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Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes

Author

Listed:
  • Sanjaya C. Abeysirigunawardena

    (Johns Hopkins University
    Kent State University)

  • Hajin Kim

    (Ulsan National Institute of Science and Technology
    Institute for Basic Science)

  • Jonathan Lai

    (University of Illinois at Urbana-Champaign)

  • Kaushik Ragunathan

    (University of Illinois at Urbana-Champaign
    University of Michigan Medical School)

  • Mollie C. Rappé

    (Johns Hopkins University
    Sandia National Laboratory)

  • Zaida Luthey-Schulten

    (University of Illinois at Urbana-Champaign)

  • Taekjip Ha

    (Johns Hopkins University
    University of Illinois at Urbana-Champaign
    Johns Hopkins University
    Howard Hughes Medical Institute)

  • Sarah A. Woodson

    (Johns Hopkins University)

Abstract

Assembly of 30S ribosomes involves the hierarchical addition of ribosomal proteins that progressively stabilize the folded 16S rRNA. Here, we use three-color single molecule FRET to show how combinations of ribosomal proteins uS4, uS17 and bS20 in the 16S 5′ domain enable the recruitment of protein bS16, the next protein to join the complex. Analysis of real-time bS16 binding events shows that bS16 binds both native and non-native forms of the rRNA. The native rRNA conformation is increasingly favored after bS16 binds, explaining how bS16 drives later steps of 30S assembly. Chemical footprinting and molecular dynamics simulations show that each ribosomal protein switches the 16S conformation and dampens fluctuations at the interface between rRNA subdomains where bS16 binds. The results suggest that specific protein-induced changes in the rRNA dynamics underlie the hierarchy of 30S assembly and simplify the search for the native ribosome structure.

Suggested Citation

  • Sanjaya C. Abeysirigunawardena & Hajin Kim & Jonathan Lai & Kaushik Ragunathan & Mollie C. Rappé & Zaida Luthey-Schulten & Taekjip Ha & Sarah A. Woodson, 2017. "Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes," Nature Communications, Nature, vol. 8(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-00536-1
    DOI: 10.1038/s41467-017-00536-1
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