Insights into the Rrf2 repressor family – the structure of CymR, the global cysteine regulator of Bacillus subtilis

Abstract

The global regulator CymR represses the transcription of a large set of genes involved in cystine uptake and cysteine biosynthesis in Bacillus subtilis and Staphylococcus aureus. This repressor belongs to the widespread and poorly characterized Rrf2 family of regulators. The crystal structure of CymR from B. subtilis reveals a biologically active dimer, where each monomer folds into two tightly packed domains: a DNA‐binding domain, which houses a winged helix–turn–helix (wHTH) motif; and a long dimerization domain, which places the wHTH motifs at the extremes. This architecture explains how these small regulators can span 23–27‐bp DNA targets. The wHTH motif of CymR resembles those of the GntR superfamily of regulators, such as FadR and HutC. Superimposing the FadR wHTH motifs bound to their DNA fragments onto the wHTH motifs of the CymR dimer structure suggests that the DNA target and/or the protein must undergo some conformational changes upon binding. The CymR structure also hints at a possible location of the Fe–S centre associated with several Rrf2‐type regulators. Structured digital abstract http://www.uniprot.org/uniprot/O34527 http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0407 to http://www.uniprot.org/uniprot/O34527 by http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0114 (View Interaction http://mint.bio.uniroma2.it/mint/search/interaction.do?interactionAc=MINT-8182482, http://mint.bio.uniroma2.it/mint/search/interaction.do?interactionAc=MINT-8182474)

Staphylococcus aureus CymR Is a New Thiol-based Oxidation-sensing Regulator of Stress Resistance and Oxidative Response

“…The reduced CymR structure revealed that CymR forms a biologically active homodimer, which consists of two domains: one winged helix-turn-helix domain and one long dimerization domain (Fig. 2, A and B), similar to a recently reported structure of B. subtilis CymR (27) except that Cys-25 is not conserved in B. subtilis CymR. A close inspection of the active cysteine in CymR revealed three major differences compared with the active cysteine residue in OhrR, which is a prototype of the OhrR/MgrA family thiol-dependent redox regulatory proteins.…”

AraC/XylS Family Stress Response Regulators Rob, SoxS, PliA, and OpiA in the Fire Blight Pathogen Erwinia amylovora

“…One of the best-studied Rrf2 proteins, IscR, represses the iscRSUA operon, encoding Fe-S cluster biosynthesis proteins (88). Several regulators of the widespread but poorly characterized Rrf2 family coordinate an Fe-S cluster that participates in signal transduction (89). The oxidation state of the Fe-S cluster may modulate the function of these regulators, as found with the [2Fe-2S]-containing transcription factor SoxR (72).…”

13. Reactivity of iron-sulfur clusters with nitric oxide

“…Although the archetypal member Rrf2 from Desulfovibrio vulgaris has not been well characterized [121], other well studied members include CymR, SaiR, IscR, RirA and RsrR. While CymR and SaiR represent regulators that do not contain a co-factor [122,123], IscR, RirA, RsrR and NsrR contain three conserved cysteine residues (Figure 7) that have been shown, or are predicted, to bind an Fe-S cluster, with the type, [2Fe-2S] or [4Fe-4S], being dependent on the particular regulator [58,68,74,124,125]. For example, IscR and RsrR are known to contain a [2Fe-2S] cluster, whereas NsrR from both Bacillus subtilis and Streptomyces coelicolor has been shown to bind a [4Fe-4S] cluster [58,68,74,125,126].…”

“…High resolution structural information is available for both CymR and IscR in the cluster-less apo form (Figure 8). Structures of IscR in the free form and in complex with type 2 promoter DNA (to which holo-and apo-IsrR binds) have been reported [122,125]. Both proteins consist of a DNA binding domain, a dimerization helix and, in the case of IscR, a sensory domain.…”

“…In the case of IscR, the three conserved Cys residues that coordinate the cluster were replaced by Ala residues to permit crystallisation. The positions of the substituted cluster ligating residues (space filling) A92, A98 and A104 are shown, along with H107, which is a cluster ligand in the wild type protein [122,125]. [68].…”