Summary: In Bacillus subtilis, the transcription factor PerR is an iron dependant sensor of H₂O₂. The sensing mechanism relies on a selective metal catalysed oxidation of two histidine residues of the regulatory site. Here we present the first crystal structure of the active PerR protein in complex with a Mn²⁺ ion. In addition, X‐ray absorption spectroscopy experiments were performed to characterize the corresponding iron form of the protein. Both studies reveal a penta‐coordinate arrangement of the regulatory site that involves three histidines and two aspartates. One of the histidine ligand belongs to the N‐terminal domain. Binding of this residue to the regulatory metal allows the protein to adopt a caliper‐like conformation suited to DNA binding. Since this histidine is conserved in all PerR and a vast majority of Fur proteins, it is likely that the allosteric switch induced by the regulatory metal is general for this family of metalloregulators.

A major public health challenge today is the resurgence of microbial infections caused by multidrug-resistant strains. Consequently, novel antimicrobial molecules are actively sought for development. In this context, the human gut microbiome is an under-explored potential trove of valuable natural molecules, such as the ribosomally-synthesized and post-translationally modified peptides (RiPPs). The biological activity of the sactipeptide subclass of RiPPs remains under-characterized. Here, we characterize an antimicrobial sactipeptide, Ruminococcin C1, purified from the caecal contents of rats mono-associated with Ruminococcus gnavus E1, a human symbiont. Its heterologous expression and post-translational maturation involving a specific sactisynthase establish a thioether network, which creates a double-hairpin folding. This original structure confers activity against pathogenic Clostridia and multidrug-resistant strains but no toxicity towards eukaryotic cells. Therefore, the Ruminococcin C1 should be considered as a valuable candidate for drug development and its producer strain R. gnavus E1 as a relevant probiotic for gut health enhancement.

The emergence of superbugs developing resistance to antibiotics and the resurgence of microbial infections have led scientists to start an antimicrobial arms race. In this context, we have previously identified an active RiPP, the Ruminococcin C1, naturally produced by Ruminococcus gnavus E1, a symbiont of the healthy human intestinal microbiota. This RiPP, subclassified as a sactipeptide, requires the host digestive system to become active against pathogenic Clostridia and multidrug-resistant strains. Here, we report its unique compact structure on the basis of four intramolecular thioether bridges introduced post-translationally by a specific radical-SAM sactisynthase. This structure confers to the Ruminococcin C1 important clinical properties including stability to digestive conditions and physicochemical treatments, a higher affinity for bacteria than simulated intestinal epithelium, a valuable activity at therapeutic doses on a range of clinical pathogens, mediated by energy resources disruption, and finally safety for human gut tissues.

Bacteria adapt to elevated levels of reactive oxygen species (ROS) by increasing the expression of detoxification enzymes and repair proteins. These defences are regulated by transcription factors that activate specific genes in response to ROS. In Bacillus subtilis, the adaptive response to peroxide stress is mainly under control of three proteins: σ^B, PerR and OhrR. σ^B is a general stress response transcription factor. PerR is a dimeric zinc protein with a regulatory site that coordinates either a Fe²⁺ or a Mn²⁺ metal ion. In the presence of iron, PerR mediates strong induction of the perRregulon in response to hydrogen peroxide (H₂O₂). In contrast to PerR, the OhrR protein is weakly activated by H₂O₂ but it shows a much higher reactivity for organic hydroperoxides. OhrR controls the expression of a thiol-dependent peroxidase that reduces organic hydroperoxides into their corresponding alcohols. In this review we emphasis peroxide sensing mechanisms for both proteins, focusing on recent biochemical and structural data.