Ripseq experiment for rfl8 targets - Functional characterization of the pentatricopeptide repeat protein PPR RFL8
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE166156 | GEO | 2021/04/27
REPOSITORIES: GEO
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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
Project description:RNaseI-RIPseq for rfl8-Functional characterization of the pentatricopeptide repeat protein PPR RFL8
| PRJNA700979 | ENA
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
Project description:ripseq experiment for rfl8 targets - Functional characterization of the pentatricopeptide repeat protein PPR RFL8
| PRJNA699482 | ENA
Project description:BackgroundThe Campanuloideae (Campanulaceae) are a highly diverse clade of angiosperms found mostly in the Northern Hemisphere, with the highest diversity in temperate areas of the Old World. Chloroplast markers have greatly improved our understanding of this clade but many relationships remain unclear primarily due to low levels of molecular evolution and recent and rapid divergence. Furthermore, focusing solely on maternally inherited markers such as those from the chloroplast genome may obscure processes such as hybridization. In this study we explore the phylogenetic utility of two low-copy nuclear loci from the pentatricopeptide repeat gene family (PPR). Rapidly evolving nuclear loci may provide increased phylogenetic resolution in clades containing recently diverged or closely related taxa. We present results based on both chloroplast and low-copy nuclear loci and discuss the utility of such markers to resolve evolutionary relationships and infer hybridization events within the Campanuloideae clade.ResultsThe inclusion of low-copy nuclear genes into the analyses provides increased phylogenetic resolution in two species-rich clades containing recently diverged taxa. We also obtain support for the placement of two early diverging lineages (Jasione and Musschia-Gadellia clades) that have previously been unresolved. Furthermore, phylogenetic analyses of PPR loci revealed potential hybridization events for a number of taxa (e.g., Campanula pelviformis and Legousia species). These loci offer greater overall topological support than obtained with plastid DNA alone.ConclusionThis study represents the first inclusion of low-copy nuclear genes for phylogenetic reconstruction in Campanuloideae. The two PPR loci were easy to sequence, required no cloning, and the sequence alignments were straightforward across the entire Campanuloideae clade. Although potentially complicated by incomplete lineage sorting, these markers proved useful for understanding the processes of reticulate evolution and resolving relationships at a wide range of phylogenetic levels. Our results stress the importance of including multiple, independent loci in phylogenetic analyses.
| S-EPMC3981779 | biostudies-literature
Project description:BackgroundPentatricopeptide repeat (PPR) proteins play an essential role in the post-transcriptional regulation of genes in plastid genomes. Although important advances have been made in understanding the functions of these genes, there is little information available on chloroplastic PPR genes in non-model plants and less in plants without chloroplasts. In the present study, a comprehensive and multifactorial bioinformatic strategy was applied to search for putative PPR genes in the foliar and meristematic tissues of green and albino plantlets of the non-model plant Agave angustifolia Haw.ResultsA total of 1581 PPR transcripts were identified, of which 282 were chloroplastic. Leaf tissue in the albino plantlets showed the highest levels of expression of chloroplastic PPRs. The search for hypothetical targets of 12 PPR sequences in the chloroplast genes of A. angustifolia revealed their action on transcripts related to ribosomes and translation, photosystems, ATP synthase, plastid-encoded RNA polymerase and RuBisCO.ConclusionsOur results suggest that the expression of PPR genes depends on the state of cell differentiation and plastid development. In the case of the albino leaf tissue, which lacks functional chloroplasts, it is possible that anterograde and retrograde signaling networks are severely compromised, leading to a compensatory anterograde response characterized by an increase in the expression of PPR genes.
| S-EPMC9295523 | biostudies-literature
Project description:The pentatricopeptide repeat (PPR) is one of the largest gene family in plants, and play important role in regulating plant growth, development and abiotic stress response. However, PPR genes have been poorly studied in grapes. In this study, based on the grape genome database, bioinformatics methods and quantitative real-time PCR (qRT-PCR) were used to identify the VvPPR family and the response to abiotic stress. A total of 181 PPR genes were identified in grape and divided into two subfamilies. Subcellular localization predicted that this gene family mainly functions in chloroplasts, nucleus, and mitochondria. Protein-protein interaction prediction indicated that there may be interaction between VvPPR44,53 and VvPPR44. The promoter region of VvPPR gene family contained various cis-acting elements, which were related to light and hormone. Expression pattern analysis showed that the VvPPR gene family was highly expressed in grape leaves, buds and carpel tissues. qRT-PCR results showed that the expression of VvPPR genes in roots was higher than stems and leaves under NAA, SA, ABA, MeJA and GA3 treatments. VvPPR8 was significantly up-regulated after GA3 and MeJA treatment for 24 h, VvPPR53 was significantly up-regulated after SA, NAA, ABA and MeJA treatment. In addition, In grape leaves, VvPPR53 was up-regulated under PEG, Nacl and 4 ℃ treatments. These data indicate that VvPPR gene family members are responsive to hormones and abiotic stresses, and that there are some differences in the degree of response and expression in different grape tissues. This study provides a certain theoretical basis for grape resistance breeding.
| S-EPMC9723081 | biostudies-literature
Project description:Pentatricopeptide repeat (PPR) proteins are helical-repeat proteins that offer a promising scaffold for the engineering of proteins to bind specified RNAs. PPR tracts bind RNA in a modular 1-repeat, 1-nucleotide fashion. An amino acid code specifying the bound nucleotide has been elucidated. However, this code does not fully explain the sequence specificity of native PPR proteins. Furthermore, it does not address nuances such as the contribution toward binding affinity of various repeat-nucleotide pairs or the impact of mismatches between a repeat and aligning nucleotide. We used an in vitro bind-n-seq approach to describe the population of sequences bound by four artificial PPR proteins built from consensus scaffolds. The specificity of these proteins can be accounted for by canonical code-based nucleotide recognition. The results show, however, that interactions near the 3'-end of binding sites make less contribution to binding affinity than do those near the 5'-end, that proteins with 11 and 14 repeats exhibit similar affinity for their intended targets but 14-repeats are more permissive for mismatches, and that purine-binding repeats are less tolerant of transversion mismatches than are pyrimidine-binding motifs. These findings have implications for mechanisms that establish PPR-RNA interactions and for optimizing PPR design to minimize off-target interactions.
| S-EPMC5861457 | biostudies-literature
Project description:Watermelon (Citrullus lanatus) is an economically important fruit crop grown for consumption of its large edible fruit flesh. Pentatricopeptide-repeat (PPR) encoding genes, one of the large gene families in plants, are important RNA-binding proteins involved in the regulation of plant growth and development by influencing the expression of organellar mRNA transcripts. However, systematic information regarding the PPR gene family in watermelon remains largely unknown. In this comprehensive study, we identified and characterized a total of 422 C. lanatus PPR (ClaPPR) genes in the watermelon genome. Most ClaPPRs were intronless and were mapped across 12 chromosomes. Phylogenetic analysis showed that ClaPPR proteins could be divided into P and PLS subfamilies. Gene duplication analysis suggested that 11 pairs of segmentally duplicated genes existed. In-silico expression pattern analysis demonstrated that ClaPPRs may participate in the regulation of fruit development and ripening processes. Genotyping of 70 lines using 4 single nucleotide polymorphisms (SNPs) from 4 ClaPPRs resulted in match rates of over 0.87 for each validated SNPs in correlation with the unique phenotypes of flesh color, and could be used in differentiating red, yellow, or orange watermelons in breeding programs. Our results provide significant insights for a comprehensive understanding of PPR genes and recommend further studies on their roles in watermelon fruit growth and ripening, which could be utilized for cultivar development of watermelon.
| S-EPMC7650700 | biostudies-literature
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