Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics of Arabidopsis seedlings during de-etiolation

ABSTRACT: Light triggers chloroplast differentiation whereby the etioplast transforms into a photosynthesizing chloroplast and the thylakoid rapidly emerges. However, the sequence of events during chloroplast differentiation remains poorly understood. Here we used whole-seedling proteome data to quantify changes in protein abundances during the course of de-etiolation within the first four days of light exposure. This data complements quantitative lipid and (ultra)structural data described in Pipitone et al. (doi: https://doi.org/10.1101/2020.08.30.274043).

INSTRUMENT(S): Q Exactive HF-X

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

TISSUE(S): Seedling

SUBMITTER: Barbara Pfister

LAB HEAD: Samuel Christian Zeeman

PROVIDER: PXD021518 | Pride | 2021-02-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20190716_002_S200328_T72h_1_72h.raw	Raw
	20190716_003_S200316_T12h_1_12h.raw	Raw
	20190716_004_S200309_T4h_2_4h.raw	Raw
	20190716_005_S200321_T24h_2_24h.raw	Raw
	20190716_007_S200327_T48h_4_48h.raw	Raw

Items per page:

1 - 5 of 38

Similar Datasets

Gene expression in pif1pif3pif4pif5 mutant under dark or red light conditions

Project description:Light initiates the seedling deetiolation transition by promoting major changes in gene expression mainly regulated by phytochrome (phy) photoreceptors. During the initial dark-to-light transition, phy photoactivation induces rapid changes in gene expression that eventually lead to the photomorphogenic development. Recent reports indicate that this process is achieved by phy-induced degradation of Phy-Interacting bHLH transcription Factors (PIFs) PIF1, PIF3 PIF4 and PIF5, which are partly redundant constitutive repressors of photomorphogenesis that accumulate in darkness. In order to test whether light/phy-regulated gene expression occurs through these PIFs, we have performed whole-genome expression analysis in the pif1pif3pif4pif5 quadruple mutant (pifq). Wild-type and pifq mutant seeds were plated on GM medium without sucrose at room temperature. During this procedure the seeds were routinely exposed to white light (WL) for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness, induced to germinate with a 5-min red pulse (Rp) (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before exposure to a terminal 5-min far red pulse (FRp) (58 μmol/m2/s) to suppress pseudo-dark effects. Seeds were then placed in either dark (D) or constant red light (Rc) (6.7 μmol/ m2/s) at 21°C for 45h (2d-old seedlings). Alternatively, 2d-old dark-grown seedlings were treated with 1h of red light (R1) (7.5 μmol/m2/s). Seed samples were harvested after stratification (5d stratified seeds).

2009-10-31 | E-GEOD-17159 | biostudies-arrayexpress

Light- and plastid-regulated transcriptomes in Arabidopsis seedlings

Project description:Plastids emit signals that broadly affect cellular processes. Based on previous genetic analyses, we propose that plastid signaling regulates the downstream components of a light signaling network and that these interactions coordinate chloroplast biogenesis with both the light environment and development by regulating gene expression. We tested these ideas by analyzing light-regulated and plastid-regulated transcriptomes. We found that the plastid is a major regulator of light signaling, attenuating the expression of more than half of all light-regulated genes in our dataset and changing the nature of light regulation for a smaller fraction of these light-regulated genes. Our analyses provide evidence that light and plastid signaling are interactive processes and are consistent with these interactions serving as major drivers of chloroplast biogenesis and function. Four biological replicates were grown separately under the same conditions. Arabidopsis seedlings were grown in the presence (+Lin) or absence (-Lin) of lincomycin in 0.5 µmol m-2 s-1 blue plus red (BR) light for 6 days. After 6 days of growth in 0.5 µmol m-2 s-1 of BR light, seedlings were transferred to 60 µmol m-2 s-1 BR light. 50-100 seedlings were collected before (0 h) and 0.5 h, 1 h, 4 h, and 24 h after the 0.5 to 60 µmol m-2 s-1 BR-fluence-rate shift for RNA extraction and hybridization on Affymetrix microarrays.

2012-03-02 | E-GEOD-24517 | biostudies-arrayexpress

RNA-seq of Arabidopsis thaliana wild-type and a putative chloroplast ribosome biogenesis mutant AtRsgA homozygous knockout

Project description:In this study, we have characterized a putative chloroplast ribosome assembly factor. To elucidate transcriptional responses caused by decreased chloroplast function, we have measured the transcriptome of wild-type and knock-down seedlings.

2018-08-16 | E-MTAB-6866 | biostudies-arrayexpress

Alfalfa_salt_stress_PRM_protomics

Project description:The dataset presented here is about global protein levels in a common alfalfa cultivar, Medicago sativa L. (cv. Nongjing No 1), with exposure to 200mM salt stress for 14 days using parallel proteomics monitoring (PRM) based targeted proteomics approach.

2020-02-18 | PXD017166 | Pride

JHI Hv GC whirly

Project description:The WHIRLY1 protein, which binds to single stranded DNA in plastids and the nucleus, is involved in chloroplast to nucleus signaling but its precise functions remain to be characterized. Here we investigated WHIRLY1 functions in photosynthesis and nitrogen metabolism using transgenic barley lines (W1-1, W1-7 and W1-9) with less than 2% of the wild type WHIRLY1 protein. The WHIRLY1-deficient lines had significantly more leaf chlorophyll with lower chlorophyll a/b ratios and less protein than the wild type when grown with either 5mM KNO3 (nitrogen replete) or 0.1mM KNO3 (nitrogen deficient). Relatively few leaf transcripts were changed in abundance as a result of WHIRLY1 deficiency but a small suite of chloroplast mRNAs was decreased including transcripts encoding proteins of the the NAD(P)H dehydrogenase (NDH) complex. Photosynthesis, stomatal conductance and transpiration were changed in W1-7 leaves compared to the wild type. The W1-7 leaves had significantly less glutamine, threonine, methionine, serine, succinate, fumarate, malate and citrate, as well as decreased transcripts encoding key enzymes of chloroplast amino acid biosynthesis, particularly the branched chain and shikimate pathways. These data demonstrate that Whirly 1 fulfils crucial roles in the regulation of photosynthesis and associated processes such as chloroplast amino acid synthesis

2014-10-01 | E-MTAB-2242 | biostudies-arrayexpress

ccr1-1

Project description:Regulation of carotenoid composition and shoot branching in Arabidopsis by a chromatin modifying histone methyltransferase, SDG8<br>Comparison of transcript profiles between wild type Columbia and ccr1 (carotenoid and chloroplast regulatory) mutant, which contains a mutation in At1g77300 (SDG8)

2009-10-01 | E-MEXP-1787 | biostudies-arrayexpress

Structural re-arrangements of the thylakoid membranes are required for the activation of the Plastid Terminal Oxidase (PTOX) as a safety valve for photoprotection

Project description:Changing climate impacts all aspects of plant physiology, photosynthesis being particularly affected. Weather extremes result in imbalances between light capture and its assimilation, leading to photoinhibition of photosynthesis, which affects plant growth and crop yields. The Plastid Terminal Oxidase (PTOX) has been suggested as a photoprotective safety valve for photosynthesis. However, a photoprotective activity has only been observed in a small number of species and its mode of activation remains elusive. Previous attempts to induce photoprotective PTOX activity in additional species have failed. Here, we show for the first time that photoprotection by PTOX can be transferred to non-extremophile species, and that can reduce photoinhibition and ROS production under stress. Our findings provide a basis for new approaches to redesign photosynthesis using PTOX, to help crops face the challenges raised by the current climate change scenario.

2023-11-28 | E-MTAB-12913 | biostudies-arrayexpress

Impact of rhamnolipids (RLs), natural defense elicitors, on shoot and root proteomes of Brassica napus by a Tandem Mass tags (TMTs) labeling approach

Project description:The rapeseed crop (Brassica napus) is valued mainly for animal feed, food oil and biofuel production. This plant is particularly susceptible to many pathogens like parasitic plants, fungi or animals attacking aerial or root parts. Conventional plant protection products, used intensively in agriculture, have a negative impact on the environment (air and water quality, biodiversity, etc.) as well as on human health. There is therefore a growing demand for the development of new, more planet-friendly alternative protection methods such as biocontrol compounds. Natural rhamnolipids (RLs) can be used as elicitors of plant defense mechanisms. Indeed, these glycolipids, from bacteria secretome, are biodegradable, non-toxic and they are known for their stimulating and protective effects, in particular on rapeseed against filamentous fungi. Characterizing the organ responsiveness to defense stimulating compounds like RLs is missing. This analysis is crucial in the frame of optimizing the effectiveness of RLs against various diseases. A TMT labeling of the proteins extracted from the shoots and roots of B. napus has been performed and showed a differential pattern of protein abundance between them. These results have allowed identifying several protein families possibly involved in the differential responses observed in shoots and roots of rapeseed upon RLs treatment. In particular, quantitative proteomic analysis highlighted differential accumulation of parietal and cytoplasmic defense or stress proteins in response to treatments with RLs with a clear effect of the type of application (foliar spraying or root absorption). These results must be considered for further use of RLs to fight specific rapeseed pathogens.

2023-01-24 | PXD038531 | Pride

Expression data from WT (Columbia) and pifq (pif1pif3pif4pif5) mutant Arabidopsis seedlings

Project description:Plants respond to changes in the red:far red ratio (R:FR) of incident light. A reduction in this ratio (increase in FR) results in the Shade Avoidance Response (SAR) with associated changes in gene expression. The Phyotchrome-Interacting Factors (PIFs) are bHLH transcription factors known to be involved in the SAR. An analysis of changes in gene expression in WT and quadruple pif1pif3pif4pif5 (pifq; Leivar et al., 2008 (PMID 19920208)) mutant seedlings in response to an increase in FR should identify primary targets of PIF signaling. We used microarrays to examine the SAR in WT (Columbia) and pifq mutant Arabidopsis seedlings. Arabidopsis WT and pifq mutant seeds were plated on GM medium without sucrose at room temperature. During this procedure, the seeds were routinely exposed to white light (WL) for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness, and then grown in WL (19 umol/m2/s, R/FR ratio of 6.48) for 2 days at 21°C (WL0 samples). Two-day-old WL-grown seedlings were then maintained in the same fluence rate of WL supplemented with far-red light (WL-FR, R/FR ratio of 0.006) for 1 (FR1), 3 (FR3) or 24 (FR24) hours before harvesting. Control seedlings were also maintained in parallel in the same fluence rate of WL for 24h (WL24) before harvesting. Three different biological replicates of each treatment were grown separately and extracted, processed, and analyzed independently.

2012-08-01 | E-GEOD-28297 | biostudies-arrayexpress

Time-resolved transcript, protein and metabolite profiling of Arabidopsis roots in simulated microgravity

Project description:Arabidopsis seedlings were grown for 1 week in Aradishes and then subjected to 5 min to 10 h of simulated microgravity using a 2D clinostat. RNA; proteins and metabolites were extracted and analyzed by RNA.seq and label free quantitative MS.

2022-12-31 | E-MTAB-4873 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data