A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity

  1. Chen Qiu
  2. Vandita D Bhat
  3. Sanjana Rajeev
  4. Chi Zhang
  5. Alexa E Lasley
  6. Robert N Wine
  7. Zachary T Campbell  Is a corresponding author
  8. Traci M T Tanaka Hall  Is a corresponding author
  1. National Institute of Environmental Health Sciences, National Institutes of Health, United States
  2. University of Texas at Dallas, United States

Abstract

In the Caenorhabditis elegans germline, fem-3 Binding Factor (FBF) partners with LST-1 to maintain stem cells. A crystal structure of an FBF-2/LST-1/RNA complex revealed that FBF-2 recognizes a short RNA motif different from the characteristic 9-nt FBF binding element, and compact motif recognition coincided with curvature changes in the FBF-2 scaffold. Previously we engineered FBF-2 to favor recognition of shorter RNA motifs without curvature change (Bhat, Qiu, et al. 2019). In vitro selection of RNAs bound by FBF-2 suggested sequence specificity in the central region of the compact element. This bias, reflected in the crystal structure, was validated in RNA-binding assays. FBF-2 has the intrinsic ability to bind to this shorter motif. LST-1 weakens FBF-2 binding affinity for short and long motifs, which may increase target selectivity. Our findings highlight the role of FBF scaffold flexibility in RNA recognition and suggest a new mechanism by which protein partners refine target site selection.

Data availability

Atomic coordinates and structure factors are deposited under RCSB PDB ID 6PUN. SEQRS sequence data are available through the Dryad Digital Repository, accession number doi:10.5061/dryad.30501q7.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Chen Qiu

    Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Vandita D Bhat

    Department of Biological Sciences, University of Texas at Dallas, Richardson, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Sanjana Rajeev

    Department of Biological Sciences, University of Texas at Dallas, Richardson, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Chi Zhang

    Department of Biological Sciences, University of Texas at Dallas, Richardson, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Alexa E Lasley

    Department of Biological Sciences, University of Texas at Dallas, Richardson, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Robert N Wine

    Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Zachary T Campbell

    Department of Biological Sciences, University of Texas at Dallas, Richardson, United States
    For correspondence
    zachary.campbell@utdallas.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3768-6996
  8. Traci M T Tanaka Hall

    Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States
    For correspondence
    hall4@niehs.nih.gov
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6166-3009

Funding

National Institutes of Health (ZIA ES50165)

  • Traci M T Tanaka Hall

National Institutes of Health (R01NS100788)

  • Zachary T Campbell

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

Reviewing Editor

  1. Timothy W Nilsen, Case Western Reserve University, United States

Version history

  1. Received: June 4, 2019
  2. Accepted: August 9, 2019
  3. Accepted Manuscript published: August 9, 2019 (version 1)
  4. Version of Record published: August 16, 2019 (version 2)
  5. Version of Record updated: August 30, 2019 (version 3)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

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  1. Chen Qiu
  2. Vandita D Bhat
  3. Sanjana Rajeev
  4. Chi Zhang
  5. Alexa E Lasley
  6. Robert N Wine
  7. Zachary T Campbell
  8. Traci M T Tanaka Hall
(2019)
A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity
eLife 8:e48968.
https://doi.org/10.7554/eLife.48968

Share this article

https://doi.org/10.7554/eLife.48968

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