1. Biochemistry and Chemical Biology
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Allosteric mechanism of the V. vulnificus adenine riboswitch resolved by four-dimensional chemical mapping

  1. Siqi Tian
  2. Wipapat Kladwang
  3. Rhiju Das  Is a corresponding author
  1. Stanford University, United States
Research Article
  • Cited 5
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Cite this article as: eLife 2018;7:e29602 doi: 10.7554/eLife.29602

Abstract

The structural interconversions that mediate the gene regulatory functions of RNA molecules may be different from classic models of allostery, but the relevant structural correlations have remained elusive in even intensively studied systems. Here, we present a four-dimensional expansion of chemical mapping called lock-mutate-map-rescue (LM2R), which integrates multiple layers of mutation with nucleotide-resolution chemical mapping. This technique resolves the core mechanism of the adenine-responsive V. vulnificus add riboswitch, a paradigmatic system for which both Monod-Wyman-Changeux (MWC) conformational selection models and non-MWC alternatives have been proposed. To discriminate amongst these models, we locked each functionally important helix through designed mutations and assessed formation or depletion of other helices via compensatory rescue evaluated by chemical mapping. These LM2R measurements give strong support to the pre-existing correlations predicted by MWC models, disfavor alternative models, and suggest additional structural heterogeneities that may be general across ligand-free riboswitches.

Article and author information

Author details

  1. Siqi Tian

    Department of Biochemistry, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Wipapat Kladwang

    Department of Biochemistry, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Rhiju Das

    Department of Biochemistry, Stanford University, Stanford, United States
    For correspondence
    rhiju@stanford.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7497-0972

Funding

National Institutes of Health (R01GM102519)

  • Rhiju Das

National Institutes of Health (R35GM122579)

  • Rhiju Das

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

Reviewing Editor

  1. Anna Marie Pyle, Yale University, United States

Publication history

  1. Received: June 15, 2017
  2. Accepted: February 13, 2018
  3. Accepted Manuscript published: February 15, 2018 (version 1)
  4. Version of Record published: March 12, 2018 (version 2)

Copyright

© 2018, Tian 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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