The β subunit gate loop is required for RNA polymerase modification by RfaH and NusG

Mol Cell. 2011 Jul 22;43(2):253-62. doi: 10.1016/j.molcel.2011.05.026.


In all organisms, RNA polymerase (RNAP) relies on accessory factors to complete synthesis of long RNAs. These factors increase RNAP processivity by reducing pausing and termination, but their molecular mechanisms remain incompletely understood. We identify the β gate loop as an RNAP element required for antipausing activity of a bacterial virulence factor RfaH, a member of the universally conserved NusG family. Interactions with the gate loop are necessary for suppression of pausing and termination by RfaH, but are dispensable for RfaH binding to RNAP mediated by the β' clamp helices. We hypothesize that upon binding to the clamp helices and the gate loop RfaH bridges the gap across the DNA channel, stabilizing RNAP contacts with nucleic acid and disfavoring isomerization into a paused state. We show that contacts with the gate loop are also required for antipausing by NusG and propose that most NusG homologs use similar mechanisms to increase RNAP processivity.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Binding Sites
  • DNA-Directed RNA Polymerases / chemistry*
  • DNA-Directed RNA Polymerases / genetics
  • DNA-Directed RNA Polymerases / metabolism
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Models, Molecular
  • Operon
  • Peptide Elongation Factors / chemistry*
  • Peptide Elongation Factors / genetics
  • Peptide Elongation Factors / metabolism
  • Protein Conformation
  • Thermus thermophilus / metabolism
  • Trans-Activators / chemistry*
  • Trans-Activators / genetics
  • Trans-Activators / metabolism
  • Transcription Factors / chemistry*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism


  • Bacterial Proteins
  • Escherichia coli Proteins
  • NusG protein, E coli
  • Peptide Elongation Factors
  • RfaH protein, E coli
  • Trans-Activators
  • Transcription Factors
  • DNA-Directed RNA Polymerases
  • RNA polymerase beta subunit