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An artificial PPR scaffold for programmable RNA recognition

Author

Listed:
  • Sandrine Coquille

    (University of Geneva)

  • Aleksandra Filipovska

    (Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia
    School of Chemistry and Biochemistry, The University of Western Australia)

  • Tiongsun Chia

    (Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia)

  • Lional Rajappa

    (University of Geneva)

  • James P. Lingford

    (Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia)

  • Muhammad F.M. Razif

    (Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia
    Present address: Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia)

  • Stéphane Thore

    (University of Geneva)

  • Oliver Rackham

    (Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia
    School of Chemistry and Biochemistry, The University of Western Australia)

Abstract

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.

Suggested Citation

  • Sandrine Coquille & Aleksandra Filipovska & Tiongsun Chia & Lional Rajappa & James P. Lingford & Muhammad F.M. Razif & Stéphane Thore & Oliver Rackham, 2014. "An artificial PPR scaffold for programmable RNA recognition," Nature Communications, Nature, vol. 5(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms6729
    DOI: 10.1038/ncomms6729
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