Flavodentata
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE71149 | GEO | 2016/02/12
SECONDARY ACCESSION(S): PRJNA290457
REPOSITORIES: GEO
Similar Datasets
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 The editing level of rpoC1 varies from one tissue to the other and because the main macroscopic phenotype of the flv/dot4 mutant are white leaf margins. We compared the leaf border to the leaf center of wild-type Col0 plants but also the leaf borders of col0 and flv/dot4 knock out mutants by sequencing total RNA depleted from rRNA to get a global view of gene expression (including post-transcrional modifications) of the 3 plant genomes: nucleus, chloroplast and mitochondria. mRNA seq on wild-type Col and FLV mutants knock out.
2016-02-12 | E-GEOD-71149 | biostudies-arrayexpress
Project description:In Trypanosoma brucei, most mitochondrial mRNAs undergo U-insertion/deletion editing, and 3′ adenylation and uridylation. The internal sequence changes and terminal extensions are coordinated: Pre-editing addition of the short (A) tail protects the edited transcript against 3′-5′ degradation, while post-editing A/U-tailing renders mRNA competent for ribosome recruitment. Participation of a poly(A) binding protein (PABP) in coupling of editing and 3′ modification processes has been inferred, but its identity and mechanism of action remained elusive. We report identification of KPAF4, a pentatricopeptide repeat-containing PABP which sequesters the A-tail and impedes exonucleolytic degradation. Conversely, KPAF4 inhibits uridylation of A-tailed transcripts and, therefore, premature A/U-tailing of partially-edited mRNAs. This quality check point prevents translation of incompletely edited mRNAs. Our findings also implicate the RNA editing substrate binding complex (RESC) in mediating the interaction between the 5′-end bound pyrophosphohydrolase MERS1 and 3′-end associated KPAF4 to enable mRNA circularization. This event is critical for transcript stability during the editing process.
2019-04-02 | PXD012008 | Pride
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
Project description:Chloroplast gene expression is controlled by numerous nuclear-encoded RNA-binding proteins. Among them, pentatricopeptide repeat (PPR) proteins are known to be a key player in posttranscriptional regulation in chloroplasts. However, the functions of many PPR proteins remain unknown. In this study, we characterized the function of a chloroplast-localized P-class PPR protein PpPPR_21 in Physcomitrella patens. Knockout (KO) mutants of PpPPR_21 exhibited a reduced growth of the protonemata and lower photosynthetic activity. Immuno-blot analysis and blue-native gel analysis showed a remarkable reduction of the photosystem II (PSII) reaction center protein and poorly formation of the PSII super-complexes in the KO mutants. To access whether PpPPR_21 is involved in the chloroplast gene expression, chloroplast genome-wide microarray analysis and northern blot hybridization were performed. These analyses indicated that the psbI-ycf12 transcript encoding the low molecular weight subunits of PSII, did not accumulate in the KO mutants while other psb transcripts accumulated at similar levels of WT and the KO mutants. A complemented PpPPR_21 KO moss transformed with the cognate full-length PpPPR_21 cDNA rescued the psbI transcript accumulation level. RNA binding experiments showed that the recombinant PpPPR_21 bound efficiently to the 5’-untraslated and translated region of the psbI mRNA. The present study suggests that PpPPR_21 may be essential for accumulation of a stable psbI-ycf12 mRNA.
2019-03-26 | GSE121554 | 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 the expression of PROTON GRADIENT REGULATION 3 (PGR3), a PPR protein required for translating several thylakoid-localised photosynthetic components and ribosome subunits within chloroplasts. Loss of NOT4A function leads to a strong depletion of cytochrome b6f and NDH complexes, as well plastid 30S ribosomes, which reduces mRNA translation and negatively impacts photosynthetic capacity, causing pale-yellow and slow-growth phenotypes. Quantitative transcriptome and proteome analyses reveal that PGR3 is misregulated in not4a. We show that the molecular not4a defects mimic those of a pgr3 mutant, and that normal plastid function is restored through transgenic PGR3 expression. Our work identifies NOT4A as crucial for ensuring robust photosynthetic function during development and stress-response, through promoting PGR3 production and chloroplast translation.
2020-11-17 | GSE161571 | 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:The P-class pentatricopeptide repeat protein binds to the 5’ untranslated and translated regions of chloroplast psbI-ycf12 transcript and is involved in mRNA stability
| PRJNA497789 | ENA
Project description:We extended the investigation of nuclear transcript changes under drought to an overarching characterization of the post(transcriptome), including alternative splicing of nuclear transcripts, accumulation of organellar (chloroplast and mitochondrion) transcripts, editing and splicing of organellar transcripts, and furthermore, accumulation of transposable elements. To this end, long non-coding (lncRNA-Seq) instead of mRNA-Seq was applied, because the lncRNA-Seq workflow employs library preparation after ribosomal RNA depletion instead of library preparation of enriched mRNAs (mRNA-Seq).
2023-08-09 | GSE202931 | 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