to identify genes differentially expressed in EST-inducible EBE over-expression line #14 compared to wild-type plants, 45 min after 2µM EST induction. Three independent biological replications were performed. In order to identify potential direct/early target genes of EBE transcription factor, estradiol inducible overexpression system was used. Three week old Arabidopsis EBE-XVE (line 14) and WT seedlings were treated with ß-estradiol (2µM) for 45 min. RNA was isolated from shoot and subjected to hybridization on Affymetrix microarrays. Experiment was performed in 3 biological replications and genes differentially expressed between estradiol treated EBE-XVE and WT plants were identified as potential early targets of EBE.

2013-03-30 | E-GEOD-27855 | biostudies-arrayexpress

Nanopore sequencing of estradiol and DMSO treated XVE:ROS1-YFP plants

Project description:Transgenic plants carrying an estradiol-inducible ROS1-YFP construct (XVE:ROS1-YFP) were subjected to long-read sequencing (Oxford Nanopore Technologies) to assess the global impacts of ROS1 activity on the methylome of Arabidopsis thaliana (ecotype Col-0).

2022-11-07 | GSE211295 | GEO

Transcription profiling of Arabidopsis ppi2 mutants

Project description:Arabidopsis ppi2 plants have a T-DNA insertion in atToc159 and thus display a severe defect in protein import into chloroplasts. These mutants have an albino phenotype and also are seedling lethal. We used microarrays to detail the induced genes in ppi2 plants compard to wild type plants. Experiment Overall Design: Arabidopsis plants, wild-type and ppi2 plants, were grown for 10 or 20 days, respectively, and total RNA was used for analysis.

2009-08-22 | E-GEOD-17675 | biostudies-arrayexpress

Host- and stage-dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis

Project description:Arbuscular mycorrhizal fungi arguably form the most successful and wide-spread endosymbiosis with plants. In general terms there is very little host-specificity in this interaction, indicating an extremely broad compatibility. However, host preferences as well as varying symbiotic efficiencies have been observed, the molecular basis of which is still largely unknown. Secreted proteins (SPs) may act as fungal effectors to control symbiotic efficiency in a host-dependent manner. Therefore, we studied whether AM fungi adjust their secretome in a host- and stage-dependent manner to contribute to their extremely wide host-range. We investigated the expression of SP encoding genes of R. irregularis DAOM197198 in three evolutionary distantly related plant species, Medicago truncatula (Medicago), Nicotiana benthamiana (Nicotiana) and Allium schoenoprasum (Chives). In addition we used laser microdissection in combination with RNAseq to study SP expression at different stages of the symbiotic interaction in Medicago. Our data indicate that the vast majority of 288 expressed SPs show equal expression levels in the interaction with all three host plants. In addition, a subset (~15%) of the SPs show significant differential expression depending on the host plant and/or environmental condition. This host-dependent expression appears to be controlled locally in the hyphal network in response to host metabolic cues. Overall, this study offers a comprehensive analysis of the R. irregularis secretome, which now offers a solid basis to direct functional studies on the role of fungal SPs in AM symbiosis.

2018-03-27 | GSE99655 | GEO

Gene expression profile in selenophosphate synthetase 1 (SPS1) knockdown Drosophila SL2 cell

Project description:Selenophosphate, which is the active donor of selenium in selenocysteine (Sec) biosynthesis is synthesized from selenite and ATP by an enzyme designated as selenophosphate synthetase (SPS).There are two isoforms of SPS in higher eukaryotes,SPS1 and SPS2. Initially, both SPS1 and SPS2 were thought to be involved in selenophosphate synthesis. However, it was subsequently shown that only SPS2 catalyzes selenophosphate synthesis. Although SPS1 is an essential gene in Drosophila, its function has not been determined. To identify transcriptional profile of SPS1 knockdown cells, which could offer valuable clues to identify molecular mechanism of SPS1, we introduced RNAi using its cognate double-stranded RNA into Drosophila SL2 cells, and then microarray analysis was carried out.

2009-08-18 | GSE17685 | GEO

Genome wide expression analysis of EST-induced EBE-XVE using Affymetrix ATH1 array

2013-03-30 | GSE27855 | GEO

Proteomics analysis unraveled paraquat-induced cholesterol biosynthesis dysregulation in human brain microvascular endothelial cells

Project description:Despite its banishment in several countries, Paraquat (PQ) is still one of the most commonly used herbicides in agriculture. This compound is known to induce damaging effects on human or animal brain cells such as glial cells or neurons through biological processes as redox by generation of Reactive Oxygen Species (ROS). This specific perturbation has already proven its association for increasing the risk of developing a long-term brain impairment in in vitro and in vivo studies using brain cells. However, there is few evidence of PQ effect on Human Brain Microvascular Endothelial Cells (HBMECs), a particular cell type acting as a macromolecule permeability regulator in the Blood-Brain Barrier (BBB). The present study aimed at unraveling biological mechanisms associated to the exposition of 1, 10 and 100 µM of PQ for 24h on HBMECs. High-throughput mass spectrometry-based proteomics using data-independent acquisition (DIA) was applied. Biological pathway enrichment and cellular assays such as mitochondrial respiration and cholesterol level of PQ-treated HBMECs were performed to verify proteomics results. Proteomic experiment reported a total of 3753 quantified proteins out of which 419 were significantly modulated by paraquat exposure. Biological pathway enrichment revealed that the modified proteins are involved in pathways such as the ubiquinone metabolism, a pathway directly linked to mitochondrial complex I proteins. This study also unveiled the modulation of the cholesterol metabolism. In conclusion, most of the highly differentially expressed proteins (DEPs) in PQ-treated HBMECs were associated to the ubiquinone metabolism pathway confirming the well know mechanism of PQ inducing oxidative stress and inhibit mitochondrial complex I activity. Additionally, this study also described the cholesterol biosynthesis modulation on primary human brain endothelial cells not yet described.

2022-02-17 | PXD026975 | Pride

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