Metalloregulators respond to metal ions to regulate transcription of metal homeostasis genes. MerR-family metalloregulators act on Ï 70 -dependent suboptimal promoters and operate via a unique DNA distortion mechanism in which both the apo and holo forms of the regulators bind tightly to their operator sequence, distorting DNA structure and leading to transcription repression or activation, respectively. It remains unclear how these metalloregulatorâDNA interactions are coupled dynamically to RNA polymerase (RNAP) interactions with DNA for transcription regulation. Using single-molecule FRET, we study how the copper efflux regulator (CueR)-a Cu + -responsive MerR-family metalloregulator-modulates RNAP interactions with CueR's cognate suboptimal promoter PcopA, and how RNAP affects CueRâPcopA interactions. We find that RNAP can form two noninterconverting complexes at PcopA in the absence of nucleotides: a dead-end complex and an open complex, constituting a branched interaction pathway that is distinct from the linear pathway prevalent for transcription initiation at optimal promoters. Capitalizing on this branched pathway, CueR operates via a "biased sampling" instead of "dynamic equilibrium shifting" mechanism in regulating transcription initiation; it modulates RNAP's binding-unbinding kinetics, without allowing interconversions between the deadend and open complexes. Instead, the apo-repressor form reinforces the dominance of the dead-end complex to repress transcription, and the holo-activator form shifts the interactions toward the open complex to activate transcription. RNAP, in turn, locks CueR binding at PcopA into its specific binding mode, likely helping amplify the differences between apo-and holo-CueR in imposing DNA structural changes. Therefore, RNAP and CueR work synergistically in regulating transcription.single-molecule FRET | protein-DNA interaction dynamics | MerR-family regulators | metal-responsive transcription regulation M aintaining cellular metal homeostasis is essential for bacteria, which often dwell in environments with high concentrations of metals. Some of these metals are purely toxic to bacteria, such as Cd and Hg. Many others are required for cellular function, such as Zn and Cu, but can be toxic in excess. Cells have thus developed many ways to regulate intracellular metal concentrations (1-9). Metal-responsive transcriptional regulation is one of them, where metalloregulators respond to intracellular metal ions and regulate transcription of metal efflux, uptake, or other metal homeostasis genes (4-9).In Gram-negative bacteria, MerR-family metalloregulators act on Ï 70 -dependent suboptimal promoters to repress or activate transcription of metal resistance genes (7,8). These suboptimal promoters have elongated spacing, 19-20 bp (Fig. 1), compared with the optimal 17 ± 1 bp, between the â35 and â10 elements. This elongated spacing causes a misalignment of these two recognition elements, impairing proper interactions with the RNA polymerase (RNAP) and leading to a weak basal leve...