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

MerR, the metalloregulator of the mercury resistance (mer) operon, binds th e operator (merO) between -10 and -35 of the merTPCAD promoter (P-T) and se questers RNA polymerase (RNAP) in a closed complex. MerR represses P-T unti l Hg(II) induces it to underwind merO DNA and thus facilitate open complex formation. We used cross-linking to determine if direct contacts between Me rR and RNAP also occur during this process. MerR cross-linked to the alpha, beta, and sigma(70) subunits of RNAP alone, indicating stable contacts whi ch were further stabilized upon forming the preinitiation complex at P-T. H g(II) did not eliminate any of the MerR-RNAP cross-links but did increase t he relative abundance of a MerR dimer conformer. Interference by MerR with self-cross-links among RNAP subunits and the formation of an electrophoreti cally stable association between MerR and RNAP also indicated MerR-RNAP int eractions. 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 tra nscription-competent complex.