A [FeFe] Hydrogenase-Rubrerythrin Chimeric Enzyme Functions to Couple H2 Oxidation to Reduction of H2O2 in the Foodborne Pathogen Clostridium perfringens

[FeFe] hydrogenases are a diverse class of H2-activating enzymes with a wide range of utilities in nature. As H2 is a promising renewable energy carrier, exploration of the increasingly realized functional diversity of [FeFe] hydrogenases is instrumental for understanding how these remarkable enzymes can benefit society and inspire new technologies. In this work, we uncover the properties of a highly unusual natural chimera composed of a [FeFe] hydrogenase and rubrerythrin as a single polypeptide. The unique combination of [FeFe] hydrogenase with rubrerythrin, an enzyme that functions in H2O2 detoxification, raises the question of whether catalytic reactions, such as H2 oxidation and H2O2 reduction, are functionally linked. Herein, we express and purify a representative chimera from Clostridium perfringens (termed CperHydR) and apply various electrochemical and spectroscopic approaches to determine its activity and confirm the presence of each of the proposed metallocofactors. The cumulative data demonstrate that the enzyme contains a surprising array of metallocofactors: the catalytic site of [FeFe] hydrogenase termed the H-cluster, two [4Fe-4S] clusters, two rubredoxin Fe(Cys)4 centers, and a hemerythrin-like diiron site. The absence of an H2-evolution current in protein film voltammetry highlights an exceptional bias of this enzyme toward H2 oxidation to the greatest extent that has been observed for a [FeFe] hydrogenase. Here, we demonstrate that CperHydR uses H2, catalytically split by the hydrogenase domain, to reduce H2O2 by the diiron site. Structural modeling suggests a homodimeric nature of the protein. Overall, this study demonstrates that CperHydR is an H2-dependent H2O2 reductase. Equipped with this information, we discuss the possible role of this enzyme as a part of the oxygen-stress response system, proposing that CperHydR constitutes a new pathway for H2O2 mitigation.

Oxygen tolerance in anaerobes as a virulence factor and a health-beneficial property

Oxygen tolerance of anaerobes is a virulence factor, but can also be a beneficial property. Many species have evolved to tolerate or take advantage of the presence of low, especially nanaerobic (≤0.14 %) oxygen concentrations. Oxygen tolerance is genus-, species- and strain-dependent according to their protective mechanisms. It was better expressed in some pathogenic species such as Bacteroides fragilis, Clostridioides difficile, and Clostridium perfringens, as well as in Akkermansia muciniphila than in other potential probiotics such as Alistipes, Blautia and Roseburia spp. Different degrees of oxygen sensitivity were found between the strains of Anaerostipes, Faecalibacterium, and Bifidobacterium spp. Importantly, clostridial spores and anaerobes in biofilms are protected from oxidation. Rubrerythrins and flavodiiron proteins and two regulators (sigma factor B and PerR) contribute to C. difficile protection from reactive oxygen species (ROS). The frequent pathogen, B. fragilis, has numerous protective factors such as enzymes (catalase, superoxide dismutase, alkyl hydroperoxidase, thioredoxin peroxidase, and aerobic-type NrdAB ribonucleotide reductase), and nanaerobic respiration. Seven proteins confer strain-specific oxygen adaptation of Faecalibacterium prausnitzii. Oxygen tolerance protects anaerobes from ROS, shields their DNA and modulates gene expression. Furthermore, oxygen can induce mutations leading to antibiotic resistance as shown in Prevotella melaninogenica. Some Faecalibacterium, Anaerostipes, Bifidobacterium, and Akkermansia strains from the intestinal microbiota exhibiting oxygen tolerance may become next-generation probiotic candidates. Further studies are needed to reveal oxygen effects on more anaerobic species and strains, and the influence of oxygen on antibiotic resistance. More studies on oxygen-tolerant probiotic strains can be useful to optimize biotechnological methods.

Responses of Clostridia to oxygen: from detoxification to adaptive strategies

Clostridia comprise bacteria of environmental, biotechnological and medical interest and many commensals of the gut microbiota. Because of their strictly anaerobic lifestyle, oxygen is a major stress for Clostridia. However, recent data showed that these bacteria can cope with O₂ better than expected for obligate anaerobes through their ability to scavenge, detoxify and consume O₂ . Upon O₂ exposure, Clostridia redirect their central metabolism onto pathways less O₂ -sensitive and induce the expression of genes encoding enzymes involved in O₂ -reduction and in the repair of oxidized damaged molecules. While Faecalibacterium prausnitzii efficiently consumes O₂ through a specific extracellular electron shuttling system requiring riboflavin, enzymes such as rubrerythrins and flavodiiron proteins with NAD(P)H-dependent O₂ - and/or H₂ O₂ -reductase activities are usually encoded in other Clostridia. These two classes of enzymes play indeed a pivotal role in O₂ tolerance in Clostridioides difficile and Clostridium acetobutylicum. Two main signalling pathways triggering O₂ -induced responses have been described so far in Clostridia. PerR acts as a key regulator of the O₂ - and/or reactive oxygen species-defence machinery while in C. difficile, σ^B , the sigma factor of the general stress response also plays a crucial role in O₂ tolerance by controlling the expression of genes involved in O₂ scavenging and repair systems.

Type E Botulinum Neurotoxin-Producing Clostridium butyricum Strains Are Aerotolerant during Vegetative Growth

Botulinum neurotoxins, the causative agents of the potentially fatal disease of botulism, are produced by certain Clostridium strains during vegetative growth, usually in anaerobic environments. Our findings indicate that, contrary to current understanding, the growth of neurotoxigenic C. butyricum strains and botulinum neurotoxin type E production can continue upon transfer from anaerobic to aerated conditions and that adaptation of strains to oxygenated environments requires global changes in proteomic and metabolic profiles. We hypothesize that aerotolerance might constitute an unappreciated factor conferring physiological advantages on some botulinum toxin-producing clostridial strains, allowing them to adapt to otherwise restrictive environments.

Clostridium butyricum, the type species of the genus Clostridium, is considered an obligate anaerobe, yet it has been shown to grow in the presence of oxygen. C. butyricum strains atypically producing the botulinum neurotoxin type E are the leading cause of type E human botulism in Italy. Here, we show that type E botulinum neurotoxin-producing C. butyricum strains growing exponentially were able to keep growing and producing toxin in vitro upon exposure to air, although less efficiently than under ideal oxygen-depleted conditions. Bacterial growth in air was maintained when the initial cell density was higher than 10³ cells/ml. No spores were detected in the cultures aerated for 5 h. To understand the biological mechanisms allowing the adaptation of vegetative cells of C. butyricum type E to oxygen, we compared the proteome and metabolome profiles of the clostridial cultures grown for 5 h under either aerated or anaerobic conditions. The results indicated that bacterial cells responded to oxygen stress by slowing growth and modulating the expression of proteins involved in carbohydrate uptake and metabolism, redox homeostasis, DNA damage response, and bacterial motility. Moreover, the ratio of acetate to butyrate was significantly higher under aeration. This study demonstrates for the first time that a botulinum neurotoxin-producing Clostridium can withstand oxygen during vegetative growth.

IMPORTANCE Botulinum neurotoxins, the causative agents of the potentially fatal disease of botulism, are produced by certain Clostridium strains during vegetative growth, usually in anaerobic environments. Our findings indicate that, contrary to current understanding, the growth of neurotoxigenic C. butyricum strains and botulinum neurotoxin type E production can continue upon transfer from anaerobic to aerated conditions and that adaptation of strains to oxygenated environments requires global changes in proteomic and metabolic profiles. We hypothesize that aerotolerance might constitute an unappreciated factor conferring physiological advantages on some botulinum toxin-producing clostridial strains, allowing them to adapt to otherwise restrictive environments.

In vitro inhibition of Streptococcus mutans biofilm formation on hydroxyapatite by subinhibitory concentrations of anthraquinones

We report that certain anthraquinones (AQs) reduce Streptococcus mutans biofilm formation on hydroxyapatite at concentrations below the MIC. Although AQs are known to generate reactive oxygen species, the latter do not underlie the observed effect. Our results suggest that AQs inhibit S. mutans biofilm formation by causing membrane perturbation.

Antimicrobial properties of salt (NaCl) used for the preservation of natural casings

The antimicrobial properties of salt (NaCl) used for the preservation of natural casings were studied by investigating the survival of six bacterial species in natural casings at different water activity (aw) levels. Individual sheep casings were inoculated with ca. 10(5) colony-forming units (cfu) g(-1) of Escherichia coli, Salmonella typhimurium, Listeria monocytogenes, Staphylococcus aureus, Clostridium perfringens and 10(2)cfu g(-1) of E. coli O157:H7. The casings were stored at 20+/-1.5 degrees C in different brines and dry salt, giving aw-levels of 0.90 aw, 0.87aw, 0.85 aw, 0.83 aw and 0.75 aw. Samples were taken at day 1, 3, 6, 8, 13, 20, 27 and 30 after inoculation and the number of bacteria present was determined. Based on survival curves, death rates (day(-1)) were calculated to quantify the reduction in log10 cfu g(-1) per day. The influence of aw on death rates was higher for Gram-negative bacteria than for Gram-positive bacteria. The death rates were overall higher for Gram-negatives than for Gram-positives. No clear reduction in the survival of C. perfringens in relation to any aw level was observed in this study. These results indicate that the antimicrobial properties of salt used for the preservation of natural casings are sufficient to reduce the bacterial contamination (except for Clostridium spores) well below acceptable levels at a water activity level of 0.85 or lower during a 30-day storage period.

Avoiding high-valent iron intermediates: superoxide reductase and rubrerythrin

The Fenton or Fenton-type reaction between aqueous ferrous ion and hydrogen peroxide generates a highly oxidizing species, most often formulated as hydroxyl radical or ferryl ([Fe(IV)O](2+)). Intracellular Fenton-type chemistry can be lethal if not controlled. Nature has, therefore, evolved enzymes to scavenge superoxide and hydrogen peroxide, the reduced dioxygen species that initiate intracellular Fenton-type chemistry. Two such enzymes found predominantly in air-sensitive bacteria and archaea, superoxide reductase (SOR) and rubrerythrin (Rbr), functioning as a peroxidase (hydrogen peroxide reductase), contain non-heme iron. The iron coordination spheres in these enzymes contain five or six protein ligands from His and Glu residues, and, in the case of SOR, a Cys residue. SOR contains a mononuclear active site that is designed to protonate and rapidly expel peroxide generated as a product of the enzymatic reaction. The ferrous SOR reacts adventitiously but relatively slowly (several seconds to a few minutes) with exogenous hydrogen peroxide, presumably in a Fenton-type reaction. The diferrous active site of Rbr reacts more rapidly with hydrogen peroxide but can divert Fenton-type reactions towards the two-electron reduction of hydrogen peroxide to water. Proximal aromatic residues may function as radical sinks for Fenton-generated oxidants. Fenton-initiated damage to these iron active sites may become apparent only under extremely oxidizing intracellular conditions.

Microbial detoxification of superoxide: the non-heme iron reductive paradigm for combating oxidative stress

A reductive paradigm has emerged in recent years for detoxification of superoxide and other redox active diatomic molecules in air-sensitive bacteria and archaea. Adventitiously generated superoxide in many anaerobic or microaerophilic bacteria and archaea is scavenged by superoxide reductase (SOR) rather than the classical superoxide dismutases characteristic of aerobic microbes. SORs contain a novel five-coordinate, square-pyramidal [Fe(His)4(Cys)] ferrous active site, which adds a sixth glutamate ligand upon oxidation. This Account summarizes the recently elucidated structural and mechanistic features of SORs. The non-heme iron reductive scavenging paradigm in these air-sensitive microbes also extends to recently characterized enzymes that scavenge hydrogen peroxide and nitric oxide and to oxygen sensing proteins.

CdeA of Clostridium difficile, a New Multidrug Efflux Transporter of the MATE Family

The cdeA gene, cloned from Clostridium difficile clinical strain 714 under the control of its natural promoter made Escherichia coli and Clostridium perfringens resistant to ethidium bromide and acriflavin but had no effect on the susceptibility of the hosts to the following antibiotics: norfloxacin, ciprofloxacin, gentamicin, erythromycin, tetracyclin, and chloramphenicol. However, it was responsible for fluoroquinolone resistance in E. coli when it was cloned under the control of the Plac promoter. Quantitative reverse transcriptase (RT)-PCR showed that growth of C. difficile clinical strain 253 in the presence of subinhibitory concentrations of ethidium bromide significantly increased the transcription of cdeA, but this was not observed with ciprofloxacin. The deduced protein was homologous to the protein sequences of known efflux pumps from the third cluster (the so-called DinF branch) of the multidrug and toxic compound extrusion (MATE) family. CdeA caused ethidium bromide energy-dependent efflux in whole cells of E. coli. Efflux activity was stimulated by addition of Na+ ions, suggesting that CdeA, like other pumps of the MATE family, is a Na+-coupled efflux pump. CdeA is the first multidrug efflux transporter identified in C. difficile.

Oxidative stress response in Clostridium perfringens

Clostridium perfringens, a strictly anaerobic bacterium, is able to survive when exposed to oxygen for short periods of time and exhibits a complex adaptive response to reactive oxygen species, both under aerobic and anaerobic conditions. However, this adaptive response is not completely understood. C. perfringens possesses specialized genes that might be involved in this adaptive process, such as those encoding superoxide dismutase (SOD), superoxide reductase and alkyl hydroperoxide reductase, but their contribution to the oxidative stress response and their control mechanisms are unknown. By a combination of functional complementation of Escherichia coli strains impaired in either SOD, alkyl hydroperoxide reductase (AhpC) or catalase activity (Cat), transcription analysis and characterization of mutants impaired in regulatory genes, it was concluded that: (i) the product of the sod gene is certainly essential to scavenge superoxide radicals, (ii) the ahpC gene, which is fully induced in all oxidative stress conditions, is probably involved in the scavenging of all intracellular peroxides, (iii) the three rubrerythrin (rbr) genes of C. perfringens do not encode proteins with in vivo H(2)O(2) reductase activity, and (iv) the two rubredoxin (rub) genes do not contribute to the hypothetical superoxide reductase activity, but are likely to belong to an electron transfer chain involved in energy metabolism.

Identification of the Clostridium perfringens genes involved in the adaptive response to oxidative stress

Clostridium perfringens is a ubiquitous gram-positive pathogen that is present in the air, soil, animals, and humans. Although C. perfringens is strictly anaerobic, vegetative and stationary cells can survive in a growth-arrested stage in the presence of oxygen and/or low concentrations of superoxide and hydroxyl radicals. Indeed, it possesses an adaptive response to oxidative stress, which can be activated in both aerobic and anaerobic conditions. To identify the genes involved in this oxidative stress response, C. perfringens strain 13 mutants were generated by Tn916 insertional mutagenesis and screened for resistance or sensitivity to various oxidative stresses. Three of the 12 sensitive mutants examined harbored an independently inserted single copy of the transposon in the same operon as two genes orthologous to the ydaD and ycdF genes of Bacillus subtilis, which encode a putative NADPH dehydrogenase. Complementation experiments and knockout experiments demonstrated that these genes are both required for efficient resistance to oxidative stress in C. perfringens and are probably responsible for the production of NADPH, which is required for maintenance of the intracellular redox balance in growth-arrested cells. Other Tn916 disrupted genes were also shown to play important roles in the oxidative stress response. This is the first time that some of these genes (e.g., a gene encoding an ATP-dependent RNA helicase, the beta-glucuronidase gene, and the gene encoding the atypical iron sulfur prismane protein) have been shown to be involved in the oxidative response.