Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tma108, a putative M1 aminopeptidase, is involved in ribosome specialization in Saccharomyces cerevisiae

ABSTRACT: We performed subcellular fractionation of the polysomes associated with the mitochondrial surface (mitopolysomes) in wild type or Tma108 deleted yeast strains and measured the mRNA enrichment in these fractions by competitive hybridization on microarrays against the corresponding total RNAs. This was used to measure the mitopolysomes enrichment of all yeast mRNAs and to compare these enrichments between wild type and tma108 mutant.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Frederic Devaux

PROVIDER: E-MTAB-3922 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Tma108, a putative M1 aminopeptidase, is a specific nascent chain-associated protein in Saccharomyces cerevisiae.

Delaveau Thierry T Davoine Dimitri D Jolly Ariane A Vallot Antoine A Rouvière Jérôme O JO Gerber Athenaïs A Brochet Sandra S Plessis Marion M Roquigny Roxane R Merhej Jawad J Leger Thibaut T Garcia Camille C Lelandais Gaëlle G Laine Elodie E Palancade Benoit B Devaux Frédéric F Garcia Mathilde M

Nucleic acids research 20160831 18

The discovery of novel specific ribosome-associated factors challenges the assumption that translation relies on standardized molecular machinery. In this work, we demonstrate that Tma108, an uncharacterized translation machinery-associated factor in yeast, defines a subpopulation of cellular ribosomes specifically involved in the translation of less than 200 mRNAs encoding proteins with ATP or Zinc binding domains. Using ribonucleoparticle dissociation experiments we established that Tma108 dir ...[more]

PMID: 27580715

Similar Datasets

Tma108, a putative M1 aminopeptidase, is involved in ribosome specialization in Saccharomyces cerevisiae

Project description:We performed RIP (RNA-IP experiments) in the yeast Saccharomyces cerevisiae, immunoprecipitating either Tma108, Scp160, Tma46 or Rpl16. The RNAs present in the IPs were analyzed by microarray competitive hybridization against total RNAs (Input). Our goal was to identify the RNAs which are targeted, directly or indirectly, by these four proteins.

2015-12-24 | E-MTAB-3881 | biostudies-arrayexpress

Tma108, a putative M1 aminopeptidase, defines specialized ribosomes in Saccharomyces cerevisiae

Project description:Ribosome specialization is an emerging concept which challenges the common assumption that translation relies on a standardized molecular machinery. In this work, we demonstrate that Tma108, a yeast uncharacterized translation machinery-associated factor, defines a subpopulation of the cellular ribosomes specifically involved in the translation of less than 200 mRNAs encoding proteins with ATP or zinc binding domains. Ribonucleoparticle dissociation experiments support the fact that Tma108 directly interacts with the nascent protein chain. Comparative genomic analyses and molecular modeling point out Tma108 as an original M1 metallopeptidase with specific residues in the catalytic pocket which may explain its selectivity. The involvement of Tma108 in co-translational regulations is attested by the drastic perturbation of the subcellular localization of ATP2 mRNA, one of its targets, upon TMA108 inactivation. Tma108 is an unique example of a nascent chain-associated factor with high selectivity and illustrates the existence of specific translation-associated factors, besides RNA binding proteins.

2016-09-27 | PXD003174 | Pride

A SUMO-dependent feedback loop senses and controls the biogenesis of nuclear pore subunits

Project description:We analyzed the impact on steady-state transcriptome of the deletion of the hnRNP K-like protein Hek2 in yeast using two-colour microarray hybridization. RNA extracted from wild type and hek2delta cells were reverse-transcribed, labelled with Cy3 or Cy5 and competitively hybridized onto Agilent custom S. cerevisiae microarrays.

2018-01-31 | E-MTAB-6065 | biostudies-arrayexpress

Tma108, a putative M1 aminopeptidase, is a specific nascent chain-associated protein in Saccharomyces cerevisiae.

Project description:The discovery of novel specific ribosome-associated factors challenges the assumption that translation relies on standardized molecular machinery. In this work, we demonstrate that Tma108, an uncharacterized translation machinery-associated factor in yeast, defines a subpopulation of cellular ribosomes specifically involved in the translation of less than 200 mRNAs encoding proteins with ATP or Zinc binding domains. Using ribonucleoparticle dissociation experiments we established that Tma108 directly interacts with the nascent protein chain. Additionally, we have shown that translation of the first 35 amino acids of Asn1, one of the Tma108 targets, is necessary and sufficient to recruit Tma108, suggesting that it is loaded early during translation. Comparative genomic analyses, molecular modeling and directed mutagenesis point to Tma108 as an original M1 metallopeptidase, which uses its putative catalytic peptide-binding pocket to bind the N-terminus of its targets. The involvement of Tma108 in co-translational regulation is attested by a drastic change in the subcellular localization of ATP2 mRNA upon Tma108 inactivation. Tma108 is a unique example of a nascent chain-associated factor with high selectivity and its study illustrates the existence of other specific translation-associated factors besides RNA binding proteins.

| S-EPMC5062994 | biostudies-literature

Stress response in yeasts

Project description:Transcriptome response of the yeasts C. glabrata and S. cerevisiae treated by an antifungal agent, benomyl Keywords: time course; stress response We performed microarray analyses of the transcriptome response of the yeasts Candida glabrata and Saccharomyces cerevisiae, treated by an antifungal agent, benomyl. The C. glabrata cells were submitted to 20 Î¼g/mL of benomyl for 2, 4, 10, 20, 40 and 80 minutes. The labelled cDNA from treated cells were competitively hybridized on microarrays versus cDNA from mock treated cells.

2010-06-20 | E-GEOD-10244 | biostudies-arrayexpress

IRAP Inhibitors: M1-Aminopeptidase Family Inspiration.

Project description:The insulin regulated aminopeptidase (IRAP) has been proposed as an important therapeutic target for indications including Alzheimer's disease and immune disorders. To date, a number of IRAP inhibitor designs have been investigated but the total number of molecules investigated remains quite small. As a member the M1 aminopeptidase family, IRAP shares numerous structural features with the other M1 aminopeptidases. The study of those enzymes and the development of inhibitors provide key learnings and new approaches and are potential sources of inspiration for future IRAP inhibitors.

| S-EPMC7546331 | biostudies-literature

Transcriptome analyses of a C. glabrata strain deleted for the transcription factor Aft2.

Project description:In these experiments, we compared the transcriptomes of a wild type strain and an aft2 deleted strain of the pathogenic yeast Candida glabrata. The comparisons were performed in four different growth conditions: iron starvation (BPS treatment), selenite treatment, cadmium treatment and optimal growth conditions (YPD).

2018-11-12 | E-MTAB-7042 | biostudies-arrayexpress

RIP-ChIP analyses of N-acetyltransferases binding preferences in yeast

Project description:We performed RIP (RNA-IP experiments) in the yeast Saccharomyces cerevisiae, immunoprecipitating either Ard1, Mak3, Nat3 subunits of N-acetyltransefrases in yeast or the ribosomal protein Rpl16 as a control. The RNAs present in the IPs were analyzed by microarray competitive hybridization against total RNAs (Input). Our goal was to identify the RNAs which are targetted, directly or indirectly, by these four proteins.

2022-12-31 | E-MTAB-11772 | biostudies-arrayexpress

Biochemical and cellular characterisation of the Plasmodium falciparum M1 alanyl aminopeptidase (PfM1AAP) and M17 leucyl aminopeptidase (PfM17LAP).

Project description:The Plasmodium falciparum M1 alanyl aminopeptidase and M17 leucyl aminopeptidase, PfM1AAP and PfM17LAP, are potential targets for novel anti-malarial drug development. Inhibitors of these aminopeptidases have been shown to kill malaria parasites in culture and reduce parasite growth in murine models. The two enzymes may function in the terminal stages of haemoglobin digestion, providing free amino acids for protein synthesis by the rapidly growing intra-erythrocytic parasites. Here we have performed a comparative cellular and biochemical characterisation of the two enzymes. Cell fractionation and immunolocalisation studies reveal that both enzymes are associated with the soluble cytosolic fraction of the parasite, with no evidence that they are present within other compartments, such as the digestive vacuole (DV). Enzyme kinetic studies show that the optimal pH of both enzymes is in the neutral range (pH 7.0-8.0), although PfM1AAP also possesses some activity (< 20%) at the lower pH range of 5.0-5.5. The data supports the proposal that PfM1AAP and PfM17LAP function in the cytoplasm of the parasite, likely in the degradation of haemoglobin-derived peptides generated in the DV and transported to the cytosol.

| S-EPMC7858622 | biostudies-literature

The M1 aminopeptidase NPEPPS is a novel regulator of cisplatin sensitivity

Project description:Platinum-based chemotherapeutics are used in many combination regimens in cancer. Despite extensive use across diverse cancer types, there is room for improved efficacy and patient selection for treatment. Here, we use bladder cancer to address both issues. A multi-omic assessment of five human bladder cancer cell lines and their chemotherapy resistant derivatives, coupled with in vitro whole-genome CRISPR screens were used to define functional drivers of treatment resistance. We identified 46 genes that sensitized the resistant cell lines to cisplatin plus gemcitabine (GemCis), a standard combination therapy in bladder cancer. Most genes were involved with DNA damage and repair pathways, which have previously been associated with enhanced sensitivity to cisplatin. Evaluating expression of the 46 genes in the whole transcriptome and proteome data in parental and resistant lines identified the puromycin sensitive aminopeptidase, NPEPPS, as a novel hit. Depletion of NPEPPS resulted in sensitizing resistant bladder cancer cells to cisplatin in vitro and in xenograft experiments. Pharmacologic inhibition of NPEPPS with tosedostat in cells and in chemoresistant, bladder cancer patient-derived tumoroids improved response to cisplatin. Prior work found NPEPPS in a protein complex with volume regulated anion channels (VRACs) in several cell line models. Interestingly, depletion of two VRAC subunits, LRRC8A and LRRC8D, known importers of intracellular cisplatin, enhanced resistance to cisplatin. Our findings support NPEPPS as a novel and druggable driver of cisplatin resistance with the potential for rapid translation to clinical investigation.

2023-12-31 | GSE171537 | 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