Active site opening and closure control translocation of multisubunit RNA polymerase

Nucleic Acids Res. 2012 Aug;40(15):7442-51. doi: 10.1093/nar/gks383. Epub 2012 May 8.


Multisubunit RNA polymerase (RNAP) is the central information-processing enzyme in all cellular life forms, yet its mechanism of translocation along the DNA molecule remains conjectural. Here, we report direct monitoring of bacterial RNAP translocation following the addition of a single nucleotide. Time-resolved measurements demonstrated that translocation is delayed relative to nucleotide incorporation and occurs shortly after or concurrently with pyrophosphate release. An investigation of translocation equilibrium suggested that the strength of interactions between RNA 3' nucleotide and nucleophilic and substrate sites determines the translocation state of transcription elongation complexes, whereas active site opening and closure modulate the affinity of the substrate site, thereby favoring the post- and pre-translocated states, respectively. The RNAP translocation mechanism is exploited by the antibiotic tagetitoxin, which mimics pyrophosphate and induces backward translocation by closing the active site.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / enzymology
  • Catalytic Domain
  • DNA / chemistry
  • DNA / metabolism
  • DNA-Directed RNA Polymerases / chemistry*
  • DNA-Directed RNA Polymerases / metabolism*
  • Dicarboxylic Acids / chemistry
  • Dicarboxylic Acids / pharmacology
  • Diphosphates / metabolism
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / pharmacology
  • Fluorescent Dyes
  • Nucleotides / metabolism
  • Organophosphorus Compounds / chemistry
  • Organophosphorus Compounds / pharmacology
  • Protein Subunits / chemistry
  • Protein Subunits / metabolism
  • Protein Transport / drug effects
  • RNA / chemistry
  • RNA / metabolism
  • Transcription, Genetic*


  • Dicarboxylic Acids
  • Diphosphates
  • Enzyme Inhibitors
  • Fluorescent Dyes
  • Nucleotides
  • Organophosphorus Compounds
  • Protein Subunits
  • diphosphoric acid
  • RNA
  • tagetitoxin
  • DNA
  • DNA-Directed RNA Polymerases