Stabilisation of the RirA [4Fe–4S] cluster results in loss of iron-sensing function

Abstract

The regulator RirA senses Fe through its [4Fe–4S] cluster, which may have only three Cys ligands from the protein. Addition of a likely fourth Asp ligand stabilised the cluster, rendering it unable to sense Fe and locked into its DNA-binding state.

Iron-sulfur protein odyssey: exploring their cluster functional versatility and challenging identification

“…The aspartic acid ligand in NsrR is critical to sense NO and the absence of a fourth ligand in RirA is critical to enable cluster disassembly in low-iron condition. 16 , 69 , 71 These coordination patterns might help create hypotheses regarding specific functions of the Fe-S proteins. Advances in the development of methods to predict Fe-S cluster binding sites in silico and in cellulo have contributed and will continue to contribute—with notably the development of tools to predict the structures of proteins exceeding 2700 residues and of multimeric protein complexes—to the identification of new Fe-S members, helping to better understand the roles of these important proteins.…”

“…Other members of the Rrf2 family that can sense iron limitation include RisR and RirA that are both harboring a [4Fe-4S] cluster. 68 , 69 Myxococcus xanthus holo-RisR is a repressor of both the isc and suf operons, in contrast to holo-IscR that represses only the isc operon. The cluster is coordinated by three cysteines and an unknown fourth ligand.…”

“…RirA cluster was proposed to be coordinated by three cysteines and a non-protein ligand such as water; this would be functionally relevant as the introduction of a fourth cysteine ligand significantly reduced the lability of the fourth iron atom and the ability of the [4Fe-4S] to disassemble under iron depletion. 69 It could be hypothesized that RisR fourth iron may also be ligated by a non-protein ligand, as both clusters sense low-iron concentration.…”

Regulatory and Sensing Iron–Sulfur Clusters: New Insights and Unanswered Questions

“…Iron-sulfur clusters exhibit a variety of structures and geometries depending on the number of iron and sulfur atoms in the cluster and the coordinating residues present in the protein. The coordinating amino acids found in most Fe-S cluster proteins are largely comprised of cysteine and histidine, but occasionally aspartate, glutamate, lysine, serine, and threonine are also coordinating residues [36,37]. The most common iron-sulfur cluster geometries found in biological systems are [2Fe-2S], [4Fe-4S], and [3Fe-4S] (Figure 2, left) [3,38,39].…”

“…Like the mammalian system, there is redundancy to modulate such an important physiological function, and rhizobium has an additional non-Fe-S cluster-binding co-regulator similar to IRP2, known as the iron response regulator (Irr), which aids in the modulation of intracellular iron levels [183]. When RirA is in its holo [4Fe-4S] cluster form, it represses iron uptake by binding to the iron response operator (IRO) box, a DNA sequence present in promoters of multiple genes [8,27,37,143]. Binding to the IRO box by RirA suppresses the transcription of iron uptake genes (Figure 3).…”