Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

YBEY is an essential biogenesis factor for mitochondrial ribosomes

ABSTRACT: The aim was to evaluate the protein composition of human mitoribosomes in YBEY knockout cells. We compared the parental cell line HEK293T-REx with the YBEY knockout cells HEK293T-RExΔYBEY.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Early Embryonic Cell

DISEASE(S): Mitochondrial Metabolism Disease

SUBMITTER: Goran Mitulović

LAB HEAD: Goran Mitulovic

PROVIDER: PXD015310 | Pride | 2020-03-02

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	C7_8C_KO3_1.raw	Raw
	C7_8C_KO3_1_A.raw	Raw
	C7_8C_KO3_2_A.raw	Raw
	C7_8C_KO3_3_A.raw	Raw
	F6_8C_KO2_1.msf	Msf

Items per page:

1 - 5 of 33

Publications

YBEY is an essential biogenesis factor for mitochondrial ribosomes.

Summer Sabrina S Smirnova Anna A Gabriele Alessandro A Toth Ursula U Fasemore Akinyemi Mandela AM Förstner Konrad U KU Kuhn Lauriane L Chicher Johana J Hammann Philippe P Mitulović Goran G Entelis Nina N Tarassov Ivan I Rossmanith Walter W Smirnov Alexandre A

Nucleic acids research 20200901 17

Ribosome biogenesis requires numerous trans-acting factors, some of which are deeply conserved. In Bacteria, the endoribonuclease YbeY is believed to be involved in 16S rRNA 3'-end processing and its loss was associated with ribosomal abnormalities. In Eukarya, YBEY appears to generally localize to mitochondria (or chloroplasts). Here we show that the deletion of human YBEY results in a severe respiratory deficiency and morphologically abnormal mitochondria as an apparent consequence of impaired ...[more]

PMID: 32182356

Similar Datasets

Mitochondrial phosphoproteomes are functionally specialized across tissues

Project description:Mitochondria are essential organelles involved in critical biological processes such as energy metabolism and cell survival. Their dysfunction is linked to numerous human pathologies that often manifest in a tissue-specific manner. Accordingly, mitochondria fitness depends on versatile proteomes specialized to meet diverse tissue-specific requirements. Furthermore, increasing evidence suggests that phosphorylation may also play an important role in regulating tissue-specific mitochondrial functions and pathophysiology. We hypothesized that recent advances in mass spectrometry (MS)-based proteomics would now enable in-depth measurement toof quantitatively profile mitochondrial proteomes along with their matching phosphoproteomes across tissues. We isolated mitochondria from mouse heart, skeletal muscle, brown adipose tissue, kidney, liver, brain, and spleen by differential centrifugation followed by separation on Percoll gradients and high resolution MS analysis of the proteomes and phosphoproteomes. This in-depth map substantially quantifies known and predicted mitochondrial proteins and provides a resource of core and tissue modulated mitochondrial proteins (mitophos.biochem.mpg.de). We also uncover tissue-specific repertoires of dozens of kinases and phosphatases. Predicting kinase substrate associations for different mitochondrial compartments indicates tissue-specific regulation at the phosphoproteome level. Illustrating the functional value of our resource, we reproduce mitochondrial phosphorylation events on DRP1 responsible for its mitochondrial recruitment and fission imitation initationinitiation and describe phosphorylation clusters on MIGA2 linked to mitochondrial fusion.

2023-11-03 | PXD030062 | Pride

Understanding the role of yeast Yme1 in mitochondrial finction using biochemical and proteomics analysis

Project description:Mitochondrial proteome comparison between S. cerevisiae BY4741 WT and Yme1 deletion mutant. Mitochondria were isolated by fractionation as described by Titorenko et al. (2009). Briefly, cells were grown in YPGal and harvested at later exponential phases of OD ~1.5. After pre- treatment with DTT buffer (100 mM Tris-H 2 SO 4 pH 9.4, 10 mM DTT) at 30°C for 20 minutes, the cell wall was digested with zymolyase 20T (Seikagaku Corporation, Japan) in zymolyase buffer (20mM potassium phosphate buffer pH 7.4, 1.2M sorbitol) for 1 hour at 30˚ with shaking at 70 rpm. The resulting spheroblasts were checked under a light microscope to confirm cell wall digestion. Then, the spheroblasts were lysed in homogenization buffer (20mM HEPES-KOH pH7.4, 0.6M sorbitol, 1mM phenylmethylsulfonyl fluoride (PMSF)) on- ice using a glass Teflon homogenizer. The resulting spheroblasts were subjected to two centrifugation steps at 1500 ×g to remove the cell debris and nuclei. Crude mitochondrial materials were isolated from the supernatant by centrifugation at 12,000 ×g at 4˚C for 10 minutes, then resuspended in SEM buffer (250mM sucrose, 0.6M Sorbitol, 20mM HEPES- KOH pH7.4). Protein concentration were checked by measuring absorbance at 280 nm, assuming an absorbance value of A280=0.21 would equate to 10 mg/ml of crude mitochondrial extract. After adjusting to final concentration of 10 mg/ml the crude mitochondria were then flash frozen and stored at −80°C.

2022-11-11 | PXD036367 | Pride

A proteomics approach to study the role of lipid droplets in plant defense

Project description:Lipid Droplets (LDs), classically viewed as lipid storage particles, are recently emerging as dynamic organelles associated with stress responses and development; however, their involvement in plant immunity has been little investigated. Here we studied LDs in Arabidopsis thaliana leaves that respond to Pseudomonas syringae pv. tomato DC3000 avrRpm1 by inducing a hypersensitive defense reaction (HR), as well as during senescence. We established a protocol to reproducibly isolate LDs from a limited amount of tissue and performed a proteomic analysis of LDs from Pseudomonas-infected (for 24 h and 72 h) and senescent leaves. The proteomes defined shared ~50% similarity, with an enrichment of proteins associated with the Gene Ontology terms “transport” and “responses to stress”. As validation, we confirmed LD localization of glycerol-3-phosphate-acetyltransferase 8 (GPAT8) and GPAT4, enzymes required for e.g., cutin biosynthesis, by transient expression of GFP fusions in HR-induced leaves of Nicotiana benthamiana. Similarly, we proved the localization to LDs of aldehyde dehydrogenase 3F1 (ALDH3F1), α-dioxygenase1 (α-DOX1) and caleosin3 (CLO3), all involved in the synthesis of fatty acid derivatives. Moreover, we found that PAD3 (phytoalexin deficient 3) was distributed in patches along the ER and plasma membrane, and in LDs near dead cells. The nature of these proteins and of the additional components characterized in the LDs, together with the phenotypic examination of selected mutants, established a functional link between LDs and plant immunity. Our data suggest that these organelles participate in protein trafficking and in lipid changes that affect the interaction of plants with invading pathogens.

2022-02-23 | PXD011499 | Pride

Cryphonectria parasitica mitochondria LC-MS/MS

Project description:Here we report a comprehensive and comparative study comprising mitochondrion quantification, reactive oxygen species (ROS) and respiratory efficiency, and quantitative mitochondrial proteomics of the wild-type and virus-infected strains of the chestnut blight fungus. Our data show that hypovirus infection increases the total number of mitochondria, lowers the general ROS level, but increases the mitochondrial respiratory efficiency. Quantification of mitochondrial proteomes revealed that a set of proteins functioning in energy metabolism and mitochondrial morphogenesis as well as virulence were regulated by the virus.

2023-10-24 | PXD041756 | Pride

RB is a cell cycle-regulated repressor of cohesin-dependent loop formation

Project description:Chromatin organization and cell cycle are tightly intertwined in eukaryotes, but the underlying mechanisms remain unclear. We investigated how the retinoblastoma protein (RB), a key cell cycle regulator, influences chromatin architecture. Chromosome conformation capture assays reveal that RB loss increases the number and size of cohesin-dependent loops and strengthens topologically associating domains (TADs). RB shows extensive colocalization with cohesin in the human genome, and it impacts cohesin’s distribution on chromatin. Active RB evicted cohesin from RB-bound TAD boundaries, repressed insulator activity, and enhanced the expression of non-E2F target genes that are important for cell adhesion. We conclude that RB has a central role in the interplay between cell cycle and chromatin organization. This role safeguards chromatin architecture and controls transcription.

2024-11-01 | E-MTAB-13566 | biostudies-arrayexpress

Cardiac Atrial Compartmentalisation Proteomics: A Modified Density Gradient Method to Analyse Endo-lysosomal Proteins

Project description:Evidence that lysosomes are important in cardiac physiology and pathology is now emerging. We describe a label-free method suitable for small cardiac tissue biopsies based on a density-separated fractionation protocol, which allows us to study endo-lysosomal (EL) proteins in guinea pig atria. The three most relevant density gradient fractions obtained were analysed using Western Blot, enzyme activity assay and MS/MS peptide analysis (adapted discontinuous Percoll, and sucrose differential density gradient). These fractions comprise whole tissue lysate; sarcoplasmic reticulum (SR), mitochondrial proteins (Mito) (1.3 g/mL); and ‘pure’ EL with negligible contamination from SR or Mito (1.04 g/mL). Kyoto Encyclopedia of Genes and Genomes, Reactome, Panther and Gene Ontology pathway analysis showed good coverage of RAB proteins, lysosomal cathepsins (including cardiac-specific cathepsin D) in the purified EL fraction. The most significant EL proteins recovered included catalytic activity proteins. We thus present a comprehensive protocol and dataset of guinea-pig atrial EL focussed organelle proteomics

2021-09-09 | PXD021277 | Pride

Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues

Project description:We have identified tens of thousands of short extrachromosomal circular DNAs (microDNA) in mouse tissues as well as mouse and human cell lines. These microDNAs are 200-400 bp long, derived from unique non-repetitive sequence and are enriched in the 5' untranslated regions of genes, exons and CpG islands. Chromosomal loci that are enriched sources of microDNA in adult brain are somatically mosaic for micro-deletions that appear to arise from the excision of microDNAs. Germline microdeletions identified by the "Thousand Genomes" project may also arise from the excision of microDNAs in the germline lineage. We have thus identified a new DNA entity in mammalian cells and provide evidence that their generation leaves behind deletions in different genomic loci. Circular DNA profiling by high throughput sequencing

2012-02-27 | E-GEOD-36088 | biostudies-arrayexpress

DNA-seq of mitochondrial DNA from liver of OGG1 and MUTYH deficient mice that have been bred for five consecutive generations

Project description:Studying whether removal of base-excision repair from mitochondria will result into increase in mitochondrial DNA (mtDNA) mutation load. The endogenous genes of OGG1 and MUTYH DNA glycosylases were modified to lack the genomic region encoding for the predicted mitochondrial targeting sequence. The mouse lines used: A mouse line that lacks the region encoding for the mitochondrial targeting sequence (L2 to W23) of OGG1 (Ogg1 dMTS mice). A mouse line that lacks the region encoding the mitochondrial targeting sequence (K2 to P33) of MUTYH (Mutyh dMTS mice). To accumulate mutations to the mitochondrial DNA these mice were bred double homozygous Mutyh dMTS x Ogg1 dMTS mice as a maternal lineage for five consecutive generations and mitochondrial DNA from liver was extracted from the offspring and sequenced with Illumina. OGG1 and MUTYH are involved in repair of 8-oxo-dG from DNA. 8-oxo-dG can be a mutagenic lesion because some DNA repair polymerases are known to erroneously incorporate adenosine opposite to 8-oxo-dG during replication leading to GC>TA transversion mutations.

2018-07-13 | E-MTAB-6532 | biostudies-arrayexpress

High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins

Project description:At every cell cycle, faithful inheritance of metazoan genomes requires the concerted activation of thousands of DNA replication origins. However, which genetic and chromatin features define metazoan replication start sites remains largely unknown. Here, we delineate the origin repertoire of the Drosophila genome at high resolution. We address the role of origin-proximal G-quadruplexes and show their ability to transiently stall replication forks in vivo. We dissect the chromatin configuration of replication origins and identify a rich spatial organization of chromatin features at initiation sites. DNA shape and chromatin configurations, not strict sequence specificity, mark and predict replication origins in higher eukaryotes. We further examine the link between transcription and origin firing and reveal that modulation of origin activity across cell types is intimately linked to cell-type-specific transcriptional programs. Our study unravels conserved origin features and provides unique insights into the relationship between DNA topology, chromatin, transcription and replication initiation across metazoa. Our dataset consists of SNS-Seq profiles in Drosophila S2 and Bg3 cells. Small nascent leading strands (SNS) have been purified with an enhanced sensitivity SNS purification protocol. For standard SNS-Seq experiments (from pooled gradient fractions, denoted as "pool"), SNS were purified from two biological replicates. For single-fraction SNS-Seq experiments, two libraries were prepared for each fraction. The genomic coordinates of S2 and Bg3 replication origins are also provided.

2015-04-23 | E-GEOD-65692 | biostudies-arrayexpress

Proteome profiling of extracellular vesicles from neurosurgical aspirates identifies CCT6A as a potential glioblastoma biomarker with prognostic significance

Project description:Glioblastoma, WHO-grade IV glioma, carries a dismal prognosis owing to its infiltrative growth rates and limited treatment options. Glioblastoma-derived extracellular vesicles (EVs; 30-1000nm membranous particles) influence the microenvironment to mediate tumour aggressiveness and carry oncogenic cargo across the blood-brain-barrier into the circulation. As such, EVs are biomarker reservoirs with enormous potential for assessing glioblastoma tumours in situ. Neurosurgical aspirates are rich sources of EVs, isolated directly from glioma microenvironments. Quantitative LC-MS/MS compared EV proteomes enriched from glioblastoma (n=15) and glioma grade II-III (n=7) aspirates and identified 298 differentially-abundant proteins (p-value<0.00496). Along with previously reported glioblastoma-associated biomarkers, levels of all eight subunits of the key molecular chaperone, T-complex protein 1 Ring complex (TRiC), were higher in glioblastoma-EVs, including CCT2, CCT3, CCT5, CCT6A, CCT7 and TCP1 (p<0.00496). Analogous increases in TRiC transcript levels and DNA copy numbers were detected in silico; CCT6A had the greatest induction of expression and amplification in glioblastoma and showed a negative association with survival (p=0.006). CCT6A is co-localised with EGFR at 7p11.2, with a strong tendency for co-amplification (p<0.001). Immunohistochemistry corroborated the CCT6A proteomics measurements and indicated a potential link between EGFR and CCT6A tissue expressions. Putative EV-biomarkers described here should be further assessed in peripheral blood.

2022-03-01 | PXD010247 | 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