Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1260963 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33482721_1.fastq.gz | Fastqsanger.gz | |||
| SRR33482721_2.fastq.gz | Fastqsanger.gz | |||
| SRR33482722_1.fastq.gz | Fastqsanger.gz | |||
| SRR33482722_2.fastq.gz | Fastqsanger.gz | |||
| SRR33482723_1.fastq.gz | Fastqsanger.gz |
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Project description:Study of the role of the FLV/DOT4 protein in post-transcriptional regulation of chloroplast gene expression. DOT4 is a pentatricopeptide repeat protein targeted to the chloroplast which regulates the editing of the rpoC1 transcript
2016-02-12 | GSE71149 | GEO
Project description:Co-immunoprecipitation of the maize pentatricopeptide protein PPR4 and extraction of bound RNA. RNA is labelled and hybridized to a maize chloroplast genome tiling array in order to identify target RNA species of PPR4.
2022-11-22 | E-MEXP-716 | biostudies-arrayexpress
Project description:Targeted inhibition of mitochondrial oxidative phosphorylation (OXPHOS) complex generation is an emerging and promising cancer treatment strategy, but limited targets and specific inhibitors have been reported. Leucine-rich pentatricopeptide repeat-containing protein (LRPPRC) is an atypical RNA-binding protein that regulates the stability of all 13 mitochondrial DNA-encoded mRNA (mt-mRNA) and thus participates in the synthesis of the OXPHOS complex. LRPPRC is also a prospective therapeutic target for lung adenocarcinoma, serving as a promising target for OXPHOS inhibition. In this study, we identified Demethylzeylasteral (T-96), a small molecule extracted from the Chinese herb Tripterygium wilfordii Hook. f., as a novel inhibitor of LRPPRC. T-96 directly bound to the RNA-binding domain of LRPPRC, inhibiting its interaction with mt-mRNA. This led to instability in both mt-mRNA and LRPPRC protein. Treatment with T-96 significantly reduced the mRNA and protein levels of the OXPHOS complex. As a consequence of LRPPRC inhibition, T-96 treatment induced a defect in the synthesis of the OXPHOS complex, inhibiting mitochondrial aerobic respiration and ATP synthesis. Moreover, T-96 exhibited potent antitumor activity for lung adenocarcinoma in vitro and in vivo, and the antitumor effect of T-96 was dependent on LRPPRC expression. In conclusion, this study not only identified the first traditional Chinese medicine monomer inhibitor against OXPHOS complex biosynthesis as well as a novel target of Demethylzeylasteral, but also shed light on the unique antitumor mechanism of bioactive compounds derived from traditional Chinese medicine.
2024-10-09 | GSE279114 | GEO
Project description:Mitochondria are responsible for energy production through aerobic respiration and represent the powerhouse of eukaryotic cells. Their metabolism and gene expression processes combine bacterial-like features and traits that evolved in eukaryotes. Among mitochondrial gene expression processes, translation remains the most elusive. In plants, while numerous pentatricopeptide repeat (PPR) proteins are involved in all steps of gene expression, their function in translation remains unclear. Here we present the biochemical characterisation of Arabidopsis mitochondrial ribosomes and identify their protein subunit composition. Complementary biochemical approaches identify 19 plant specific mitoribosome proteins, among which 10 are PPR proteins. The knock out mutations of ribosomal PPR (rPPR) genes result in distinct macroscopic phenotypes including lethality or severe growth delays. The molecular analysis of rppr1 mutants using ribosome profiling as well as the analysis of mitochondrial protein levels reveal that rPPR1 is a generic translation factor, which is a novel function for PPR proteins. Finally, single particle cryo-electron microscopy reveals the unique structural architecture of Arabidopsis mitoribosomes, characterised by a very large small ribosomal subunit, larger than the large subunit, bearing an additional RNA domain grafted onto the head. Overall, our results show that Arabidopsis mitoribosomes are substantially divergent from bacterial and other eukaryote mitoribosomes, both in terms of structure and of protein content.
2018-10-03 | GSE119655 | GEO
Project description:Plastids contain multiple copies of the plastid chromosome, folded together with proteins and RNA into nucleoids. The degree to which components of the plastid gene expression and protein biogenesis machineries are nucleoid associated, and the factors involved in plastid DNA organization, repair, and replication, are poorly understood. To provide a conceptual framework for nucleoid function, we characterized the proteomes of highly enriched nucleoid fractions of proplastids and mature chloroplasts isolated from the maize (Zea mays) leaf base and tip, respectively, using mass spectrometry. Quantitative comparisons with proteomes of unfractionated proplastids and chloroplasts facilitated the determination of nucleoid-enriched proteins. This nucleoid-enriched proteome included proteins involved in DNA replication, organization, and repair as well as transcription, mRNA processing, splicing, and editing. Many proteins of unknown function, including pentatricopeptide repeat (PPR), tetratricopeptide repeat (TPR), DnaJ, and mitochondrial transcription factor (mTERF) domain proteins, were identified. Strikingly, 70S ribosome and ribosome assembly factors were strongly overrepresented in nucleoid fractions, but protein chaperones were not. Our analysis strongly suggests that mRNA processing, splicing, and editing, as well as ribosome assembly, take place in association with the nucleoid, suggesting that these processes occur cotranscriptionally. The plastid developmental state did not dramatically change the nucleoid-enriched proteome but did quantitatively shift the predominating function from RNA metabolism in undeveloped plastids to translation and homeostasis in chloroplasts. This study extends the known maize plastid proteome by hundreds of proteins, including more than 40 PPR and mTERF domain proteins, and provides a resource for targeted studies on plastid gene expression. Details of protein identification and annotation are provided in the Plant Proteome Database.
2023-09-28 | PXD045331 | Pride
Project description:As one of the largest protein family in landplants pentatricopeptide repeat (PPR) proteins offer a wide research array. They are mostly involved in the RNA processing steps in Chloroplasts and Mitochondria. Recently it has been shown, that they are not only involved in the RNA processing steps, but are also part of the mitoribosome (rPPRs) as regulators of translation and ribosome stabilizers. This experiment focuses on a non-previously reported rPPR protein. The RNA-Seq data are needed for a ribosome profiling experiment that aimed to analyze DWEORG1's impact on mitochondrial translation. Arabidopsis mutants are compared to the wild type using duplicates for the RNA-Seq experiment. RNASEQ (determining the transcript abundance) and RIBOSEQ ( for detecting ribosome occupancy on each transcript) of wild type and mutants were conducted to determine the translational efficiency of mitochondrial transcripts in the mutant and wild type. The plants were grown in the Greenhouse under long day conditions. Flowers were harvested simultaneously for all genotypes, snap-frozen in liquid nitrogen and stored at -80°C until use.Total RNA was prepared from a mix of flower buds and open flowers.For total RNA extraction from flowers Trizol was used. Total RNA were treated with Dnase and depleted of rRNAs using the RiboMinusTM Plant Kit for RNA-Seq (invitrogen), following the manufacturer’s instructions.The sequencing libraries of two biological repeats per genotype were prepared using the NEXTflex Rapid Directional RNA-Seq Kit (Bioo Scientific) following the manufacturer's instructions. For sequencing Illumina NextSeq 500 75 bp single reads were used. The reads were than mapped to the Col-0 mitochondrial genome of Arabidopsis thaliana acccession JF729201.
2022-07-13 | E-MTAB-11928 | biostudies-arrayexpress
Project description:Mammalian mitochondrial ribosomes are unique molecular machines that translate 11 leaderless mRNAs. To date it is not clear how mitoribosomes recognize and initiate translation in the absence of untranslated regions in the mitochondrial mRNAs. Translation initiation in mitochondria shares similarities with prokaryotic systems, such as the formation of a ternary complex of fMet-tRNAMet, mRNA and the 28S subunit, but differs in the requirements for initiation factors. Mitochondria have two initiation factors, MTIF2 that closes the decoding centre and stabilizes the binding of the fMet-tRNAMet to the leaderless mRNAs, and MTIF3 whose role is not clear. We knocked out Mtif3 in mice and show that this protein is essential for embryo development and heart- and skeletal muscle-specific loss of MTIF3 causes premature death. We identify increased but uncoordinated mitochondrial protein synthesis in mice lacking MTIF3 that results in loss of specific respiratory complexes. Therefore, we show that coordinated assembly of OXPHOS complexes requires stoichiometric levels of nuclear and mitochondrially-encoded protein subunits in vivo. Our ribosome profiling and transcriptomic analyses show that MTIF3 is required for recognition and regulation of translation initiation of mitochondrial mRNAs, but not dissociation of the ribosome subunits.
2020-01-13 | GSE131154 | GEO
Project description:Chloroplast function requires the coordinated action of nuclear- and chloroplast-derived proteins, including several hundred nuclear-encoded pentatricopeptide repeat (PPR) proteins that regulate plastid mRNA metabolism. Despite their large number and importance, regulatory mechanisms controlling PPR expression are poorly understood. Here we show that the Arabidopsis NOT4A ubiquitin-ligase positively regulates PROTON GRADIENT 3 (PGR3), a PPR protein required for translating 30S ribosome subunits and several thylakoid-localised photosynthetic components within chloroplasts.
2021-09-09 | PXD022584 | Pride