Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantification of proteins and oxidized proteins in wild type and CLPP deficient mouse heart mitochondria.

ABSTRACT: We studied consequences of CLPP deletion to mitochondrial proteome and redox-proteome.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Heart

SUBMITTER: Ilka Wittig

LAB HEAD: Aleksandra Trifunovic

PROVIDER: PXD017464 | Pride | 2020-03-05

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	P18_033_Nmodule_Redox_2nd_FullProteome_KO1_B.raw	Raw
	P18_033_Nmodule_Redox_2nd_FullProteome_KO1_C.raw	Raw
	P18_033_Nmodule_Redox_2nd_FullProteome_KO1_D.raw	Raw
	P18_033_Nmodule_Redox_2nd_FullProteome_KO1_E.raw	Raw
	P18_033_Nmodule_Redox_2nd_FullProteome_KO2_B.raw	Raw

Items per page:

1 - 5 of 51

Publications

A salvage pathway maintains highly functional respiratory complex I.

Szczepanowska Karolina K Senft Katharina K Heidler Juliana J Herholz Marija M Kukat Alexandra A Höhne Michaela Nicole MN Hofsetz Eduard E Becker Christina C Kaspar Sophie S Giese Heiko H Zwicker Klaus K Guerrero-Castillo Sergio S Baumann Linda L Kauppila Johanna J Rumyantseva Anastasia A Müller Stefan S Frese Christian K CK Brandt Ulrich U Riemer Jan J Wittig Ilka I Trifunovic Aleksandra A

Nature communications 20200402 1

Regulation of the turnover of complex I (CI), the largest mitochondrial respiratory chain complex, remains enigmatic despite huge advancement in understanding its structure and the assembly. Here, we report that the NADH-oxidizing N-module of CI is turned over at a higher rate and largely independently of the rest of the complex by mitochondrial matrix protease ClpXP, which selectively removes and degrades damaged subunits. The observed mechanism seems to be a safeguard against the accumulation ...[more]

PMID: 32242014

Similar Datasets

Quantification of oxidized proteins in wild type and Nox2 deficient mouse dorsal root ganglia

Project description:Here we studied the NOX2 dependent redox-proteome in dorsal root ganglia in mice. The overall goal was to assess the degree of NOX2-dependent changes in oxidised proteins following exposure to enriched enviroment and sciatic nerve axotomy in dorsal root ganglia.

2020-10-13 | PXD018085 | Pride

Protein expression and oxidation in the hippocampus of neuronal nucleoredoxin knockout (Nestin-NXN-/-) versus floxed control mice (NXN-flfl)

Project description:Nucleoredoxin (NXN) is a thioredoxin-like member of the large group of redoxins which maintain redox balances in the cell. Its primary localization is the cytoplasm, and it is highly expressed in neurons. It has been described as a redox regulator of WNT signaling via maintenance of the redox balance of Disheveled (Dvl). Previous proteomic analyses in NXN-knockdown SH-SY5Y cells found a high fraction of reduced proteins involved in development and cell differentiation. The results suggested NXN mainly acted as oxidase under the culture conditions. The functions in vivo are not known, but full deletion of NXN is embryonically lethal owing to cranial deformities. We have generated mice with a pan-neuronal Nestin-Cre driven deletion of NXN (Nestin-NXN-/-) to study its functions in neurons. Nestin-NXN-/- develop normally and are healthy up to old age. They show a loss of exploratory and playful behavior but have no deficits of cognitive functions, social behavior or readouts of anxiety. Using a Yeast-2-Hybrid screen, calcium calmodulin kinase 2a was identified as interaction partner. Camk2a is crucial for long-term potentiation and thereby learning and memory but is also associated with psychiatric diseases, and it is regulated via redox modification of cysteines that impact on the autophosphorylation status of a critical threonine. Camk2a colocalized and co-precipitated with NXN and its activity depended on the presence of NXN. To further study the functions of NXN in neurons we performed a proteomic screen of the hippocampal proteome and the redox proteome using the BIAM switch method.

2021-09-10 | PXD024624 | Pride

Quantification of sulfenic acid on model protein

Project description:Aldolase contains eight free cysteine residues without disulfide formation in its native state, which makes it a suitable model to manipulate the oxidative modifications on cysteine. H2O2 was chosen to treat aldolase since the principle product between which is sulfenic acid.To assess the reduction of the newly formed sulfenic acids on aldolase by arsenite, a differential alkylation strategy was adapted.To further investigate the formation of other reversible cysteine oxidations such as disulfide on aldolase, arsenite was replaced by DTT in the differential alkylation method to reduce all the reversible cysteine oxidations.To further validate the selectivity of the reducing ability of arsenite on sulfenic acid but not other oxidative modifications especially disulfide, lysozyme was employed in the differential alkylation method. Lysozyme has 8 cysteine residues all bound into disulfide bonds, thereby was not treated with H2O2 to avoid further oxidation.

2016-10-10 | PXD003348 | Pride

Genome-wide maps of chromatin state in HSC, Pro B and mature B cells

Project description:We have used a genome-wide ChIP-sequencing approach to define and investigate the dynamics of the cis-regulatory landscape in three developmental stages of the murine hematopoietic system. To this end, we have compared the profiles of H3K4me3, H3K4me1, H3K27ac, H3K27me3 and H3K9me2 in HSCs, committed pro-B and splenic mature B cells. We find the enhancer repertoire to be dynamically reshaped during hematopoiesis progression, surprisingly only a small fraction of primed enhancers in HSCs or committed progenitors become activated in subsequent stages. In turn, the majority of active enhancers in terminally differentiated cells are not primed in earlier stages. We also found that The heterochromatin mark H3K9me2 covers large domains that remain largerly invariant across the three stages and are depleted in both active chromatin marks and the Polycomb related mark H3K27me3. Investigating enhancer dynamics in 3 different stages of B cell development

2015-10-19 | E-GEOD-60005 | biostudies-arrayexpress

Coordinated miRNA activity mediates the cellular transition into dormancy during embryonic diapause

Project description:Dormancy is a key feature of stem cell function in adult tissues as well as embryonic cells in the context of diapause. The establishment of dormancy is an active process that involves extensive transcriptional, epigenetic, and metabolic rewiring. How these processes are coordinated to successfully transition cells to the resting dormant state is not known. Here we show that microRNA activity, which is normally dispensable for pre-implantation development, is essential for the adaptation of early mouse embryos to the dormant state of diapause. In particular, the pluripotent epiblast depends on miRNA activity, the absence of which results in loss of pluripotency and embryo collapse. Through tissue-specific small RNA profiling of single embryos and computational analyses of miRNA targets, we identified the miRNA-protein network of diapause. Individual miRNA function contributes to combinatorial regulation by the network of most notably RNA processing and chromatin modifier proteins. Without miRNAs, multiple nuclear and cytoplasmic bodies show aberrant expression and structure in normal ESCs and fail to reorganize in response to stress. We find extensive alternative splicing in wild-type, but not miRNA-deficient ESCs, of cell cycle and metabolic regulators. Our results reveal that miRNAs are critical for the transcriptional and structural rewiring of pluripotent cells in response to stress and to establish dormancy in the pluripotent state.

2024-03-26 | PXD044550 | Pride

ChIP-Seq of fly Schneider S2 cells to investigate CID islands

Project description:The centromere-specific Histone H3-variant CENH3 (also known as CENP-A) is considered to be an epigenetic mark for establishment and propagation of centromere identity. Pulse-induction of CENH3 (Drosophila CID) in Schneider S2 cells incorporates into noncentromeric regions and generates CID islands that resist clearing from chromosome arms for multiple cell generations. We demonstrate that CID islands represent functional ectopic kinetochores, which are non-randomly distributed on the chromosome and display a preferential localization near telomeres and pericentric heterochromatin in transcriptionally silent, intergenic chromatin domains. Although overexpression of heterochromatin protein 1 (HP1) or increasing Histone acetylation interferes with CID islands formation on a global scale, induction of a locally defined region of synthetic heterochromatin by targeting HP1-LacI fusions to stably integrated Lac Operator arrays produces a proximal hotspot for CID islands formation. These data suggest that the characteristics of regions bordering heterochromatin promote de novo kinetochore assembly and thereby contribute to centromere identity.

2011-07-15 | E-MTAB-652 | biostudies-arrayexpress

3D-printed wound dressings containing a fosmidomycin-derivative prevent Acinetobacter baumannii biofilm formation in vitro and in vivo

Project description:Two Acinetobacter baumannii strains with low susceptibility to fosmidomycin and two reference with high susceptibility to fosmidomycin were DNA-sequenced to investigate the genomic determinants of fosmidomycin resistance.

2022-12-21 | E-MTAB-12357 | biostudies-arrayexpress

Mutant Huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure

Project description:Expansion of the poly-glutamine (Q) tract in the protein Huntingtin (HTT) causes the neurodegenerative disorder Huntington’s disease (HD). Emerging evidence suggests that mutant HTT (mHTT) disrupts brain development. To gain mechanistic insights into the neurodevelopmental impact of human mHTT, we engineered induced pluripotent stem cells to introduce a 70Q expansion or remove the poly-Q tract. mHTT introduction caused aberrant development of cerebral organoids with loss of neural progenitor organization. The early neurodevelopmental signature of mHTT highlighted the dysregulation of coiled-coil-helix-coiled-coil-helix domain containing 2 (CHCHD2), which is involved in mitochondrial integrated stress response. CHCHD2 repression was associated with abnormal mitochondrial morpho-dynamics and elevated resting energy expenditure. Elimination of the poly-Q tract reverted CHCHD2 expression and mitochondrial defects. Hence, mHTT-mediated disruption of human neurodevelopment is paralleled by aberrant neurometabolic programming mediated by dysregulation of CHCHD2, which could then represent a target of early intervention for HD.

2024-06-21 | PXD041846 | Pride

Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human brain

Project description:5-hydroxymethylcytosine (5-hmC) is a newly discovered modified form of cytosine that has been suspected to be an important epigenetic modification in neurodevelopment. While DNA methylation dynamics have already been implicated during neurodevelopment, little is known about hydroxymethylation in this process. Here we report DNA hydroxymethylation dynamics during cerebellum development in the human brain. Overall, we find a positive correlation between 5-hmC levels and cerebellum development. Genome-wide profiling reveals that 5-hmC is highly enriched on specific gene regions, including exons and especially the untranslated regions (UTRs), but it is depleted on introns and intergenic regions. Furthermore, we have identified fetus-specific and adult-specific differentially hydroxymethylated regions (DhMRs), most of which overlap with genes and CpG island shores. Surprisingly, during development DhMRs are highly enriched in genes encoding mRNAs that can be regulated by fragile X mental retardation protein (FMRP), some of which are disrupted in autism, as well as in many known autism genes. Our results suggest that 5-hmC-mediated epigenetic regulation may broadly impact the development of the human brain, and its dysregulation could contribute to the molecular pathogenesis of neurodevelopmental disorders. We generated comprehensive genome-wide profiles of 5hmC in human cerebellum.

2012-09-30 | E-GEOD-40539 | biostudies-arrayexpress

‘Shotgun’ Proteome Analyses Do Not Require Alkylation of Cysteine

Project description:It is a common belief that reduction of disulfide bridges and alkylation of thiols in proteins are indispensable steps in proteomic sample preparation. Since this chemical procedure is often incomplete and prone to side reactions and can results in various artefacts we reexamined its importance. We found that the reduction and alkylation do not increase the depth of analysis and quality of proteomic quantification therefore these steps are unessential in shotgun-type investigations of proteomes. Moreover, we found that compared to a standard procedure using iodoacetamide for thiol-alkylation, sample preparation under conditions protecting thiols from oxidation improves quality of peptides and allows identifying of 10-20% more peptides and proteins. Excluding the thiol-alkylation from proteomic sample preparation, shorten the workflows, and decreases the probability of biases resulting from occurrence of artificially modified peptides.

2020-01-21 | PXD014000 | Pride

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