Looking for mitochondrial associated RNA
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE9393 | GEO | 2008/06/01
SECONDARY ACCESSION(S): PRJNA103117
REPOSITORIES: GEO
Similar Datasets
Project description:We investigated the peripheral mitochondrial localization of nuclear-encoded mRNAs (MLR) in various conditions in which translation was inhibited or the mRNA binding protein context altered (Delta puf3). We used cell fractionation protocols together with microarray to assess the distribution of mRNAs between free and mitochondrion-bound polysomes. Keywords: Mitochondrial-associated RNA localization in cells GSM239122-GSM239127: mitochondrial associated RNA (three biological replicates each in dye swap) GSM239128-GSM239131: mitochondrial associated RNA in presence of 200µg/ml cycloheximide (two biological replicates each in dye swap) GSM239132-GSM239135: mitochondrial associated RNA in presence of 2.1mM puromycin (two biological replicates each in dye swap) GSM239136-GSM239139: mitochondrial associated RNA in Delta Puf3 strain (two biological replicates each in dye swap)
2008-06-01 | E-GEOD-9393 | biostudies-arrayexpress
Project description:In order to identify what RNA messengers are being translated at the ER membrane, membrane-associated polysomes were separated from free polysomes by subcellular fractionation of WT and delta-egd1/delta-egd2 yeast strains and associated RNA was isolated and then identified by microarray analysis.
2013-04-05 | GSE45795 | GEO
Project description:In order to identify what RNA messengers are being translated at the ER membrane, membrane-associated polysomes were separated from free polysomes by subcellular fractionation of WT and delta-egd1/delta-egd2 yeast strains and associated RNA was isolated and then identified by microarray analysis. Set of arrays that are part of repeated experiments
2013-04-05 | E-GEOD-45795 | biostudies-arrayexpress
Project description: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.
2015-12-24 | E-MTAB-3922 | biostudies-arrayexpress
Project description:Pbp1 (polyA-binding protein - binding protein 1) is a stress granule marker and polyglutamine expansions in its mammalian ortholog ataxin-2 have been linked to neurodegenerative conditions. Pbp1 was recently shown to form intracellular assemblies that function in the negative regulation of TORC1 signaling under respiratory conditions. Furthermore, it was observed that loss of Pbp1 leads to mitochondrial dysfunction. Here, we show that loss of Pbp1 leads to a specific decrease in mitochondrial proteins whose encoding mRNAs are targets of the RNA-binding protein Puf3, suggesting a functional relationship between Pbp1 and Puf3. We found that Pbp1 stabilizes and promotes the translation of Puf3-target mRNAs in respiratory conditions, such as those involved in the assembly of cytochrome c oxidase. We further show that Pbp1 and Puf3 associate through their respective low complexity domains, which is required for target mRNA stabilization and translation. Our findings reveal a key role for Pbp1-containing assemblies in enabling the translation of mRNAs critical for mitochondrial biogenesis and respiration under metabolically challenging conditions. They may further explain prior associations of Pbp1/ataxin-2 with stress granule biology and RNA metabolism.
2023-05-08 | GSE227356 | GEO
Project description:Current evidence suggests that nuclear-encoded mitochondrial proteins can be locally translated at the mitochondrial surface and co-translationally or post-translationally imported into mitochondria. mRNA localization on the mitochondrial membrane, a prerequisite for localized translation, remains uncharacterized in higher eukaryotic organisms. We employed fractionation-sequencing to profile mitochondria-associated mRNAs in zebrafish larvae. Our transcriptome-wide analysis reveals the localization of mRNAs of only 12% of the nuclear-encoded mitochondrial proteins to the mitochondrial surface, which suggests that post-translational import is the dominant mode of protein import to mitochondria. Additionally, the mRNAs which were localized to the mitochondrial membrane consisted mostly of those encoding proteins involved in mitochondrial dynamics, suggesting their site-specific translation. Finally, we show that the loss of function of the MIA pathway responsible for the post-translational import of a subclass of mitochondrial proteins, triggers mitochondrial localization of mRNAs encoding proteins that are imported to mitochondria via other pathways. Thus, our study suggests that mRNA targeting and localized translation could be relevant in higher eukaryotes to combat stress conditions affecting mitochondrial biogenesis in general.
2023-10-28 | GSE160355 | GEO
Project description:The Puf family of RNA-binding proteins regulate gene expression by controlling protein synthesis or stimulating RNA decay. Puf3p is one of six related proteins in Saccharomyces cerevisiae characterised as targeting and regulating decay of nuclear-encoded mRNAs specifying mitochondrial proteins. Much prior work has examined how Puf3p regulates COX17 mRNA. We undertook a genome-wide approach to quantitatively assess the impact of loss of PUF3 on gene expression. Comparing transcript levels in wild-type and puf3∆ cells revealed that that only a small fraction of mRNA levels alter, suggesting Puf3p determines mRNA stability for only some target mRNAs.
2016-03-31 | E-MTAB-3407 | biostudies-arrayexpress
Project description:Translational regulation can be studied on a global scale by integrating polysome fractionation of mRNAs with microarray hybridization. This approach is based on the fact that translationally quiescent mRNAs are sequestered within messenger ribonucleoprotein (mRNP) particles or associated with single ribosomes (monosomes), whereas actively translated mRNAs are associated with multiple ribosomes (polysomes). The mRNAs associated within these fractions are then used to interrogate microarrays, providing insight into how the translational state of individual mRNAs is modified by environmental cues. In this study, we coupled polysome fractionation with microarray detection in order to identify changes in the translation state of the A. fumigatus transcriptome under conditions that perturb ER homeostasis such as chemical stress (DTT, tunicamycin) or thermal stress (shift from 25 degrees celsius to 37 degrees celsius).
2014-10-24 | E-MTAB-2027 | biostudies-arrayexpress
Project description:The hypothesis tested in the present study was that PRR16/Largen influences mRNA translation to control mammalian cell size. Results provide important information of the effects of PRR16/Largen on translation of particular sets of mRNAs encoding histones, mitochondrial, and vascular transport proteins. mRNAs obtained from heavy and light polysomes in PRR16/Largen-overexpressing cells subjected to the identification of mRNAs enriched in heavy polysomes compared to control cells.
2014-01-28 | E-GEOD-54383 | biostudies-arrayexpress
Project description:Recent studies of the Puf family of RNA-binding proteins revealed that besides their traditional roles in translational regulation of mRNAs, some Puf proteins are also involved in ribosome biogenesis by binding rRNA. In this study, we report the role of a Puf-like protein (Puf3) in ribosome biogenesis in Plasmodium falciparum and Plasmodium yoelii. Secondary structure prediction suggested that the RNA-binding domain of Puf3 consists of 11 pumilio repeats, similar to human Puf-A/yeast Puf6, which is involved in ribosome biogenesis. Neither pfpuf3 nor pypuf3 could be genetically disrupted, suggesting they may be essential for the intraerythrocytic developmental cycle (IDC). A time-course study of PfPuf3 protein indicated that PfPuf3 was expressed during the entire IDC, with peak expression in early trophozoites. Cellular fractionation of PfPuf3 revealed that it is preferentially partitioned to the nuclear rather than the cytoplasmic fractions, which is consistent with a nuclear localization of PfPuf3::GFP and PyPuf3::GFP as seen by immunofluorescence. Further, we found PfPuf3 co-localized with a well-known nucleolus maker, PfNop1, demonstrating that PfPuf3 is a nucleolar protein. This localization is in contrast to the cytoplasmic localization of PfPuf1 and PfPuf2, but matches the localization of human Puf-A and yeast Puf6. Affinity purification of a C-terminal PTP-tagged variant of PfPuf3 revealed an association with 32 proteins associated with the 60S ribosome, and an enrichment of 28S rRNA and internal transcribed spacer 2. Taken together, these results demonstrate a nucleolar localization of PfPuf3 and suggest an essential function of PfPuf3 in ribosomal biogenesis.
2018-03-12 | PXD007978 | Pride