1. Structural Biology and Molecular Biophysics
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Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand

  1. Jiacheng Zhang
  2. Bhaskar Chetnani
  3. Eric D Cormack
  4. Dulce Alonso
  5. Wei Liu
  6. Alfonso Mondragon
  7. Jingyi Fei  Is a corresponding author
  1. University of Chicago, United States
  2. Northwestern University, United States
Research Article
  • Cited 12
  • Views 2,194
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Cite this article as: eLife 2018;7:e39518 doi: 10.7554/eLife.39518

Abstract

T-box riboswitches are cis-regulatory RNA elements that regulate the expression of proteins involved in amino acid biosynthesis and transport by binding to specific tRNAs and sensing their aminoacylation state. While the T-box modular structural elements that recognize different parts of a tRNA have been identified, the kinetic trajectory describing how these interactions are established temporally remains unclear. Using smFRET, we demonstrate that tRNA binds to the riboswitch in two steps, first anticodon recognition followed by the sensing of the 3' NCCA end, with the second step accompanied by a T-box riboswitch conformational change. Studies on site-specific mutants highlight that specific T-box structural elements drive the two-step binding process in a modular fashion. Our results set up a kinetic framework describing tRNA binding by T-box riboswitches, and propose such binding mechanism is kinetically beneficial for efficient, co-transcriptional recognition of the cognate tRNA ligand.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. smFRET trajectories of each data sets included in the manuscript are available in Source Data.

Article and author information

Author details

  1. Jiacheng Zhang

    Institute for Biophysical Dynamics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Bhaskar Chetnani

    Department of Molecular Biosciences, Northwestern University, Evanston, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Eric D Cormack

    The University of Chicago College, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Dulce Alonso

    Department of Molecular Biosciences, Northwestern University, Evanston, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Wei Liu

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Alfonso Mondragon

    Department of Molecular Biosciences, Northwestern University, Evanston, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0423-6323
  7. Jingyi Fei

    Institute for Biophysical Dynamics, University of Chicago, Chicago, United States
    For correspondence
    jingyifei@uchicago.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9775-3820

Funding

Chicago Community Trust

  • Jingyi Fei

Chicago Community Trust

  • Alfonso Mondragon

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

Reviewing Editor

  1. Gisela Storz, National Institute of Child Health and Human Development, United States

Publication history

  1. Received: June 27, 2018
  2. Accepted: September 24, 2018
  3. Accepted Manuscript published: September 25, 2018 (version 1)
  4. Version of Record published: October 22, 2018 (version 2)

Copyright

© 2018, Zhang 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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