CBR antimicrobials alter coupling between the bridge helix and the β subunit in RNA polymerase

Nat Commun. 2014 Mar 6;5:3408. doi: 10.1038/ncomms4408.


Bacterial RNA polymerase (RNAP) is a validated target for antibacterial drugs. CBR703 series antimicrobials allosterically inhibit transcription by binding to a conserved α helix (β' bridge helix, BH) that interconnects the two largest RNAP subunits. Here we show that disruption of the BH-β subunit contacts by amino-acid substitutions invariably results in accelerated catalysis, slowed-down forward translocation and insensitivity to regulatory pauses. CBR703 partially reverses these effects in CBR-resistant RNAPs while inhibiting catalysis and promoting pausing in CBR-sensitive RNAPs. The differential response of variant RNAPs to CBR703 suggests that the inhibitor binds in a cavity walled by the BH, the β' F-loop and the β fork loop. Collectively, our data are consistent with a model in which the β subunit fine tunes RNAP elongation activities by altering the BH conformation, whereas CBRs deregulate transcription by increasing coupling between the BH and the β subunit.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amidines / chemistry
  • Amidines / metabolism*
  • Amidines / pharmacology
  • Amino Acid Substitution
  • Anti-Infective Agents / chemistry
  • Anti-Infective Agents / metabolism*
  • Anti-Infective Agents / pharmacology
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Biocatalysis / drug effects
  • DNA-Directed RNA Polymerases / chemistry
  • DNA-Directed RNA Polymerases / genetics
  • DNA-Directed RNA Polymerases / metabolism*
  • Hydroxylamines / chemistry
  • Hydroxylamines / metabolism*
  • Hydroxylamines / pharmacology
  • Kinetics
  • Models, Molecular
  • Molecular Structure
  • Protein Binding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Protein Subunits / chemistry
  • Protein Subunits / genetics
  • Protein Subunits / metabolism


  • Amidines
  • Anti-Infective Agents
  • Bacterial Proteins
  • CBR 703
  • Hydroxylamines
  • Protein Subunits
  • DNA-Directed RNA Polymerases