1. Biochemistry and Chemical Biology
  2. Microbiology and Infectious Disease

Transcription inhibition by the depsipeptide antibiotic salinamide A

  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  Is a corresponding author
  1. Rutgers University, United States
  2. University of California, San Diego, United States
https://doi.org/10.7554/eLife.02451
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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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  3. Download .RIS

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

Share this article

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

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Further reading

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    GE23077 binds to the RNA polymerase ‘i’ and ‘i+1’ sites and prevents the binding of initiating nucleotides

    Yu Zhang, David Degen ... Richard H Ebright
    Research Article

    Using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic GE23077 (GE) binds directly to the bacterial RNA polymerase (RNAP) active-center ‘i’ and ‘i+1’ nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. The target-based resistance spectrum for GE is unusually small, reflecting the fact that the GE binding site on RNAP includes residues of the RNAP active center that cannot be substituted without loss of RNAP activity. The GE binding site on RNAP is different from the rifamycin binding site. Accordingly, GE and rifamycins do not exhibit cross-resistance, and GE and a rifamycin can bind simultaneously to RNAP. The GE binding site on RNAP is immediately adjacent to the rifamycin binding site. Accordingly, covalent linkage of GE to a rifamycin provides a bipartite inhibitor having very high potency and very low susceptibility to target-based resistance.