1. Structural Biology and Molecular Biophysics
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Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts

  1. Hande Boyaci
  2. James Chen
  3. Mirjana Lilic
  4. Margaret Palka
  5. Rachel Anne Mooney
  6. Robert Landick
  7. Seth A Darst  Is a corresponding author
  8. Elizabeth A Campbell  Is a corresponding author
  1. The Rockefeller University, United States
  2. University of Wisconsin-Madison, United States
Research Article
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Cite this article as: eLife 2018;7:e34823 doi: 10.7554/eLife.34823

Abstract

Fidaxomicin (Fdx) is an antimicrobial RNA polymerase (RNAP) inhibitor highly effective against Mycobacterium tuberculosis RNAP in vitro, but clinical use of Fdx is limited to treating Clostridium difficile intestinal infections due to poor absorption. To identify the structural determinants of Fdx binding to RNAP, we determined the 3.4 Å cryo-electron microscopy structure of a complete M. tuberculosis RNAP holoenzyme in complex with Fdx. We find that the actinobacteria general transcription factor RbpA contacts fidaxomycin, explaining its strong effect on M. tuberculosis. Additional structures define conformational states of M. tuberculosis RNAP between the free apo-holoenzyme and the promoter-engaged open complex ready for transcription. The results establish that Fdx acts like a doorstop to jam the enzyme in an open state, preventing the motions necessary to secure promoter DNA in the active site. Our results provide a structural platform to guide development of anti-tuberculosis antimicrobials based on the Fdx binding pocket.

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The following previously published data sets were used

Article and author information

Author details

  1. Hande Boyaci

    Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. James Chen

    Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Mirjana Lilic

    Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Margaret Palka

    Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Rachel Anne Mooney

    Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Robert Landick

    Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Seth A Darst

    Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
    For correspondence
    darst@rockefeller.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8241-3153
  8. Elizabeth A Campbell

    Laboratory of Molecular Biophysics, The Rockefeller University, New York, United States
    For correspondence
    elizabeth.campbell0@gmail.com
    Competing interests
    The authors declare that no competing interests exist.

Funding

The Rockefeller University (Women in Science Fellowship)

  • Hande Boyaci

National Institute of General Medical Sciences (R01 GM38660)

  • Robert Landick

National Institute of General Medical Sciences (R35 GM118130)

  • Seth A Darst

National Institute of General Medical Sciences (R01 GM114450)

  • Elizabeth A 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. Gisela Storz, National Institute of Child Health and Human Development, United States

Publication history

  1. Received: January 4, 2018
  2. Accepted: February 13, 2018
  3. Accepted Manuscript published: February 26, 2018 (version 1)
  4. Version of Record published: March 5, 2018 (version 2)

Copyright

© 2018, Boyaci 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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