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.

Reviewing Editor

  1. Gisela Storz, National Institute of Child Health and Human Development, United States

Version history

  1. Received: February 2, 2014
  2. Accepted: April 18, 2014
  3. Accepted Manuscript published: April 30, 2014 (version 1)
  4. Version of Record published: May 21, 2014 (version 2)

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.

Metrics

  • 3,127
    views
  • 429
    downloads
  • 72
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  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

Further reading

    1. Biochemistry and Chemical Biology
    2. Plant Biology
    Henning Mühlenbeck, Yuko Tsutsui ... Cyril Zipfel
    Research Article

    Transmembrane signaling by plant receptor kinases (RKs) has long been thought to involve reciprocal trans-phosphorylation of their intracellular kinase domains. The fact that many of these are pseudokinase domains, however, suggests that additional mechanisms must govern RK signaling activation. Non-catalytic signaling mechanisms of protein kinase domains have been described in metazoans, but information is scarce for plants. Recently, a non-catalytic function was reported for the leucine-rich repeat (LRR)-RK subfamily XIIa member EFR (elongation factor Tu receptor) and phosphorylation-dependent conformational changes were proposed to regulate signaling of RKs with non-RD kinase domains. Here, using EFR as a model, we describe a non-catalytic activation mechanism for LRR-RKs with non-RD kinase domains. EFR is an active kinase, but a kinase-dead variant retains the ability to enhance catalytic activity of its co-receptor kinase BAK1/SERK3 (brassinosteroid insensitive 1-associated kinase 1/somatic embryogenesis receptor kinase 3). Applying hydrogen-deuterium exchange mass spectrometry (HDX-MS) analysis and designing homology-based intragenic suppressor mutations, we provide evidence that the EFR kinase domain must adopt its active conformation in order to activate BAK1 allosterically, likely by supporting αC-helix positioning in BAK1. Our results suggest a conformational toggle model for signaling, in which BAK1 first phosphorylates EFR in the activation loop to stabilize its active conformation, allowing EFR in turn to allosterically activate BAK1.

    1. Biochemistry and Chemical Biology
    2. Neuroscience
    Katarzyna Marta Zoltowska, Utpal Das ... Lucía Chávez-Gutiérrez
    Research Article

    Amyloid β (Aβ) peptides accumulating in the brain are proposed to trigger Alzheimer’s disease (AD). However, molecular cascades underlying their toxicity are poorly defined. Here, we explored a novel hypothesis for Aβ42 toxicity that arises from its proven affinity for γ-secretases. We hypothesized that the reported increases in Aβ42, particularly in the endolysosomal compartment, promote the establishment of a product feedback inhibitory mechanism on γ-secretases, and thereby impair downstream signaling events. We conducted kinetic analyses of γ-secretase activity in cell-free systems in the presence of Aβ, as well as cell-based and ex vivo assays in neuronal cell lines, neurons, and brain synaptosomes to assess the impact of Aβ on γ-secretases. We show that human Aβ42 peptides, but neither murine Aβ42 nor human Aβ17–42 (p3), inhibit γ-secretases and trigger accumulation of unprocessed substrates in neurons, including C-terminal fragments (CTFs) of APP, p75, and pan-cadherin. Moreover, Aβ42 treatment dysregulated cellular homeostasis, as shown by the induction of p75-dependent neuronal death in two distinct cellular systems. Our findings raise the possibility that pathological elevations in Aβ42 contribute to cellular toxicity via the γ-secretase inhibition, and provide a novel conceptual framework to address Aβ toxicity in the context of γ-secretase-dependent homeostatic signaling.