1. Structural Biology and Molecular Biophysics

Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch

  1. My-Tra Le  Is a corresponding author
  2. Wojciech K Kasprzak
  3. Taejin Kim
  4. Feng Gao
  5. Megan YL Young
  6. Xuefeng Yuan
  7. Bruce A Shapiro
  8. Joonil Seog
  9. Anne E Simon  Is a corresponding author
  1. University of Maryland, United States
  2. Leidos Biomedical Research, Inc., United States
  3. National Cancer Institute, United States
  4. College of Plant Protection, Shandong Agricultural University, China
https://doi.org/10.7554/eLife.22883
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  1. My-Tra Le
  2. Wojciech K Kasprzak
  3. Taejin Kim
  4. Feng Gao
  5. Megan YL Young
  6. Xuefeng Yuan
  7. Bruce A Shapiro
  8. Joonil Seog
  9. Anne E Simon
(2017)
Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch
eLife 6:e22883.
https://doi.org/10.7554/eLife.22883
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Abstract

Turnip crinkle virus contains a T-shaped, ribosome-binding, translation enhancer (TSS) in its 3'UTR that serves as a hub for interactions throughout the region. The viral RNA-dependent RNA polymerase (RdRp) causes the TSS/surrounding region to undergo a conformational shift postulated to inhibit translation. Using optical tweezers (OT) and steered molecular dynamic simulations (SMD), we found that the unusual stability of pseudoknotted element H4a/Ψ3 required five upstream adenylates, and H4a/Ψ3 was necessary for cooperative association of two other hairpins (H5/H4b) in Mg2+. SMD recapitulated the TSS unfolding order in the absence of Mg2+, showed dependence of the resistance to pulling on the 3D orientation and gave structural insights into the measured contour lengths of the TSS structure elements. Adenylate mutations eliminated one-site RdRp binding to the 3'UTR, suggesting that RdRp binding to the adenylates disrupts H4a/Ψ3, leading to loss of H5/H4b interaction and promoting a conformational switch interrupting translation and promoting replication.

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Author details

  1. My-Tra Le

    Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
    For correspondence
    my.letra@gmail.com
    Competing interests
    The authors declare that no competing interests exist.

  2. Wojciech K Kasprzak

    Basic Science Program, Leidos Biomedical Research, Inc., Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Taejin Kim

    RNA Biology Laboratory, National Cancer Institute, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Feng Gao

    Department of Cell Biology and Molecular Genetics, University of Maryland, College Pak, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Megan YL Young

    Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Xuefeng Yuan

    Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
    Competing interests
    The authors declare that no competing interests exist.

  7. Bruce A Shapiro

    RNA Biology Laboratory, National Cancer Institute, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Joonil Seog

    Department of Materials Science and Engineering, University of Maryland, College Park, United States
    Competing interests
    The authors declare that no competing interests exist.

  9. Anne E Simon

    Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States
    For correspondence
    simona@umd.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6121-0704

Funding

National Science Foundation (MCB-1411836)

  • My-Tra Le
  • Feng Gao
  • Megan YL Young
  • Xuefeng Yuan
  • Anne E Simon

National Institutes of Health (R21AI117882-01)

  • My-Tra Le
  • Feng Gao
  • Anne E Simon

National Cancer Institute (Intramural)

  • Wojciech K Kasprzak
  • Taejin Kim
  • Bruce A Shapiro

National Institutes of Health (T32GM080201)

  • Megan YL Young

National Institutes of Health (2T32AI051967-06A1)

  • Megan YL Young
  • Anne E Simon

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2017, Le et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. My-Tra Le
  2. Wojciech K Kasprzak
  3. Taejin Kim
  4. Feng Gao
  5. Megan YL Young
  6. Xuefeng Yuan
  7. Bruce A Shapiro
  8. Joonil Seog
  9. Anne E Simon
(2017)
Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch
eLife 6:e22883.
https://doi.org/10.7554/eLife.22883

Share this article

https://doi.org/10.7554/eLife.22883

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