ArticleBMC evolutionary biology2012
Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures.
Article in BMC evolutionary biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- LRPPRC: A Multifunctional Protein Involved in Energy Metabolism and Human Disease.Frontiers in physiology · 2019Pooled it
- Conservation of the moss RNA editing factor PPR78 despite the loss of its known cytidine-to-uridine editing sites is explained by a hidden extra target.The Plant cell · 2024Article
- A Genome-Wide Analysis of the Pentatricopeptide Repeat Protein Gene Family in Two Kiwifruit Species with an Emphasis on the Role of RNA Editing in Pathogen Stress.International journal of molecular sciences · 2023Article
- Emergence of Novel RNA-Editing Sites by Changes in the Binding Affinity of a Conserved PPR Protein.Molecular biology and evolution · 2022Article
- Identification and expression analysis of the grape pentatricopeptide repeat (PPR) gene family in abiotic stress.Physiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- Article
- Plant mitochondrial RNA editing factors can perform targeted C-to-U editing of nuclear transcripts in human cells.Nucleic acids research · 2022Article
- An Overview of Pentatricopeptide Repeat (PPR) Proteins in the MossPlants (Basel, Switzerland) · 2022Review
- Advancing organelle genome transformation and editing for crop improvement.Plant communications · 2021Review
- One C-to-U RNA Editing Site and Two Independently Evolved Editing Factors: Testing Reciprocal Complementation with DYW-Type PPR Proteins from the MossThe Plant cell · 2020Article
- The dual-targeted RNA editing factor AEF1 is universally conserved among angiosperms and reveals only minor adaptations upon loss of its chloroplast or its mitochondrial target.Plant molecular biology · 2020Article
- Establishment of a Heterologous RNA Editing Event in Chloroplasts.Plant physiology · 2019Article
- Multifarious Evolutionary Pathways of a Nuclear RNA Editing Factor: Disjunctions in Coevolution of DOT4 and Its Chloroplast Target rpoC1eU488SL.Genome biology and evolution · 2019Article
- Expected and unexpected evolution of plant RNA editing factors CLB19, CRR28 and RARE1: retention of CLB19 despite a phylogenetically deep loss of its two known editing targets in Poaceae.BMC evolutionary biology · 2018Article
- The Pentatricopeptide Repeat Gene Family inMolecules (Basel, Switzerland) · 2018Article
- Functional divergence and origin of the DAG-like gene family in plants.Scientific reports · 2017Article
- Mitochondrial-nuclear co-evolution leads to hybrid incompatibility through pentatricopeptide repeat proteins.EMBO reports · 2017Article
- Frequent chloroplast RNA editing in early-branching flowering plants: pilot studies on angiosperm-wide coexistence of editing sites and their nuclear specificity factors.BMC evolutionary biology · 2016Article
- Genome-wide transcript profiling reveals the coevolution of plastid gene sequences and transcript processing pathways in the fucoxanthin dinoflagellate Karlodinium veneficum.Molecular biology and evolution · 2014Article
- Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing.BMC plant biology · 2013Article
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3 authors.
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Abstract
backgroundPentatricopeptide repeat (PPR) proteins are required for numerous RNA processing events in plant organelles including C-to-U editing, splicing, stabilization, and cleavage. Fifteen PPR proteins are known to be required for RNA editing at 21 sites in Arabidopsis chloroplasts, and belong to the PLS class of PPR proteins. In this study, we investigate the co-evolution of four PPR genes (CRR4, CRR21, CLB19, and OTP82) and their six editing targets in Brassicaceae species. PPR genes are composed of approximately 10 to 20 tandem repeats and each repeat has two α-helical regions, helix A and helix B, that are separated by short coil regions. Each repeat and structural feature was examined to determine the selective pressures on these regions.
resultsAll of the PPR genes examined are under strong negative selection. Multiple independent losses of editing site targets are observed for both CRR21 and OTP82. In several species lacking the known editing target for CRR21, PPR genes are truncated near the 17th PPR repeat. The coding sequences of the truncated CRR21 genes are maintained under strong negative selection; however, the 3' UTR sequences beyond the truncation site have substantially diverged. Phylogenetic analyses of four PPR genes show that sequences corresponding to helix A are high compared to helix B sequences. Differential evolutionary selection of helix A versus helix B is observed in both plant and mammalian PPR genes.
conclusionPPR genes and their cognate editing sites are mutually constrained in evolution. Editing sites are frequently lost by replacement of an edited C with a genomic T. After the loss of an editing site, the PPR genes are observed with three outcomes: first, few changes are detected in some cases; second, the PPR gene is present as a pseudogene; and third, the PPR gene is present but truncated in the C-terminal region. The retention of truncated forms of CRR21 that are maintained under strong negative selection even in the absence of an editing site target suggests that unrecognized function(s) might exist for this PPR protein. PPR gene sequences that encode helix A are under strong selection, and could be involved in RNA substrate recognition.
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