Article | Published:

Protein-guided RNA dynamics during early ribosome assembly

Nature volume 506, pages 334338 (20 February 2014) | Download Citation

Abstract

The assembly of 30S ribosomes requires the precise addition of 20 proteins to the 16S ribosomal RNA. How early binding proteins change the ribosomal RNA structure so that later proteins may join the complex is poorly understood. Here we use single-molecule fluorescence resonance energy transfer (FRET) to observe real-time encounters between Escherichia coli ribosomal protein S4 and the 16S 5′ domain RNA at an early stage of 30S assembly. Dynamic initial S4–RNA complexes pass through a stable non-native intermediate before converting to the native complex, showing that non-native structures can offer a low free-energy path to protein–RNA recognition. Three-colour FRET and molecular dynamics simulations reveal how S4 changes the frequency and direction of RNA helix motions, guiding a conformational switch that enforces the hierarchy of protein addition. These protein-guided dynamics offer an alternative explanation for induced fit in RNA–protein complexes.

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Acknowledgements

This work was supported by grants from the National Institutes of Health (R01 GM60819 to S.A.W.; R01 GM65367 to T.H.) and from the National Science Foundation (NSF) (PHY0822613 to T.H. and MCB12-44570 to Z. L.-S.). Supercomputer computing time was provided by NSF XSEDE (TG-MCA03S027). T.H. is an investigator with the Howard Hughes Medical Institute.

Author information

Author notes

    • Hajin Kim
    •  & Sanjaya C. Abeysirigunawarden

    These authors contributed equally to this work.

    • Hajin Kim
    • , Megan Mayerle
    •  & Kaushik Ragunathan

    Present addresses: School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea (H.K.); Department of Biochemistry and Biophysics, University of California at San Francisco, 600 16th Street, San Francisco, California 94143-2200, USA (M.M.); Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, LHRRB-517, Boston, Massachusetts 02115-5730, USA (K.R.).

Affiliations

  1. Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA

    • Hajin Kim
    • , Zaida Luthey-Schulten
    •  & Taekjip Ha
  2. Howard Hughes Medical Institute, Urbana, Illinois 61801, USA

    • Hajin Kim
    •  & Taekjip Ha
  3. T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA

    • Sanjaya C. Abeysirigunawarden
    •  & Sarah A. Woodson
  4. Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA

    • Ke Chen
    • , Kaushik Ragunathan
    • , Zaida Luthey-Schulten
    •  & Taekjip Ha
  5. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA

    • Ke Chen
    • , Zaida Luthey-Schulten
    •  & Taekjip Ha
  6. CMDB Program, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA

    • Megan Mayerle
    •  & Sarah A. Woodson

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Contributions

H.K., S.C.A., Z.L.-S., T.H. and S.A.W. designed the research. H.K., S.C.A., K.R. and M.M. conducted experiments, S.C.A. and M.M. provided samples, K.C. performed molecular dynamics simulations, H.K. and K.R. analysed the data and H.K. and S.A.W. wrote the paper with input from other authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Taekjip Ha or Sarah A. Woodson.

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https://doi.org/10.1038/nature13039

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