Meddling with Metal Sensors: Fur-Family Proteins as Signaling Hubs

Abstract

The ferric uptake regulator (Fur) protein is the founding member of the FUR superfamily of metalloregulatory proteins that control metal homeostasis in bacteria. FUR proteins regulate metal homeostasis in response to the binding of iron (Fur), zinc (Zur), manganese (Mur), or nickel (Nur). FUR family proteins are generally dimers in solution, but the DNA-bound complex can involve a single dimer, a dimer-of-dimers, or an extended array of bound protein. Elevated FUR levels due to changes in cell physiology increase DNA occupancy and may also kinetically facilitate protein dissociation. Interactions between FUR proteins and other regulators are commonplace, often including cooperative and competitive DNA-binding interactions within the regulatory region. Further, there are many emerging examples of allosteric regulators that interact directly with FUR family proteins. Here, we focus on newly uncovered examples of allosteric regulation by diverse Fur antagonists (Escherichia coli YdiV/SlyD, Salmonella enterica EIIA^Ntr, Vibrio parahaemolyticus FcrX, Acinetobacter baumannii BlsA, Bacillus subtilis YlaN, and Pseudomonas aeruginosa PacT) as well as one Zur antagonist (Mycobacterium bovis CmtR). Small molecules and metal complexes may also serve as regulatory ligands, with examples including heme binding to Bradyrhizobium japonicum Irr and 2-oxoglutarate binding to Anabaena FurA. How these protein-protein and protein-ligand interactions act in conjunction with regulatory metal ions to facilitate signal integration is an active area of investigation.

Keywords: activator; allosteric regulation; metal homeostasis; metalloregulation; repressor; transcription.

FIG 1

Space-filling representation of Fur protein (from Magnetospirillum gryphiswaldense MSR-1) (62) that was activated by Mn²⁺ and bound to operator DNA. (A) A dimer of Fur protein (with one protomer in purple and another in pink) bound to the P. aeruginosa feoAB1 operator site (PDB: 4RB3). Bases that match the 7-1-7 consensus (TGATAATnATTATCA) for Fur binding are in bold. (B) Two Fur dimers in complex with a consensus 19 bp Fur box (PDB: 4RB1), which can be represented as two overlapping 7-1-7 consensus sites (61).

FIG 2

Schematic illustration of a representative Fur family protein binding to DNA as a dimer and the regulatory impact of allosteric regulators and protein-facilitated operator dissociation. Most antagonists likely act from solution to impede the binding of the metalloregulator to DNA (gray line). Once bound, protein still in solution is postulated to interact transiently with DNA-bound protein to form an unstable ternary complex that can then resolve to yield either a direct substitution (with no change in regulation) or the dissociation of both dimers (leading to either derepression or a loss of activation), as described in (72–74).

FIG 3

Summary of protein and small molecule antagonists that affect the function of FUR regulators. FUR regulators most commonly require a divalent metal ion (M²⁺) to activate DNA-binding. However, numerous other factors have now been revealed that can also modulate FUR function, often by acting as antagonists of DNA-binding. The signals that control the expression and activity of each of these effectors are only partially understood (see the text for details).