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Half_edit - A new predictive method for E+ PPR binding

ABSTRACT: ngs2018_04_half_edit-half_edit - Is there some transcriptomic defects in these different PPR KO mutants? - Identification of RNA editing defects in 3 differents KO mutants for E+ PPR. Results will be compared to different predictive methods in order to find out which one is the more accurate. Also looking for other transcriptomic defects in a pure-PPR.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE144674 | GEO | 2020/03/30

REPOSITORIES: GEO

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half_edit - A new predictive method for E+ PPR binding

Project description:half_edit - A new predictive method for E+ PPR binding

| PRJNA604567 | ENA

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

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

Search for mitochondrial editing defect in an Arabidopsis PPR mutant

Project description:ngs2019_18_eplus-eplus-search for mitochondrial editing defect in an arabidopsis PPR mutant Annotation, RNA/Small-RNA quantification: editing quantification. The Mito samples were first enriched with mitochondria by a series of multi-speed centrifugations after grinding with mortar at 4°C.

2020-03-30 | GSE144560 | GEO

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

RIP-Seq analysis of non-PPR editing factors OZ1, ORRM1, RIP9/MORF9

Project description:We provide sequences of maize chlroplast RNAs associated with non-PPR editing factors through immunoprecipitation. The accumulated sequences indicate expansive role in RNA processing and potential associations of OZ1-ORRM1 complexes with the ribosome and less efficiently translated mRNAs.

2021-12-31 | GSE151702 | GEO

The whole transcriptome RNA-seq analysis of poco1, a mitochondrial PPR protein mutant in Arabidopsis thaliana

Project description:In a recent study, we showed that a T-DNA insertional mutation in a mitochondrial PPR protein, POCO1, led to the earlier floral transition (Emami and Kempken 2019). We used RNA-seq analysis to provide an overview of the global transcriptome changes in poco1 mutant during different developmental stages.

2020-05-14 | E-MTAB-8912 | biostudies-arrayexpress

salmonell inva-Trancriptomic analysis in Salmonella typhimurium infection

Project description:au10-06_salmonella - salmonell inva - Transcriptomic analysis between Salmonella wt and differents mutants in type3 secretion system. - Plants were grown during 14 days in solid medium and were transfered to liquid medium during 16 h. at 9 am samonella was added to a final concentration of OD600=0.2

2012-04-07 | GSE36699 | GEO

salmonella_prgh - Trancriptomic analysis in Salmonella typhimurium infection

Project description:au10-06_salmonella_eduardob - salmonella_prgh - Transcriptomic analysis between Salmonella wt and differents mutants in type3 secretion system - Plants were grown during 14 days in solid medium and were transfered to liquid medium during 16 h, at 9 am samonella was added to a final concentration of OD600=0.2. Keywords: normal vs disease comparison

2012-01-01 | GSE23791 | GEO

salmonella_14028s - Trancriptomic analysis in Salmonella typhimurium infection

Project description:au10-06_salmonella_eduardob - salmonella_14028s - Transcriptomic analysis between Salmonella wt and differents mutants in type3 secretion system - Plants were grown during 14 days in solid medium and were transfered to liquid medium during 16 h, at 9 am samonella was added to a final concentration of OD600=0.2. Keywords: normal vs disease comparison

2012-01-01 | GSE23790 | GEO

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