MerR cross-links to the alpha, beta, and sigma 70 subunits of RNA polymerase in the preinitiation complex at the merTPCAD promoter

Biochemistry. 1999 Mar 16;38(11):3362-8. doi: 10.1021/bi982814m.


MerR, the metalloregulator of the mercury resistance (mer) operon, binds the operator (merO)between -10 and -35 of the merTPCAD promoter (PT) and sequesters RNA polymerase (RNAP) in a closed complex. MerR represses PT until Hg(II) induces it to underwind merO DNA and thus facilitate open complex formation. We used cross-linking to determine if direct contacts between MerR and RNAP also occur during this process. MerR cross-linked to the alpha, beta, and sigma70 subunits of RNAP alone, indicating stable contacts which were further stabilized upon forming the preinitiation complex at PT. Hg(II) did not eliminate any of the MerR-RNAP cross-links but did increase the relative abundance of a MerR dimer conformer. Interference by MerR with self-cross-links among RNAP subunits and the formation of an electrophoretically stable association between MerR and RNAP also indicated MerR-RNAP interactions. This is the first evidence for stable physical contacts between MerR and RNAP and for a Hg(II)-induced allosteric change in MerR in the transcription-competent complex.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism
  • Base Sequence
  • Cross-Linking Reagents / chemistry*
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / metabolism
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics*
  • DNA-Binding Proteins / metabolism
  • DNA-Directed RNA Polymerases / chemistry*
  • DNA-Directed RNA Polymerases / metabolism
  • Dimerization
  • Glutaral / chemistry
  • Mercury / pharmacology
  • Molecular Sequence Data
  • Operon
  • Peptide Chain Initiation, Translational / genetics*
  • Promoter Regions, Genetic*
  • Protein Conformation / drug effects
  • RNA Polymerase II / chemistry
  • RNA Polymerase II / metabolism
  • Sigma Factor / chemistry
  • Sigma Factor / metabolism


  • Bacterial Proteins
  • Cross-Linking Reagents
  • DNA, Bacterial
  • DNA-Binding Proteins
  • MerR protein, Bacteria
  • Sigma Factor
  • RNA Polymerase II
  • RNA polymerase sigma 70
  • DNA-Directed RNA Polymerases
  • RNA polymerase alpha subunit
  • Mercury
  • Glutaral