Two distinct mechanisms of transcriptional regulation by the redox sensor YodB

Abstract

For bacteria, cysteine thiol groups in proteins are commonly used as thiol-based switches for redox sensing to activate specific detoxification pathways and restore the redox balance. Among the known thiol-based regulatory systems, the MarR/DUF24 family regulators have been reported to sense and respond to reactive electrophilic species, including diamide, quinones, and aldehydes, with high specificity. Here, we report that the prototypical regulator YodB of the MarR/DUF24 family from Bacillus subtilis uses two distinct pathways to regulate transcription in response to two reactive electrophilic species (diamide or methyl-p-benzoquinone), as revealed by X-ray crystallography, NMR spectroscopy, and biochemical experiments. Diamide induces structural changes in the YodB dimer by promoting the formation of disulfide bonds, whereas methyl-p-benzoquinone allows the YodB dimer to be dissociated from DNA, with little effect on the YodB dimer. The results indicate that B. subtilis may discriminate toxic quinones, such as methyl-p-benzoquinone, from diamide to efficiently manage multiple oxidative signals. These results also provide evidence that different thiol-reactive compounds induce dissimilar conformational changes in the regulator to trigger the separate regulation of target DNA. This specific control of YodB is dependent upon the type of thiol-reactive compound present, is linked to its direct transcriptional activity, and is important for the survival of B. subtilis. This study of B. subtilis YodB also provides a structural basis for the relationship that exists between the ligand-induced conformational changes adopted by the protein and its functional switch.YodB | MarR/DUF24 | transcriptional regulator | redox signaling | reactive electrophilic species

The MarR-Type Repressor MhqR Confers Quinone and Antimicrobial Resistance inStaphylococcus aureus

“…The redox-sensing MarR/DUF24-family repressors YodB and CatR of B. subtilis are inactivated by intersubunit disulfide formation in vivo that involves the conserved Cys6 or Cys7 (1, 2, 12, 13, 69). The YodB and QsrR repressor mutant proteins with single Cys6 and Cys5 sense quinones also by thiol- S -alkylation in vitro (33, 41). The MhqR repressors might be inactivated by direct binding of quinones to a specific pocket.…”

“…YodB and CatR are redox-sensing repressors that sense and respond directly to quinones by a redox-switch mechanism involving thiol oxidation at the conserved Cys6 and Cys7 residues, respectively (12, 13). The YodB repressor forms intermolecular disulfides between Cys6 and the C-terminal Cys101 or Cys108 in the opposing subunits of the YodB dimer under quinone and diamide stress in vitro and in vivo (12, 41). However, the mechanism of MhqR regulation under quinone stress is unknown thus far and may not involve a thiol-switch mechanism (69).…”

Metallochaperones and metalloregulation in bacteria

“…The C-terminal α5 site in ArsR repressors, represented by S. aureus CzrA [88], is composed of an all N/O-donor ligand set used to coordinate harder metals such as Zn II ; in some cases, the α5 site is further elaborated to bind Ni II and Co II with octahedral coordination geometries, achieved by the recruitment of N/O donors from the extreme N-terminal tail [89]. It is becoming increasingly clear that ArsRs are not restricted to metal sensing [90–98], with individual members now known to have evolved to sense ROS [93,94,98,99] and RSS [90,92] via a conserved cysteine pair in the α2 and α5 helices, while RES appear to be sensed by a cysteine in α1 helix [91]. It is important to point out here that redox-sensing ArsR family members are often misannotated as MarR family members due to known or anticipated functional similarities ( vide infra ).…”

“…Structural changes in ArsRs upon metal binding or oxidative modification are generally small, with the exception of some reactive oxygen, sulfur and electrophile species which appear to induce somewhat larger conformational changes in the homodimer that allosterically inhibit DNA binding [91–93]. It therefore remains challenging to understand how sensing is physically connected to regulation of DNA binding.…”

OhsR acts as an organic peroxide-sensing transcriptional activator using an S-mycothiolation mechanism in Corynebacterium glutamicum

“…OhrR was a redox sensor for OHPs, hypochlorous acid (HClO), H 2 O 2 , and superoxide anions [35, 44–46]. Therefore, the function of OhsR in the response to organic and inorganic oxidative stresses was studied using the plate sensitivity assay (Fig.…”