Regulation of a nickel tolerance operon conserved in Mesorhizobium strains from serpentine soils

ABSTRACT The Mesorhizobium nre (nickel resistance) operon has previously been shown to mediate Ni tolerance in serpentine soils with naturally high concentrations of this transition metal. In most serpentine-derived strains evaluated, the putative efflux genes nreX and nreY are conserved, along with a small gene (nreA) encoding a CsoR/RcnR-family transcriptional regulator. CsoR/RcnR-family regulators are small (around 100 amino acids in length), they bind transition metals, and they use an unconventional and poorly understood DNA-binding mechanism. NreA is 93 amino acids in length and belongs to a poorly characterized clade within the CsoR/RcnR family. This investigation is focused on regulatory DNA elements that functionally interact with Mesorhizobium NreA, as well as amino acid residues in NreA that influence its regulatory activity. We show that NreA is a transcriptional repressor that is responsive to exogenous Ni. The Ni-responsive promoter is immediately upstream of the nreAXY operon, resulting in a leaderless transcript. A partially palindromic operator sequence occupies the spacer region between the −35 and −10 promoter elements. Mutational analysis of the operator highlights functionally crucial base pairs occupying opposite ends of the palindromic operator. Changes to conserved residues in the NreA polypeptide result in varying effects, with changes predicted to prevent Ni binding leading to a super-repressor phenotype. Structural modeling of the NreA-operator complex provides a plausible mechanism for DNA binding by a tetrameric form of NreA, with DNA contact sites along a positively charged surface, and the modeled contact sites agree well with the mutational analysis. IMPORTANCE Bacteria employ diverse mechanisms for maintaining optimal intracellular levels of bioactive metals. Isolates of Mesorhizobium bacteria from nickel-rich serpentine soils possess a small genetic region controlling Ni efflux. This region is subject to transcriptional regulation via the small repressor protein NreA. In this work, the essential components of the NreA protein and the DNA operator with which it interacts are defined, enabling potential adaptation of this system for metal sensing or other technologies requiring a compact inducible gene expression module.