Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Absolute quantification of selected photosynthetic electron transfer proteins in Chlamydomonas reinhardtii in the presence and absence of oxygen

ABSTRACT: The absolute amount of plastocyanin (PC), ferredoxin-NADP+-oxidoreductase (FNR), hydrogenase (HYDA1) and ferredoxin 5 (FDX5) were quantified in aerobic and anaerobic Chlamydomonas reinhardtii whole cells using purified (recombinant) proteins as internal standard in a mass spectrometric approach. Quantified protein amounts were related to the estimated amount of PSI. The ratios of PC to FNR to HYDA1 to FDX5 in aerobic cells were determined to be 2.1 : 1.8 : 0.005 : 0. In anaerobic cells, the ratios changed to 1.6 : 1.8 : 0.026 : 0.04 (PC : FNR : HYDA1 : Fdx5). Employing sodium dithionite and methyl viologen as electron donors the specific activity of hydrogenase in whole cells was calculated to be 382 ±96.5 μmolH2/min/mg. Importantly, these data demonstrate for competition of electrons from FDX1, HYDA1 is about 70-fold less abundant than its competitor FNR. Effective in vivo hydrogen production points to a channeling mechanism for FDX to HYDA1 electron transfer.

INSTRUMENT(S): LTQ Orbitrap XL

ORGANISM(S): Chlamydomonas Reinhardtii

TISSUE(S): Whole Body

SUBMITTER: Denitsa Nikolova

LAB HEAD: Michael Hippler

PROVIDER: PXD008313 | Pride | 2022-02-23

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	050320152ndHYDAE01-joined.csv	Csv
	050320152ndHYDAE01-qtrace-results.csv	Csv
	050320152ndHYDAE02-joined.csv	Csv
	050320152ndHYDAE02-qtrace-results.csv	Csv
	050320152ndHYDAE03-joined.csv	Csv

Items per page:

1 - 5 of 193

Similar Datasets

Genome wide effects of maternal undernutrition

Project description:DNA methylation profiles of the livers of 1 day old rats from mothers fed with three different diets during gestation. The first animal group was fed with a normal diet (c=control); second group received much less protein than normal and slighlty more carbs (p=low protein, or programmed); third group diet was same as low protein but with extra folic acid (f=low protein+folate). All diets were matched for energy. Genomic DNA from rat livers was subjected to selection according to the methyl-CpG binding domain-based (MBD) protein protocol (DNA pooled from 6 individuals per group) and the resulting fragments sequenced in high throughput. Methylated DNA was captured with MethylCap kit (Diagenode). Approximately 10 ng of captured DNA was used for library preparation (ChIP-seq DNA sample Prep Kit, Illumina).

2014-05-20 | E-GEOD-50935 | biostudies-arrayexpress

Repurposing human kinase inhibitors to create an antibiotic active against drug-resistant Staphylococcus aureus

Project description:To combat methicillin-resistant Staphylococcus aureus (MRSA) infections novel drugs are desperately needed. From a screen, we found that the anti-cancer drug sorafenib effectively kills MRSA strains. By synthetic variation of key structural features, we identified a potent analog, PK150, exhibiting activities against several pathogenic strains at sub-micromolar concentrations. The antibiotic induced rapid killing of S. aureus, including challenging persisters, and eradicated established biofilms. PK150 holds promising therapeutic potential as it did not induce in vitro resistance and exhibited oral bioavailability and in vivo efficacy. Mode of action analysis by chemical proteomics revealed several targets, including interference with menaquinone biosynthesis by inhibiting demethylmenaquinone methyltransferase and stimulation of protein secretion by altering the activity of signal peptidase IB. Reduced endogenous menaquinone levels along with enhanced levels of extracellular proteins of PK150-treated bacteria support this hypothesis. The associated antibiotic effects, especially the lack of resistance development, likely stem from the compound’s polypharmacology attribute.

2019-09-09 | PXD012946 | Pride

miRNA expression data from human high and low risk prostate carcinoma

Project description:miRNA expression of 6 high risk and 8 low risk prostate carcinoma were compared to the expression of 6 benign prostatic hyperplasia. Keywords: expression profile We used microarrays to detail the global programme of miRNA expression underlying tumorigenesis and tumor progression and identified dysregulated genes during this process

2011-07-31 | E-GEOD-18671 | biostudies-arrayexpress

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

Project description:Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. We present a protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing. This ribosome profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. Additionally, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, we describe an adaptation that reveals the sites of translation initiation by pre-treating cells with harringtonine to immobilize initiating ribosomes. The protocol we describe requires 5 - 7 days to generate a completed ribosome profiling sequencing library. Ribosome profiling in cultured mammalian cells under three different footprinting conditions

2012-07-26 | E-GEOD-37744 | biostudies-arrayexpress

DIA data analysis with unambiguously determined precursor mass

Project description:Proteomics research today no longer simply seeks exhaustive protein identification; now, robust, large-scale quantitative information is sought. For this purpose, data-independent acquisition (DIA) has emerged as a promising strategy largely owing to the developments in advanced mass spectrometers and sophisticated data analysis methods. However, the highly complex multiplexed MS/MS spectra produced by DIA remain challenging to interpret. Here, we present a novel strategy to analyze DIA data, based on unambiguous precursor mass assignment through the mPE-MMR (multiplexed post-experimental monoisotopic mass refinement) procedure, and combined with complementary multi-stage database searching. Compared to conventional spectral library searching, the accuracy and sensitivity of peptide identification were effectively increased by assigning precise precursor masses to DIA data. Additional peptides absent from spectral libraries, including sample-specific mutated peptides and post-translationally-modified peptides, were identified by MS-GF+ and MODa/MODi multi-stage database searching with the precursor masses determined. This first use of unambiguously-determined precursor masses to mine DIA data demonstrates considerable potential for further exploitation of this rich experimental data.

2019-08-19 | PXD012744 | Pride

VL30 retro-transposons are TRIM24-repressed enhancers that generate non-coding RNA to regulate gene expression in mouse hepatocytes. [RNA-Seq]

Project description:TRIM24 and TRIM33 interact to form a corepressor complex that suppresses murine hepatocellular carcinoma (HCC). TRIM24 and TRIM33 cooperatively repress retinoic acid receptor dependent activity of VL30 retro-transposons in hepatocytes in vivo. In TRIM24 knockout hepatocytes, VL30 long terminal repeats (LTRs) generate enhancer (e)RNAs and act as surrogate promoter and enhancer elements deregulating expression of neighbouring genes. We show that a VL30 LTR-derived eRNA is essential to activate the lipocalin 13 gene in hepatocytes in vivo. A further consequence of VL30 de-repression is the accumulation of retro-transcribed VL30 DNA in the cytoplasm of TRIM24-mutant hepatocytes and activation of the viral defence/interferon response. VL30 activation therefore modulates gene expression via the enhancer activity of the LTRs and by activation of the interferon response. Both of these processes are genetically linked to HCC development suggesting that VL30 repression by TRIM24 plays an important role in tumour suppression. RNA profiles in liver of wild type (WT) and Trim24-/- mice by deep sequencing using Illumina GAIIx.

2013-01-01 | E-GEOD-39851 | biostudies-arrayexpress

TAF4 promotes pre-initiation complex formation and HNF4A occupancy of regulatory elements required to activation post-natal gene expression programme in hepatocytes (RNA-seq)

Project description:The nuclear receptor HNF4A regulates embryonic and post-natal hepatocyte gene expression. Using hepatocyte-specific inactivation in mice, we show that the TAF4 subunit of TFIID acts as a cofactor for HNF4A in vivo and that HNF4A interacts directly with the TAF4-TAF12 heterodimer in vitro. In vivo, TAF4 is required to maintain HNF4A-directed embryonic gene expression at post-natal stages and for HNF4A-directed activation of post-natal gene expression. TAF4 promotes HNF4A occupancy of functional cis-regulatory elements located adjacent to the transcription start sites of post-natal expressed genes and for pre-initiation complex formation required for their expression. Promoter-proximal HNF4A-TFIID interactions are therefore required for pre-initiation complex formation and stable HNF4A occupancy of regulatory elements as two concomitant mutually dependent processes. RNA profiles in wild-type and Taf4-/- livers by deep sequencing

2014-09-25 | E-GEOD-57712 | biostudies-arrayexpress

The C-terminal tail of polycystin-1 suppresses cystic disease in a mitochondrial enzyme-dependent fashion

Project description:Autosomal dominant polycystic kidney disease (ADPKD) is the most prevalent potentially lethal monogenic disorder. Mutations in the PKD1 gene, which encodes polycystin-1 (PC1), account for approximately 78% of cases. PC1 is a large 462-kDa protein that undergoes cleavage in its N and C-terminal domains. C-terminal cleavage produces fragments that translocate to mitochondria. We show that transgenic expression of a protein corresponding to the final 200 amino acid (aa) residues of PC1 in two Pkd1-KO orthologous murine models of ADPKD suppresses cystic phenotype and preserves renal function. This suppression depends upon an interaction between the C-terminal tail of PC1 and the mitochondrial enzyme Nicotinamide Nucleotide Transhydrogenase (NNT). This interaction modulates tubular/cyst cell proliferation, the metabolic profile, mitochondrial function, and the redox state. Together, these results suggest that a short fragment of PC1 is sufficient to suppress cystic phenotype and open the door to the exploration of gene therapy strategies for ADPKD.

2023-02-17 | PXD040210 | Pride

Transcription profiling of rat liver exposed to methapyrilene - ILSI-HESI Hepatotoxicity Study: methapyrilene

Project description:This study examines the effects of an hepatotoxicant, Methapyrilene (CAS:91-80-5, CHEBI:6820). on hepatic gene expression in the Sprague-Dawley rat. Rats were treated with two dose levels of the compound for up to seven days. Gene expression profiles were generated using several different microarray platforms for an inter-laboratory comparison.

2005-07-16 | E-TOXM-14 | biostudies-arrayexpress

Transcription profiling of rat kidney exposed to different doses of Cisplatin- ILSI-HESI NephroToxicity Study - Cisplatin

Project description:Evaluation and comparison of biological responses of rats and gene expression responses of the kidney in rats exposed to different doses of Cisplatin [CAS:15663-27-1;CHEBI:27899]

2007-01-10 | E-TOXM-11 | biostudies-arrayexpress