1. Biochemistry and Chemical Biology

A dynamic RNA loop in an IRES affects multiple steps of elongation factor-mediated translation initiation

  1. Marisa Ruehle
  2. Haibo Zhang
  3. Ryan M Sheridan
  4. Somdeb Mitra
  5. Yuanwei Chen
  6. Ruben L Gonzalez
  7. Barry S Cooperman
  8. Jeffrey S Kieft  Is a corresponding author
  1. Howard Hughes Medical Institute, University of Colorado Denver School of Medicine, United States
  2. University of Pennsylvania, United States
  3. Columbia University, United States
https://doi.org/10.7554/eLife.08146
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Cite this article
  1. Marisa Ruehle
  2. Haibo Zhang
  3. Ryan M Sheridan
  4. Somdeb Mitra
  5. Yuanwei Chen
  6. Ruben L Gonzalez
  7. Barry S Cooperman
  8. Jeffrey S Kieft
(2015)
A dynamic RNA loop in an IRES affects multiple steps of elongation factor-mediated translation initiation
eLife 4:e08146.
https://doi.org/10.7554/eLife.08146
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Abstract

Internal ribosome entry sites (IRESs) are powerful model systems to understand how the translation machinery can be manipulated by structured RNAs and for exploring inherent features of ribosome function. The intergenic region (IGR) IRESs from the Dicistroviridae family of viruses are structured RNAs that bind directly to the ribosome and initiate translation by co-opting the translation elongation cycle. These IRESs require an RNA pseudoknot that mimics a codon-anticodon interaction and contains a conformationally dynamic loop. We explored the role of this loop and found that both the length and sequence are essential for translation in different types of IGR IRESs and from diverse viruses. We found that loop 3 affects two discrete elongation factor-dependent steps in the IRES initiation mechanism. Our results show how the IRES directs multiple steps after 80S ribosome placement and highlights the often underappreciated significance of discrete conformationally dynamic elements within the context of structured RNAs.

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Author details

  1. Marisa Ruehle

    Department of Biochemistry and Molecular Genetics, Howard Hughes Medical Institute, University of Colorado Denver School of Medicine, Aurora, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Haibo Zhang

    Department of Chemistry, University of Pennsylvania, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Ryan M Sheridan

    Department of Biochemistry and Molecular Genetics, Howard Hughes Medical Institute, University of Colorado Denver School of Medicine, Aurora, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Somdeb Mitra

    Department of Chemistry, Columbia University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Yuanwei Chen

    Department of Chemistry, University of Pennsylvania, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Ruben L Gonzalez

    Department of Chemistry, Columbia University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Barry S Cooperman

    Department of Chemistry, University of Pennsylvania, Philadelphia, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Jeffrey S Kieft

    Department of Biochemistry and Molecular Genetics, Howard Hughes Medical Institute, University of Colorado Denver School of Medicine, Aurora, United States
    For correspondence
    jeffrey.kieft@ucdenver.edu
    Competing interests
    The authors declare that no competing interests exist.

Copyright

© 2015, Ruehle 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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