An artificial PPR scaffold for programmable RNA recognition
Open accessAbstract
Pentatricopeptide repeat (PPR) proteins control diverse aspects of RNA metabolism in eukaryotic cells. Although recent computational and structural studies have provided insights into RNA recognition by PPR proteins, their highly insoluble nature and inconsistencies between predicted and observed modes of RNA binding have restricted our understanding of their biological functions and their use as tools. Here we use a consensus design strategy to create artificial PPR domains that are structurally robust and can be programmed for sequence-specific RNA binding. The atomic structures of these artificial PPR domains elucidate the structural basis for their stability and modelling of RNA-protein interactions provides mechanistic insights into the importance of RNA-binding residues and suggests modes of PPR-RNA association. The modular mode of RNA binding by PPR proteins holds great promise for the engineering of new tools to target RNA and to understand the mechanisms of gene regulation by natural PPR proteins.
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Biochemical analysis of PPR proteins is very challenging due to low expression levels and aggregation.
“Biochemical analysis of PPR proteins is very challenging due to low expression levels and aggregation (Krause et al. 2004; Coquille et al. 2014).”
From <i>Candida albicans</i> PPR proteins are required for the expression of respiratory Complex I subunits (2024) · cites this paper as Coquille et al. 2014
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Wenda, J. M., Drzewicka, K., Mulica, P., Tetaud, E., di Rago, J. P., Golik, P., & Łabędzka-Dmoch, K. (2024) · GENETICS · doi:10.1093/genetics/iyae124 · Cited by 2 · see citing works
- Authors
- Coquille, S., Filipovska, A., Chia, T., Rajappa, L., Lingford, J. P., Razif, M. F. M., Thore, S., & Rackham, O.
- Affiliations
- University of Geneva (CH)
- The University of Western Australia (AU)
- Corresponding author
- Thore, Stéphane
- Rackham, Oliver
- ORCID
- Venue
- Nature Communications
- Published
- 2014-12-17
- Volume
- 5
- Issue
- 1
- Pages
- 5729-5729
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2163677890
- Cited by
- 120
- References
- 61
- Citations by year
- 2026: 2 · 2025: 7 · 2024: 8 · 2023: 8 · 2022: 11 · 2021: 7 · 2020: 8 · 2019: 15 · 2018: 16 · 2017: 14 · 2016: 16 · 2015: 8
- FWCI
- 5.20
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Nature Communications (publishedVersion)
- PubMed (publishedVersion)
- Archive ouverte UNIGE (University of Geneva) (publishedVersion, other-oa)
- UWA Profiles and Research Repository (UWA) (submittedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- DORA PSI (Paul Scherrer Institute) (submittedVersion)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- Funders
- National Science Foundation
- Novartis Foundation
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (316030, 128787, 140924, 124909)
- Paul Scherrer Institut
- Novartis Stiftung für Medizinisch-Biologische Forschung
- Université de Genève
- Medical Research Council
- Australian Research Council (DP140104111, FT0991113, FT0991008)
- National Health and Medical Research Council (1058442, 1045677)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- pentatricopeptide repeat proteins, sequence-specific RNA binding, RNA-protein interactions, protein engineering, consensus design, crystal structure, RNA metabolism, gene expression regulation, RNA-binding residues
- MeSH terms
- Binding Sites, Gene Expression Regulation, Humans, Models, Molecular, Molecular Sequence Data, Protein Binding, Recombinant Proteins, RNA, Protein Engineering, RNA-Binding Proteins, Arabidopsis, Protein Structure, Tertiary, Amino Acid Motifs, Mitochondrial Proteins, Protein Stability
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