Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of phot2 phosphorylation profiles and interaction partners involved in chloroplast accumulation and avoidance responses in Arabidopsis thaliana

ABSTRACT: The project aims to use photocycle mutants to understand the importance of phot2 autophosphorylation for signaling leading to chloroplast accumulation and avoidance. The second part is focused on the identification of new interacting proteins for phot2. Characterization of proteins important for signaling leading to chloroplast avoidance. PHOT2-GFP wild type and PHOT2-V392L-GFP muteins were immunoprecipitated from leaves of transgenic Arabidopsis plants, either dark-adapted or irradiated with low or high blue light. Proteins identified by Mass Spectrometry as interacting with wild-type PHOT2-GFP and PHOT2-V392L-GFP were compared to identify proteins putatively involved in chloroplast avoidance. Phosphorylation profiles of PHOT2-GFP wild type and PHOT2-V392L-GFP were analyzed to distinguish between phosphorylation sites characteristic for chloroplast accumulation and avoidance.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Thaliana (ncbitaxon:3702)

SUBMITTER: Justyna Labuz

PROVIDER: MSV000094308 | MassIVE | Wed Mar 13 06:14:00 GMT 2024

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Shade represses photosynthetic genes by disrupting the DNA binding of GOLDEN2-LIKE1

Project description:The goal of this study is to identify transcriptome changes by the RPGE overexpression or glk1/glk2 double mutant under white light. We compared the transcriptome of RPGE2-OX (35Spro::GFP-RPGE2) with wild type (Col-0) and glk12 (glk1/glk2 double mutant) with wild type in continuous white light to investigate the expression changes of genes which are related with chloroplast development and the relationship between RPGE and GLK in the chloroplast development process.

2023-01-27 | GSE199312 | GEO

Inorganic Carbon Limitation in Cells of the Wild Type and Photorespiratory Mutants of the Cyanobacterium Synechocystis sp. Strain PCC 6803

Project description:The amount of inorganic carbon represents one of the main environmental factors determining productivity of photoautotrophic organisms. Using the model cyanobacterium Synechocystis sp. PCC 6803, we performed a first metabolome study with cyanobacterial cells shifted from high CO2 (5% in air) into conditions of low CO2 (LC; ambient air with 0.035% CO2). Using gas chromatography-mass spectrometry, 74 metabolites were reproducibly identified under different growth conditions. Shifting wild-type cells into LC conditions resulted in a global metabolic reprogramming and involved increases of, for example, 2-oxoglutarate (2OG) and phosphoenolpyruvate, and reductions of, for example, sucrose and fructose-1,6-bisphosphate. A decrease in Calvin-Benson cycle activity and increased usage of associated carbon cycling routes, including photorespiratory metabolism, was indicated by synergistic accumulation of the fumarate, malate, and 2-phosphoglycolate pools and a transient increase of 3-phosphoglycerate. The unexpected accumulation of 2OG with a concomitant decrease of glutamine pointed toward reduced nitrogen availability when cells are confronted with LC. Despite the increase in 2OG and low amino acid pools, we found a complete dephosphorylation of the PII regulatory protein at LC characteristic for nitrogen-replete conditions. Moreover, mutants with defined blocks in the photorespiratory metabolism leading to the accumulation of glycolate and glycine, respectively, exhibited features of LC-treated wild-type cells such as the changed 2OG to glutamine ratio and PII phosphorylation state already under high CO2 conditions. Thus, metabolome profiling demonstrated that acclimation to LC involves coordinated changes of carbon and interacting nitrogen metabolism. We hypothesize that Synechocystis has a temporal lag of acclimating carbon versus nitrogen metabolism with carbon leading.

2015-09-14 | MTBLS5 | MetaboLights

Targeted quantification of phosphorylation sites in S. macrospora wildtype and STRIPAK-mutants

Project description:The composition of the striatin-interacting phosphatases and kinases (STRIPAK) signaling complex is highly similar in all eukaryotes and controls for the phosphorylation and dephosphorylation of target proteins. Associated with STRIPAK are germinal center kinases (GCK), some of which are part of conserved downstream signaling pathways. Using protein samples from wild type and three STRIPAK mutants, we applied absolute quantification by parallel reaction monitoring (PRM) to analyse phosphorylation site occupancies.

2021-04-15 | PXD023130 | panorama

Sigma2 and Sigma6-mediated plastid retrograde signals control nuclear gene expression in Arabidopsis

Project description:Retrograde signaling from the chloroplast to the nucleus is necessary to regulate the chloroplast proteome during development and fluctuating environmental conditions. Although the specific chloroplast process(es) that must occur and the nature of the signal(s) that exits the chloroplast are not well understood, previous studies using drug inhibitors of chloroplast biogenesis have revealed that normal chloroplast development is required to express Photosynthesis Associated Nuclear Genes (PhANGs). In an attempt to determine which specific steps in chloroplast development are involved in retrograde signaling, we analyzed Arabidopsis mutants defective in the six genes encoding sigma factor (Sig) proteins that are utilized by the plastid-encoded RNA polymerase to transcribe specific sets of plastid genes. Here, we demonstrate that both Sig2 and Sig6 have partially redundant roles in not only plastid transcription, but also tetrapyrrole synthesis and retrograde signaling to control PhANG expression. Normal PhANG expression can be partly restored in the sig2 mutant by increasing heme synthesis. Furthermore, there is a genetic interaction between Sig and GUN (genomes uncoupled) genes to generate chloroplast-retrograde signals. These results demonstrate that defective plastid transcription is the source of at least two retrograde signals to the nucleus; one involving tetrapyrrole synthesis and the other involving the accumulation of an unknown plastid transcript. We also propose that the study of sig mutants (with defects in the expression of specific plastid genes) provides a new genetic system, which avoids the use of harsh inhibitors and their potential side effects, to monitor developmental retrograde signaling and to elucidate its mechanisms.

2012-09-18 | E-MTAB-4338 | biostudies-arrayexpress

The comparison for the transcript levels of chloroplast-encoded genes between wild type (Col-0) and pbf8 mutants

Project description:We found that thylakoid-anchored protein PBF8 is a key regulator for Photosystem I (PSI) biogenesis. To explore the role of PBF8 in regulating chloroplast gene expression, we performed the RNA-seq to compare the the transcript levels of chloroplast-encoded genes between wild type (Col-0) and pbf8 mutants. To this end, we isolated the total RNA form 12-day-old wild type and pbf8 seedlings grown on the MS medium under long-day conditions (14 h light, 10 h dark) at 22 ºC and with a light intensity of 80 µmol m-2 s-1. The rRNAs were deleted using the Ribo-Zero Kit (Epicentre). The resulting rRNA-depleted RNA was used for preparing the sequencing library with NEBNext Single Cell/Low input library Prep Kit. The libraries were pooled and sequenced on an Illumina Nova 6000 system with 150-bp pair-end reads. Finally, our results show that the transcript accumulation for chloroplast-encoded PSI subunit and assembly factor genes between the wild type (Col-0) and pbf8 samples, suggesting PBF8 may not affect the transcript levels of chloroplast-encoded PSI subunits and assembly factors in chloroplasts.

2024-01-24 | GSE239827 | GEO

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

ena-DATASET-UCSF-04-08-2016-07:03:04:493-110 - samples

Project description:We expressed PDGFRAmut, wild-type PDGFRA and a GFP control from lentivirus, in two primary GBM patient-derived cell lines that we had cultured as monolayers.

| EGAD00001002269 | EGA

The potential interacting proteins of QQS by IP-MS

Project description:To further examined the potential interacting proteins of QQS in pollen development, we performed IP-MS analysis using Arabidopsis anthers of the wild type, 35S:QQS-Flag and 35S:QQS-GFP lines at flower stage 12-15.

2024-07-20 | PXD038184 | Pride

The Thylakoid Protein NTA1 Is An Assembly Factor of Cytochrome b6f Complex Essential for Chloroplast Development in Arabidopsis

Project description:The cytochrome b6f (Cyt b6f) complex is a multisubunit protein complex in chloroplast thylakoid membranes required for photosynthetic electron transport. Here we report the isolation and characterization of the new tiny albino (nta1) mutant in Arabidopsis, which had severe defects in Cyt b6f accumulation and chloroplast development. Gene cloning unveiled that the nta1 phenotypes were caused by the disruption of a single nuclear gene, NTA1, which encodes an integral thylakoid membrane protein conserved across green algae and plants. Overexpression of NTA1 completely rescued the nta1 phenotypes, while knockout of NTA1 in wild type plants recapitulated the mutant phenotypes. Loss of NTA1 function severely impaired the accumulation of multiprotein complexes related to photosynthesis in thylakoid membranes, particularly the components of Cyt b6f. Furthermore, NTA1 was shown to directly interact with four subunits (Cyt b6/PetB, PetD, PetG and PetN) of Cyt b6f through the DUF1279 domain and C-terminal sequence to mediate their assembly. Taken together, our study identified NTA1 as a new and key regulator of chloroplast development, which plays essential roles in the assembly of Cyt b6f complex through interacting with multiple Cyt b6f subunits.

2023-02-22 | PXD038714 | Pride

Comparision of La-RNA-binding between wild type La and sumoylation deficient La mutant (K41/200R) in HEK293 cells.

Project description:We performed a RNA immunoprecipitations experiments using gfp-specific antibodies to precipitate gfp-tagged La proteins from from gfp-La wild type and sumoylation deficient La mutant (K41/200R) cells and found that specific mRNAs are preferentially enriched gfp-La wild type RIPs when compared to sumoylation deficient La mutant (K41/200R) RIPs.

2017-11-22 | GSE102842 | GEO

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