ArticleNucleic acids research2018
RNA-binding specificity landscapes of designer pentatricopeptide repeat proteins elucidate principles of PPR-RNA interactions.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Pentatricopeptide repeat proteins in crops: Advances in functional mechanisms and breeding applications.Journal of integrative plant biology · 2026Review
- Expanding the palette of cis-elements to tune the expression of chloroplast transgenes in tobacco.The Plant journal : for cell and molecular biology · 2026Article
- Structural basis of plant organelle C-to-U RNA editing by PPR-DYW proteins.Nature communications · 2026Article
- Synthetic Pentatricopeptide Repeat Proteins: Building a Toolkit for Precise RNA Control.International journal of molecular sciences · 2025Review
- RECODE: a programmable guide-free C-to-U RNA editing tool.Nucleic acids research · 2025Article
- GRASP: a modular toolkit for building synthetic pentatricopeptide repeat RNA-binding proteins.Nucleic acids research · 2025Article
- Contribution of Range-Wide and Short-Scale Chemical Soil Variation to Local Adaptation in a Tropical Montane Forest Tree.Evolutionary applications · 2025Article
- De novo RNA base editing in plant organelles with engineered synthetic P-type PPR editing factors.Nucleic acids research · 2025Article
- Pentatricopeptide repeat proteins in plants: Cellular functions, action mechanisms, and potential applications.Plant communications · 2025Review
- Targeted introduction of premature stop codon in plant mitochondrial mRNA by a designer pentatricopeptide repeat protein with C-to-U editing function.The Plant journal : for cell and molecular biology · 2025Article
- Single-molecule visualization of sequence-specific RNA binding by a designer PPR protein.Nucleic acids research · 2024Article
- GENOMES UNCOUPLED PROTEIN1 binds to plastid RNAs and promotes their maturation.Plant communications · 2024Article
- Translational activation by a synthetic PPR protein elucidates control of psbA translation in Arabidopsis chloroplasts.The Plant cell · 2024Article
- Applications of Synthetic Pentatricopeptide Repeat Proteins.Plant & cell physiology · 2024Review
- Mitochondrial atp1 mRNA knockdown by a custom-designed pentatricopeptide repeat protein alters ATP synthase.Plant physiology · 2024Article
- Chloroplast gene expression: Recent advances and perspectives.Plant communications · 2023Review
- Beyond a PPR-RNA recognition code: Many aspects matter for the multi-targeting properties of RNA editing factor PPR56.PLoS genetics · 2023Article
- Plant organellar RNA maturation.The Plant cell · 2023Review
- Engineering of pentatricopeptide repeat proteins in organellar gene regulation.Frontiers in plant science · 2023Article
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.