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RNaseI-RIPseq for rfl8-Functional characterization of the pentatricopeptide repeat protein PPR RFL8

ABSTRACT: RNaseI-RIPseq for rfl8-Functional characterization of the pentatricopeptide repeat protein PPR RFL8

PROVIDER: PRJNA700979 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13666885.fastq.gz	Fastqsanger.gz
	SRR13666886.fastq.gz	Fastqsanger.gz
	SRR13666887.fastq.gz	Fastqsanger.gz
	SRR13666888.fastq.gz	Fastqsanger.gz

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ripseq experiment for rfl8 targets - Functional characterization of the pentatricopeptide repeat protein PPR RFL8

Project description:ripseq experiment for rfl8 targets - Functional characterization of the pentatricopeptide repeat protein PPR RFL8

| PRJNA699482 | ENA

RNaseI-RIPseq for rfl8-Functional characterization of the pentatricopeptide repeat protein PPR RFL8

Project description:blanc09_ripseq_rfl8-rnasei-ripseq for rfl8-Which mitochondrial transcripts are bound by RFL8 protein? -The RNaseI-RIPseq approach to find the in vivo binding sites of RFL8 protein on mitochondrial mRNAs via co-immunoprecipitation of 3HA tag fused in C-terminal of RFL8 protein

2021-04-27 | GSE166447 | GEO

ripseq experiment for rfl8 targets - Functional characterization of the pentatricopeptide repeat protein PPR RFL8

Project description:blanc09_ripseq_rfl8-ripseq experiment for rfl8 targets-Which mitochondrial transcripts are bound by RFL8 protein? -The RIPseq approach to find the mitochondrial transcripts attached by RFL8 protein via co-immunoprecipitation of 3HA tag fused in C-terminal of RFL8 protein

2021-04-27 | GSE166156 | GEO

Genome-wide investigation of pentatricopeptide repeat (PPR) gene family in poplar and their expression analysis in response to biotic and abiotic stresses

Project description:Pentatricopeptide repeat (PPR) proteins, which are characterized by tandem 30-40 amino acid sequence motifs, constitute a large gene family in plants. These known PPR proteins have been identified to play important roles in organellar RNA metabolism and plant development in Arabidopsis and rice. However, functions of PPR genes in woody species remain still largely unknown. Here, we identified and characterized a total of 626 PPR genes containing PPR motifs in the poplar genome. A comprehensive genome-wide analysis of the poplar PPR gene family was performed, including chromosomal location, phylogenetic relationships, gene duplication. Transcriptomic analyses identified that 154 of the PtrPPR genes were induced by biotic and abiotic treatments, including Marssonina brunnea, salicylic acid (SA), methyl jasmonate (MeJA), wounding, cold and salinity. Quantitative RT-PCR analysis further confirmed the expression profiles of 11 PtrPPR genes under different stresses. Our results contribute to a more comprehensive understanding the roles of PPR proteins and provided an insight for improving the stress tolerance in poplar.

2018-01-31 | GSE109609 | GEO

Riboseq analysis of the rfl8 mutant-Functional characterization of the pentatricopeptide repeat protein PPR RFL8

Project description:Riboseq analysis of the rfl8 mutant-Functional characterization of the pentatricopeptide repeat protein PPR RFL8

| PRJNA700978 | ENA

Targeted Translation Inhibition of Chloroplast and Mitochondrial mRNAs by Designer Pentatricopeptide Repeat Proteins

Project description:Pentatricopeptide repeat (PPR) proteins are crucial for organellar gene expression. To establish a tool for gene expression manipulation in Arabidopsis chloroplasts and genetically inaccessible mitochondria, we engineered designer (dPPR) proteins to specifically inhibit the translation of chloroplast and mitochondrial mRNAs by masking their start codons.Unlike prior methods for targeted downregulation of gene expression, which relied on re-targeting natural PPR proteins to RNA sequences closely related to their original targets, our approach employs a fully synthetic P-type PPR scaffold, programmable to bind any RNA sequence of interest. Here, using dPPR-psbK and dPPR-nad7, we targeted the psbKmRNA in chloroplasts and the nad7 mRNA in mitochondria, respectively. Our results demonstrated that dPPR-psbKeffectively binds and inhibits psbK translation with high specificity, resulting in disrupted PSII supercomplexes and reduced photosynthetic efficiency. Similarly, dPPR-nad7 suppressed nad7 translation, leading to decreased NADH oxidase activity in Complex I and growth retardation. By comparing the phenotypes with tobacco psbK knockouts and bir6-2 mutants, we could exclude any physiologically relevant off-target effects. These findings highlight dPPR proteins as precise tools for targeted translation inhibition, enabling functional studies of organellar genes and offering a novel approach for manipulating mitochondrial gene expression with potential applications across diverse plant species.

2025-03-05 | PXD060146 | Pride

Two novel PLS-class pentatricopeptide repeat proteins are involved in the group II intron splicing of mitochondrial transcripts in the moss Physcomitrella patens

Project description:Pentatricopeptide repeat (PPR) proteins are RNA binding proteins that function in posttranscriptional regulation as gene-specific regulators of RNA metabolism in plant organelles. Plant PPR proteins are divided into four classes: P, PLS, E and DYW. The E- and DYW-class proteins are mainly implicated in RNA editing, whereas most of the P-class proteins predominantly participate in RNA cleavage, splicing and stabilization. In contrast, the functions of PLS-class proteins still remain obscure. Here, we report the function of PLS-class PpPPR_31 and PpPPR_9 in Physcomitrella patens. The knockout (KO) mutants of PpPPR_31 and PpPPR_9 exhibited slower protonema growth compared to the wild type. The PpPPR_31 KO mutants showed a considerable reduction in the splicing of nad5 intron 3 and atp9 intron 1. The PpPPR_9 KO mutants displayed severely reduced splicing of cox1 intron 3. An RNA electrophoresis mobility shift assay showed that the recombinant PpPPR_31 protein bound to the 5' region of nad5 exon 4 and the bulged-A region in domain VI of atp9 group II intron 1 while the recombinant PpPPR_9 bound to the translated region of ORF622 in cox1 intron 3. These results suggest that PLS-class PPR proteins may influence the splicing efficiency of mitochondrial group II introns.

2020-08-01 | GSE145050 | GEO

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

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

Riboseq analysis of the rfl8 mutant-Functional characterization of the pentatricopeptide repeat protein PPR RFL8

Project description:blanc09_ripseq_rfl8-riboseq analysis of the rfl8 mutant-Which mitochondrial transcripts are bound by RFL8 protein? -Does the RFL8 loss impact on mitochondrial translation?

2021-04-27 | GSE166446 | GEO

Genome-wide investigation of pentatricopeptide repeat (PPR) gene family in poplar and their expression analysis in response to biotic and abiotic stresses

Project description:Genome-wide investigation of pentatricopeptide repeat (PPR) gene family in poplar and their expression analysis in response to biotic and abiotic stresses

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