Transcription inhibition by the depsipeptide antibiotic salinamide A

David Degen, Yu Feng, Yu Zhang, Katherine Y. Ebright, Yon W. Ebright, Matthew Gigliotti, Hanif Vahedian-Movahed, Sukhendu Mandal, Meliza Talaue, Nancy Connell, Eddy Arnold, William Fenical, Richard H. Ebright

Research output: Contribution to journalArticlepeer-review

43 Scopus citations


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.

Original languageEnglish (US)
Article numbere02451
Issue number3
StatePublished - Apr 30 2014
Externally publishedYes


  • Allosteric inhibitor
  • Antibacterial agent
  • Antibacterial resistance
  • Antibiotic
  • Bridge helix
  • Bridge helix N-terminal hinge
  • Bridge-helix cap
  • CBR703
  • Crystal structure
  • F-loop
  • Inhibitor
  • Link region
  • Lipiarmycin
  • Myxopyronin
  • Nucleotide addition
  • RNA polymerase
  • Resistance mutant
  • Resistance spectrum
  • Rifampin
  • Rifamycin
  • Salinamide A
  • Salinamide B
  • Salinamides
  • Streptolydigin
  • Transcription
  • Transcription elongation
  • Transcription initiation
  • Trigger loop

ASJC Scopus subject areas

  • Neuroscience(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)


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