Response of Arabidopsis thaliana gene expression to NO redox forms
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ABSTRACT:
PROVIDER: PRJEB53633 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR9860244_1.fastq.gz | Fastqsanger.gz | |||
| ERR9860244_2.fastq.gz | Fastqsanger.gz | |||
| ERR9860245_1.fastq.gz | Fastqsanger.gz | |||
| ERR9860245_2.fastq.gz | Fastqsanger.gz | |||
| ERR9860246_1.fastq.gz | Fastqsanger.gz |
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Project description:Fluctuating light affects photosynthesis in chloroplasts, resulting changes of a series of redox reactions and accumulation of reactive oxygen species (ROS). Chloroplast redox regulation have been considered as “a fine regulation of protein function which is crucial for efficient photosynthesis”. However, the role of redox regulation in acclimation to fluctuating light for plants is still unclear. In this study, we performed global quantitative mapping of the Arabidopsis thaliana (wild-type and pgr5 mutant) cysteine thiol switching using the latest iodoTMT-based redox proteomics technology, systematically revealing a high-quality landscape of fluctuating light-responsive redox-modified proteins for the first time. Notably, photosynthesis-related pathway, especially PSI-related proteins, are operational thiol-switching hotspots.
2021-11-17 | PXD029772 |
Project description:Fluctuating light affects photosynthesis in chloroplasts, resulting changes of a series of redox reactions and accumulation of reactive oxygen species (ROS). Chloroplast redox regulation have been considered as “a fine regulation of protein function which is crucial for efficient photosynthesis”. However, the role of redox regulation in acclimation to fluctuating light for plants is still unclear. In this study, we performed global quantitative mapping of the Arabidopsis thaliana (wild-type and pgr5 mutant) cysteine thiol switching using the latest iodoTMT-based redox proteomics technology, systematically revealing a high-quality landscape of fluctuating light-responsive redox-modified proteins for the first time. Notably, photosynthesis-related pathway, especially PSI-related proteins, are operational thiol-switching hotspots.
2022-04-12 | PXD027929 |
Project description:DDA experiment investigating differential cystein redox modification using iodoTMT label on high light treated samples from Arabidsopsis thaliana leaves.
2024-08-23 | PXD048299 | JPOST Repository
Project description:Thiol-dependent redox regulation is essential for the rapid adaptation of chloroplast metabolism to unpredictable changes of light intensity. The disulfide reductase activity of thioredoxins (Trxs), which relies on photo-reduced ferredoxin (Fdx) and a Fdx-dependent Trx reductase (FTR), constitutes the Fdx-FTR-Trxs system, which links chloroplast redox regulation to light. In addition, chloroplasts harbor an NADPH-dependent Trx reductase (NTR) with a joint Trx domain, NTRC. The activity of these two redox systems is integrated by the balance of the hydrogen peroxide scavenging enzyme 2-Cys peroxiredoxin (2-Cys Prx), which thus plays a key role in maintaining the reducing capacity of chloroplast Trxs in response to light intensity. Based on the severe phenotype of mutant lines lacking NTRC, it is clear that this enzyme plays an essential role in chloroplast redox homeostasis. However, whether the function of NTRC depends on its capacity of reduce 2-Cys Prxs or has additional targets remains unknown. Here, we have addressed this issue by a comparative analysis of the triple mutant of Arabidopsis thaliana, ntrc-2cpab, simultaneously lacking 2-Cys Prxs and NTRC, and the double mutant 2cpab lacking 2-Cys Prxs. The phenotype of the ntrc-2cpab mutant is indistinguishable of the 2cpab mutant, as shown by growth rate, photosynthesis performance, light-dependent redox regulation of enzyme activity and comparative transcriptomics based RNA-Seq. Based on these results, we propose that the function of NTRC in chloroplast redox homeostasis is exerted by the regulation of the redox balance of 2-Cys Prxs rather than by the direct reduction of additional targets.
2021-09-09 | GSE147793 | GEO
Project description:Although plant development is highly reproducible, some stochasticity exists. This developmental stochasticity may be caused by noisy gene expression. Here we analyze the fluctuation of protein expression in Arabidopsis thaliana. Using the photoconvertible KikGR marker, we show that the protein expressions of individual cells fluctuate over time. A dual reporter system was used to study extrinsic and intrinsic noise of marker gene expression. We report that extrinsic noise is higher than intrinsic noise and that extrinsic noise in stomata is clearly lower in comparison to several other tissues/cell types. Finally, we show that cells are coupled with respect to stochastic protein expression in young leaves, hypocotyls and roots but not in mature leaves. Our data indicate that stochasticity of gene expression can vary between tissues/cell types and that it can be coupled in a non-cell-autonomous manner.
| S-EPMC5730595 | biostudies-literature
Project description:Climate change as a consequence of increasing atmospheric CO2 affects plant growth and productivity. CO2 is not only a carbon donor for photosynthesis but also an environmental signal that can perturb cellular redox homeostasis and lead to modifications of redox-sensitive proteins. Although redox regulation of protein functions has emerged as an important mechanism in several biological processes, protein redox modifications and how they function in plant CO2 response remain unclear. Here iodoTMTRAQ proteomics technology was employed to analyze changes in protein redox modifications in Arabidopsis thaliana suspension cells in response to bicarbonate (mimic of elevated CO2) in a time-course study. A total of 47 potential redox-regulated proteins were identified with functions in carbohydrate and energy metabolism, transport, ROS scavenging, cell structure modulation and protein turnover. This inventory of previously unknown protein redox switches in Arabidopsis thaliana bicarbonate responses lays a foundation for future research toward understanding the molecular mechanisms underlying plant CO2 responses.
2017-02-14 | PXD004963 | Pride
Project description:Intact mitochondria purified from Arabidopsis thaliana Col-0 seedlings were differentially labeled with iodoTMTs in the presence of different metabolic substrates. Redox proteomes were analyzed in a substrate depleted state and after addition of citrate and 2-oxoglutarate, providing the oxidation states of individual Cys-peptides.
2020-06-19 | PXD014302 | JPOST Repository
Project description:Redox regulation of auxin and strigolactone signaling in the control of Arabidopsis thaliana root growth
| PRJNA157017 | ENA
Project description:Plants aquire nitrogen from the soil, most commonly in the form of either nitrate or ammonium. Unlike ammonium, nitrate must be reduced (with NADH and ferredoxin as electron donors) prior to assimilation. Thus, nitrate nutrition imposes a substantially greater energetic cost than ammonium nutrition. Our goal was to compare the transcriptomes of nitrate-supplied and ammonium-supplied plants, with a particular interest in characterizing the differences in redox metabolism elicited by different forms of inorganic nitrogen. We used microarrays to compare the short-term transcriptional response to either nitrogen supply or ammonium supply in Arabidopsis roots. Genes upregulated or downregulated by nitrate only, ammonium only, or both ammonium and nitrate were identified and analyzed. Arabidopsis thaliana (Col-0) plants were grown hydroponically until they reached growth stage 5.10. They were then transferred to a nitrogen-free medium for 26 hr and then supplied with 1 mM nitrate or 1 mM ammonium. RNA isolation (and subsequent microarray analysis) was performed on root tissue isolated just before nitrogen supply (time 0) and at 1.5 hr and 8 hr after nitrogen supply (1.5 hr nitrate, 8 hr nitrate, 1.5 hr ammonium, 8 hr ammonium).
2011-05-28 | E-GEOD-29589 | biostudies-arrayexpress
Project description:BackgroundThe elucidation of networks from a compendium of gene expression data is one of the goals of systems biology and can be a valuable source of new hypotheses for experimental researchers. For Arabidopsis, there exist several thousand microarrays which form a valuable resource from which to learn.ResultsA novel Bayesian network-based algorithm to infer gene regulatory networks from gene expression data is introduced and applied to learn parts of the transcriptomic network in Arabidopsis thaliana from a large number (thousands) of separate microarray experiments. Starting from an initial set of genes of interest, a network is grown by iterative addition to the model of the gene, from another defined set of genes, which gives the 'best' learned network structure. The gene set for iterative growth can be as large as the entire genome. A number of networks are inferred and analysed; these show (i) an agreement with the current literature on the circadian clock network, (ii) the ability to model other networks, and (iii) that the learned network hypotheses can suggest new roles for poorly characterized genes, through addition of relevant genes from an unconstrained list of over 15,000 possible genes. To demonstrate the latter point, the method is used to suggest that particular GATA transcription factors are regulators of photosynthetic genes. Additionally, the performance in recovering a known network from different amounts of synthetically generated data is evaluated.ConclusionOur results show that plausible regulatory networks can be learned from such gene expression data alone. This work demonstrates that network hypotheses can be generated from existing gene expression data for use by experimental biologists.
| S-EPMC2760521 | biostudies-literature