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

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

PROVIDER: PRJNA431471 | ENA |

REPOSITORIES: ENA

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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

Genome-wide investigation of pentatricopeptide repeat 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 of a large gene family in plants. Some PPR proteins have been identified to play important roles in organellar RNA metabolism and organ development in Arabidopsis and rice. However, functions of PPR genes in woody species remain largely unknown. Here, we identified and characterized a total of 626 PPR genes containing PPR motifs in the Populus trichocarpa genome. A comprehensive genome-wide analysis of the poplar PPR gene family was performed, including chromosomal location, phylogenetic relationships and gene duplication. Genome-wide transcriptomic analysis showed that 154 of the PtrPPR genes were induced by biotic and abiotic treatments, including Marssonina brunnea, salicylic acid (SA), methyl jasmonate (MeJA), mechanical wounding, cold and salinity stress. Quantitative RT-PCR analysis further investigated the expression profiles of 11 PtrPPR genes under different stresses. Our results contribute to a comprehensive understanding the roles of PPR proteins and provided an insight for improving the stress tolerance in poplar.

| S-EPMC5809412 | biostudies-literature

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

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

| PRJNA700979 | ENA

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

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

Transcriptome responses to combined biotic and abiotic stresses in Arabidopsis thaliana

2013-01-31 | GSE41935 | 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

Transcriptome responses to combined biotic and abiotic stresses in Arabidopsis thaliana

Project description:Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light intensity, have profound effects on crop performance and yeilds To analyze such responses, we initially compared transcriptome changes in ten Arabidopsis thaliana ecotypes using cold, heat, high light, salt and flagellin treatments as single stress factors or their double combinations. Arabidopsis thaliana plants of ecotypes (Col, Ler, C24, Cvi, Kas1, An1, Sha, Kyo2, Eri and Kond) were subjected to the following stress treatments: Salt, Cold, Heat, High Light (HL), Salt+Heat, Salt+HL, Cold+HL, Heat+HL, as well as FLG (Flagellin, flg22 peptide), Cold+FLG, Heat+FLG

2013-01-31 | E-GEOD-41935 | biostudies-arrayexpress

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

The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3′-UTRs of yeast mitochondrial mRNAs

Project description:Stabilization of messenger RNA is an important step in posttranscriptional gene regulation. In the nucleus and cytoplasm of eukaryotic cells it is generally achieved by 5′ capping and 3′ polyadenylation, whereas additional mechanisms exist in bacteria and organelles. The mitochondrial mRNAs in the yeast Saccharomyces cerevisiae comprise a dodecamer sequence element that confers RNA stability and 3′-end processing via an unknown mechanism. Here, we isolated the protein that binds the dodecamer and identified it as Rmd9, a factor that is known to stabilize yeast mitochondrial RNA. We show that Rmd9 associates with mRNA around dodecamer elements in vivo and that recombinant Rmd9 specifically binds the element in vitro. The crystal structure of Rmd9 bound to its dodecamer target reveals that Rmd9 belongs to the family of pentatricopeptide (PPR) proteins and uses a previously unobserved mode of specific RNA recognition. Rmd9 protects RNA from degradation by the mitochondrial 3′-exoribonuclease complex mtEXO in vitro, indicating that recognition and binding of the dodecamer element by Rmd9 confers stability to yeast mitochondrial mRNAs.

2021-04-07 | GSE139514 | GEO

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