Abstract

We report that bacterial RNA polymerase (RNAP) is the functional cellular target of the depsipeptide antibiotic salinamide A (Sal), and we report that Sal inhibits RNAP through a novel binding site and mechanism. We show that Sal inhibits RNA synthesis in cells and that mutations that confer Sal-resistance map to RNAP genes. We show that Sal interacts with the RNAP active-center 'bridge-helix cap,' comprising the 'bridge-helix N-terminal hinge,' 'F-loop,' and 'link region.' We show that Sal inhibits nucleotide addition in transcription initiation and elongation. We present a crystal structure that defines interactions between Sal and RNAP and effects of Sal on RNAP conformation. We propose that Sal functions by binding to the RNAP bridge-helix cap and preventing conformational changes of the bridge-helix N-terminal hinge necessary for nucleotide addition. The results provide a target for antibacterial drug discovery and a reagent to probe conformation and function of the bridge-helix N-terminal hinge.

Article and author information

Author details

  1. David Degen

    Rutgers University, Piscataway, United States
    Competing interests
    David Degen, patents pending on Sal derivatives and on bridge-helix-cap target.
  2. Yu Feng

    Rutgers University, Piscataway, United States
    Competing interests
    Yu Feng, patents pending on Sal derivatives.
  3. Yu Zhang

    Rutgers University, Piscataway, United States
    Competing interests
    Yu Zhang, patents pending on Sal derivatives.
  4. Katherine Y Ebright

    Rutgers University, Piscataway, United States
    Competing interests
    Katherine Y Ebright, patent pending on bridge-helix-cap target.
  5. Yon W Ebright

    Rutgers University, Piscataway, United States
    Competing interests
    Yon W Ebright, patents pending on Sal derivatives.
  6. Matthew Gigliotti

    Rutgers University, Piscataway, United States
    Competing interests
    No competing interests declared.
  7. Hanif Vahedian-Movahed

    Rutgers University, Piscataway, United States
    Competing interests
    No competing interests declared.
  8. Sukhendu Mandal

    Rutgers University, Piscataway, United States
    Competing interests
    No competing interests declared.
  9. Meliza Talaue

    Rutgers University, Newark, United States
    Competing interests
    No competing interests declared.
  10. Nancy Connell

    Rutgers University, Newark, United States
    Competing interests
    No competing interests declared.
  11. Eddy Arnold

    Rutgers University, Piscataway, United States
    Competing interests
    No competing interests declared.
  12. William Fenical

    University of California, San Diego, La Jolla, United States
    Competing interests
    William Fenical, patent on SalA and SalB; patent pending on Sal derivatives.
  13. Richard H Ebright

    Rutgers University, Piscataway, United States
    For correspondence
    ebright@waksman.rutgers.edu
    Competing interests
    Richard H Ebright, patents pending on Sal derivatives and on bridge-helix-cap target.

Copyright

© 2014, Degen et al.

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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  1. David Degen
  2. Yu Feng
  3. Yu Zhang
  4. Katherine Y Ebright
  5. Yon W Ebright
  6. Matthew Gigliotti
  7. Hanif Vahedian-Movahed
  8. Sukhendu Mandal
  9. Meliza Talaue
  10. Nancy Connell
  11. Eddy Arnold
  12. William Fenical
  13. Richard H Ebright
(2014)
Transcription inhibition by the depsipeptide antibiotic salinamide A
eLife 3:e02451.
https://doi.org/10.7554/eLife.02451

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https://doi.org/10.7554/eLife.02451

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