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Protein-guided RNA dynamics during early ribosome assembly

Author

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  • Hajin Kim

    (Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Howard Hughes Medical Institute
    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.).)

  • Sanjaya C. Abeysirigunawarden

    (Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA)

  • Ke Chen

    (Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign
    University of Illinois at Urbana-Champaign)

  • Megan Mayerle

    (CMDB Program, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA
    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.).)

  • Kaushik Ragunathan

    (Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign
    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.).)

  • Zaida Luthey-Schulten

    (Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign
    University of Illinois at Urbana-Champaign)

  • Taekjip Ha

    (Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Howard Hughes Medical Institute
    Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign
    University of Illinois at Urbana-Champaign)

  • Sarah A. Woodson

    (Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA
    CMDB Program, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA)

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.

Suggested Citation

  • Hajin Kim & Sanjaya C. Abeysirigunawarden & Ke Chen & Megan Mayerle & Kaushik Ragunathan & Zaida Luthey-Schulten & Taekjip Ha & Sarah A. Woodson, 2014. "Protein-guided RNA dynamics during early ribosome assembly," Nature, Nature, vol. 506(7488), pages 334-338, February.
    • Handle: RePEc:nat:nature:v:506:y:2014:i:7488:d:10.1038_nature13039
    DOI: 10.1038/nature13039
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    Cited by:

    1. Xiaolin Niu & Zhonghe Xu & Yufan Zhang & Xiaobing Zuo & Chunlai Chen & Xianyang Fang, 2023. "Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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