Transcriptional analysis of the rubrerythrin and superoxide dismutase genes of Clostridium perfringens

Transcriptomics Uncovers the Response of Anammox Bacteria to Dissolved Oxygen Inhibition and the Subsequent Recovery Mechanism

Understanding the recovery of anaerobic ammonium-oxidizing (anammox) bacteria after inhibition by dissolved oxygen (DO) is critical for the successful applications of anammox-based processes. Therefore, the effects of oxygen exposure (2 mg L^-1 DO for 90 min) and subsequent recovery treatments [N₂ purging or nano zero-valent iron (nZVI) addition] on the activity and gene expression in a Kuenenia stuttgartiensis enrichment culture were examined. Combining the self-organizing map clustering and enrichment analysis, we proposed the oxidative stress response of anammox bacteria based on the existing concepts of oxidative stress in microbes: the DO exposure triggered a stringent response in K. stuttgartiensis, which downregulated the transcription levels of genes involved in the central metabolism and diverted energy to a flagellar assembly and metal transport modules; these changes possibly promoted survival during the inhibition of anammox activity. According to the cotranscription with central catabolism genes, putative reactive oxygen species (ROS) scavenger genes (kat and sod) were presumed to detoxify the anammox intermediates rather than ROS. In addition, both activity and mRNA profiles with appropriate amount of nZVI addition (5 and 25 mg L^-1) were close to that of control, which proved the effectiveness of nZVI addition in anammox recovery. These results would be relevant to the physio-biochemistry development of anammox bacteria and further enhancement of nitrogen removal in wastewater treatment.

Clostridium perfringens as Foodborne Pathogen in Broiler Production: Pathophysiology and Potential Strategies for Controlling Necrotic Enteritis

Clostridium perfringens (Cp.) is the cause of human foodborne desease. Meat and poultry products are identified as the main source of infection for humans. Cp. can be found in poultry litter, feces, soil, dust, and healthy birds' intestinal contents. Cp. strains are known to secrete over 20 identified toxins and enzymes that could potentially be the principal virulence factors, capable of degrading mucin, affecting enterocytes, and the small intestine epithelium, involved in necrotic enteritis (NE) pathophysiology, also leading to immunological responses, microbiota modification and anatomical changes. Different environmental and dietary factors can determine the colonization of this microorganism. It has been observed that the incidence of Cp-associated to NE in broilers has increased in countries that have stopped using antibiotic growth promoters. Since the banning of such antibiotic growth promoters, several strategies for Cp. control have been proposed, including dietary modifications, probiotics, prebiotics, synbiotics, phytogenics, organic acids, and vaccines. However, there are aspects of the pathology that still need to be clarified to establish better actions to control and prevention. This paper reviews the current knowledge about Cp. as foodborne pathogen, the pathophysiology of NE, and recent findings on potential strategies for its control.

Expression of cellulosome components and type IV pili within the extracellular proteome of Ruminococcus flavefaciens 007

BACKGROUND

Ruminococcus flavefaciens is an important fibre-degrading bacterium found in the mammalian gut. Cellulolytic strains from the bovine rumen have been shown to produce complex cellulosome structures that are associated with the cell surface. R. flavefaciens 007 is a highly cellulolytic strain whose ability to degrade dewaxed cotton, but not Avicel cellulose, was lost following initial isolation in the variant 007S. The ability was recovered after serial subculture to give the cotton-degrading strain 007C. This has allowed us to investigate the factors required for degradation of this particularly recalcitrant form of cellulose.

METHODOLOGY/PRINCIPAL FINDINGS

The major proteins associated with the bacterial cell surface and with the culture supernatant were analyzed for R. flavefaciens 007S and 007C grown with cellobiose, xylan or Avicel cellulose as energy sources. Identification of the proteins was enabled by a draft genome sequence obtained for 007C. Among supernatant proteins a cellulosomal GH48 hydrolase, a rubrerthyrin-like protein and a protein with type IV pili N-terminal domain were the most strongly up-regulated in 007C cultures grown on Avicel compared with cellobiose. Strain 007S also showed substrate-related changes, but supernatant expression of the Pil protein and rubrerythrin in particular were markedly lower in 007S than in 007C during growth on Avicel.

CONCLUSIONS/SIGNIFICANCE

This study provides new information on the extracellular proteome of R. flavefaciens and its regulation in response to different growth substrates. Furthermore it suggests that the cotton cellulose non-degrading strain (007S) has altered regulation of multiple proteins that may be required for breakdown of cotton cellulose. One of these, the type IV pilus was previously shown to play a role in adhesion to cellulose in R. albus, and a related pilin protein was identified here for the first time as a major extracellular protein in R. flavefaciens.

Effect of oxygen on the anaerobic methanotroph 'Candidatus Methylomirabilis oxyfera': kinetic and transcriptional analysis

'Candidatus Methylomirabilis oxyfera' is a denitrifying methanotroph that performs nitrite-dependent anaerobic methane oxidation through a newly discovered intra-aerobic pathway. In this study, we investigated the response of a M. oxyfera enrichment culture to oxygen. Addition of either 2% or 8% oxygen resulted in an instant decrease of methane and nitrite conversion rates. Oxygen exposure also led to a deviation in the nitrite to methane oxidation stoichiometry. Oxygen-uptake and inhibition studies with cell-free extracts displayed a change from cytochrome c to quinol as electron donor after exposure to oxygen. The change in global gene expression was monitored by deep sequencing of cDNA using Illumina technology. After 24 h of oxygen exposure, transcription levels of 1109 (out of 2303) genes changed significantly when compared with the anoxic period. Most of the genes encoding enzymes of the methane oxidation pathway were constitutively expressed. Genes from the denitrification pathway, with exception of one of the putative nitric oxide reductases, norZ2, were severely downregulated. The majority of known genes involved in the vital cellular functions, such as nucleic acid and protein biosynthesis and cell division processes, were downregulated. The alkyl hydroperoxide reductase, ahpC, and genes involved in the synthesis/repair of the iron-sulfur clusters were among the few upregulated genes. Further, transcription of the pmoCAB genes of aerobic methanotrophs present in the non-M. oxyfera community were triggered by the presence of oxygen. Our results show that oxygen-exposed cells of M. oxyfera were under oxidative stress and that in spite of its oxygenic capacity, exposure to microoxic conditions has an overall detrimental effect.

The oncopathic potency of Clostridium perfringens is independent of its alpha-toxin gene

Hypoxia in solid tumors is a major obstacle in conventional treatment because of inefficient delivery of therapeutic agents to the lesions, but offers the potential for anaerobic bacterial colonization that can lead to tumor destruction. We have previously reported a recombinant Clostridium perfringens (Cp) strain constructed by deletion of the superoxide dismutase (sod) gene and insertion of the Panton-Valentine leukocidin (PVL) gene, Cp/sod(-)/PVL, which showed elevated oxygen sensitivity, tumor selectivity, and oncopathic potency in an orthotopic model of pancreatic cancer in immune-competent and syngeneic mice, and that led to substantial prolongation of animal survival. A major limitation to Cp/sod(-)/PVL in clinical applications is that it expresses phospholipase C (plc), the alpha-toxin and the major virulence determinant in Cp that is causative in the development of gas gangrene. In this study, the plc gene in Cp/sod(-)/PVL was knocked out to create Cp/plc(-)/sod(-)/PVL, which was shown to be incapable of inducing gas gangrene in mice. Intravenous injection of Cp/plc(-)/sod(-)/PVL spores led to a significant survival advantage in tumor-bearing mice with the same efficacy as Cp/sod(-)/PVL, indicating that the oncopathic potency of Cp is independent of a functional plc gene. The treatment also did not lead to an attenuated immune response to a subsequent pathogen challenge, indicating that a systemic immune-suppressive effect in the host is absent. Consequently, Cp/plc(-)/sod(-)/PVL is a novel oncopathic bacterial agent for the effective treatment of pancreatic cancer and other poorly vascularized tumors, with a substantially enhanced safety profile, which is essential for the development of translational studies in the future.

Pathway for H2O2 and O2 detoxification in Clostridium acetobutylicum

An unusual non-haem diiron protein, reverse rubrerythrin (revRbr), is known to be massively upregulated in response to oxidative stress in the strictly anaerobic bacterium Clostridium acetobutylicum. In the present study both in vivo and in vitro results demonstrate an H2O2 and O2 detoxification pathway in C. acetobutylicum involving revRbr, rubredoxin (Rd) and NADH : rubredoxin oxidoreductase (NROR). RevRbr exhibited both NADH peroxidase (NADH : H2O2 oxidoreductase) and NADH oxidase (NADH : O2 oxidoreductase) activities in in vitro assays using NROR as the electron-transfer intermediary from NADH to revRbr. Rd increased the NADH consumption rate by serving as an intermediary electron-transfer shuttle between NROR and revRbr. While H2O2 was found to be the preferred substrate for revRbr, its relative oxidase activity was found to be significantly higher than that reported for other Rbrs. A revRbr-overexpressing strain of C. acetobutylicum showed significantly increased tolerance to H2O2 and O2 exposure. RevRbr thus appears to protect C. acetobutylicum against oxidative stress by functioning as the terminal component of an NADH peroxidase and NADH oxidase.

A genetically enhanced anaerobic bacterium for oncopathic therapy of pancreatic cancer

BACKGROUND

A major obstacle in treatment of solid tumors is the inefficient delivery of therapeutic agents to the hypoxic cores. Hypoxia offers the potential for anaerobic bacteria colonization and tumor destruction by the bacteria, and dormant spores of wild-type Clostridium perfringens (Cp) germinate and proliferate within the hypoxic cores of pancreatic tumors in mice. However, the oncopathic effects of Cp were limited by host inflammatory responses and by Cp's residual tolerance to oxygen, which caused toxic effects in animals.

METHODS

Recombinant Cp strains in which superoxide dismutase, a major oxygen tolerance gene, was deleted (Cp/sod(-)) were constructed to enhance its selective growth in tumors. In addition, Panton-Valentine Leukocidin (PVL), an inflammation-suppressing gene from Staphylococcus aureus, was inserted into the Cp/sod(-) genome to enhance its oncopathic potency. The ability of the recombinant Cp strains to kill tumors was investigated in C57/BL6 mice bearing murine PANC02 tumors. Systemic and organ toxic effects were assessed by monitoring serum chemistries and histopathological examination. Statistical tests were two-sided.

RESULTS

Cp/sod(-) showed reduced toxic effects compared with wild-type Cp when spores were administered intravenously into PANC02 tumor-bearing mice. Mice treated with Cp/sod(-)/PVL spores demonstrated a reduction in neutrophils and macrophages in tumors, logarithmically elevated growth of intratumoral bacteria, enhanced tumor necrosis, and substantially prolonged survival without apparent systemic and organ toxic effects, compared with mice treated with both wild-type Cp and Cp/sod(-) spores. Accordingly, 47% of Cp/sod(-)/PVL-treated mice (n = 15) achieved tumor-free survival for over 120 days, whereas all mice treated with Cp/sod(-) or phosphate-buffered saline (n = 10 per group) died within 50 days. The median survival for Cp/sod(-)/PVL-treated mice was 77 days (95% confidence interval [CI] = 45 to 120 days) and for Cp/sod(-)-treated mice was 30 days (95% CI = 23 to 36 days; P < .001).

CONCLUSIONS

Cp/sod(-)/PVL provides a prototype for a novel class of oncopathic microbes that may have potential for the safe and effective treatment of pancreatic cancer and other poorly vascularized tumors.

An O2-inducible rubrerythrin-like protein, rubperoxin, is functional as a H2O2 reductase in an obligatory anaerobe Clostridium acetobutylicum

Clostridium acetobutylicum, an obligatory anaerobe, is able to grow microoxically with the accumulation of two functionally unknown O2-induced proteins identified by two-dimensional electrophoresis. One was determined to be a novel type rubrerythrin-like protein, named rubperoxin (Rpr) in this study, that conserves one rubredoxin-type Fe(SCys)(4) site per polypeptide in the N-terminus. Recombinant rubperoxin expressed in E. coli purified in its oxidized form is a dimer with optical absorption maxima at 492, 377, and 277nm. Reduced rubperoxin is rapidly and fully oxidized by a half molar ratio of H2O2 per mole protein, and slowly oxidized by t-butyl hydroperoxide and O2. Cell-free extracts from microoxically grown cells efficiently reduce rubperoxin when NAD(P)H is used as the electron donor (preferentially reduced by NADH). These results strongly suggest that rubperoxin is involved in NAD(P)H-dependent H2O2 detoxification in vivo.

The rubrerythrin-like protein Hsp21 of Clostridium acetobutylicum is a general stress protein

The small heat shock protein Hsp21 of Clostridium acetobutylicum was recently identified as a rubrerythrin-like protein with a rubredoxin-like FeS(4) domain at the N-terminus and a ferritin-like diiron domain at the C-terminus. Here, we report that the two identical tandem genes rbr3A and rbr3B, which encode the heat shock protein Hsp21, show the transcription pattern of general stress genes. Northern blot analysis indicated that the transcription of the rbr3AB operon is induced by various environmental stress conditions: in addition to heat and oxidative stress, an increase of the pH of the growth medium from 4.5 to 6.2, addition of the salt NaCl (400 mM) or of the solvent butanol (3.5% v/v), and lowering the incubation temperature from 37 to 25 degrees C resulted in transiently increased transcript levels. The promoter region deduced from the 5' end of the mRNA has only limited similarity to the consensus promoter sequence of Gram-positive bacteria. A conserved inverted repeat between this promoter and the initiation codon is proposed to have a regulatory role. Although C. acetobutylicum is regarded as a strictly anaerobic bacterium, live/dead staining demonstrated that it can survive exposure to air or H(2)O(2) and other stressors to various extents.

Adaptive responses to oxygen stress in obligatory anaerobes Clostridium acetobutylicum and Clostridium aminovalericum

Clostridium acetobutylicum and Clostridium aminovalericum, both obligatory anaerobes, grow normally after growth conditions are changed from anoxic to microoxic, where the cells consume oxygen proficiently. In C. aminovalericum, a gene encoding a previously characterized H2O-forming NADH oxidase, designated noxA, was cloned and sequenced. The expression of noxA was strongly upregulated within 10 min after the growth conditions were altered to a microoxic state, indicating that C. aminovalericum NoxA is involved in oxygen metabolism. In C. acetobutylicum, genes suggested to be involved in oxygen metabolism and genes for reactive oxygen species (ROS) scavenging were chosen from the genome database. Although no clear orthologue of C. aminovalericum NoxA was found, Northern blot analysis identified many O2-responsive genes (e.g., a gene cluster [CAC2448 to CAC2452] encoding an NADH rubredoxin oxidoreductase-A-type flavoprotein-desulfoferrodoxin homologue-MerR family-like protein-flavodoxin, an operon [CAC1547 to CAC1549] encoding a thioredoxin-thioredoxin reductase-glutathione peroxidase-like protein, an operon [CAC1570 and CAC1571] encoding two glutathione peroxidase-like proteins, and genes encoding thiol peroxidase, bacterioferritin comigratory proteins, and superoxide dismutase) whose expression was quickly and synchronously upregulated within 10 min after flushing with 5% O2. The corresponding enzyme activities, such as NAD(P)H-dependent peroxide (H2O2 and alkyl hydroperoxides) reductase, were highly induced, indicating that microoxic growth of C. acetobutylicum is associated with the expression of a number of genes for oxygen metabolism and ROS scavenging.

Rubrerythrin from the hyperthermophilic archaeon Pyrococcus furiosus is a rubredoxin-dependent, iron-containing peroxidase

Rubrerythrin was purified by multistep chromatography under anaerobic, reducing conditions from the hyperthermophilic archaeon Pyrococcus furiosus. It is a homodimer with a molecular mass of 39.2 kDa and contains 2.9 +/- 0.2 iron atoms per subunit. The purified protein had peroxidase activity at 85 degrees C using hydrogen peroxide with reduced P. furiosus rubredoxin as the electron donor. The specific activity was 36 micromol of rubredoxin oxidized/min/mg with apparent K(m) values of 35 and 70 microM for hydrogen peroxide and rubredoxin, respectively. When rubrerythrin was combined with rubredoxin and P. furiosus NADH:rubredoxin oxidoreductase, the complete system used NADH as the electron donor to reduce hydrogen peroxide with a specific activity of 7.0 micromol of H(2)O(2) reduced/min/mg of rubrerythrin at 85 degrees C. Strangely, as-purified (reduced) rubrerythrin precipitated when oxidized by either hydrogen peroxide, air, or ferricyanide. The gene (PF1283) encoding rubrerythrin was expressed in Escherichia coli grown in medium with various metal contents. The purified recombinant proteins each contained approximately three metal atoms/subunit, ranging from 0.4 Fe plus 2.2 Zn to 1.9 Fe plus 1.2 Zn, where the metal content of the protein depended on the metal content of the E. coli growth medium. The peroxidase activities of the recombinant forms were proportional to the iron content. P. furiosus rubrerythrin is the first to be characterized from a hyperthermophile or from an archaeon, and the results are the first demonstration that this protein functions in an NADH-dependent, hydrogen peroxide:rubredoxin oxidoreductase system. Rubrerythrin is proposed to play a role in the recently defined anaerobic detoxification pathway for reactive oxygen species.

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.

Crystal structure of sulerythrin, a rubrerythrin-like protein from a strictly aerobic archaeon, Sulfolobus tokodaii strain 7, shows unexpected domain swapping

Sulerythrin is the first rubrerythrin-like protein to be isolated from an aerobic organism, Sulfolobus tokodaii strain 7, and it lacks a C-terminal rubredoxin-like FeS(4) domain. The protein purified from Sulfolobus cells was crystallized, and the crystal structure was determined at 1.7 A resolution. The dimer of sulerythrin exhibited "domain-swapping" at the loop connecting alphaB and alphaC, hybrid four-helix bundles consisting of alphaA/B and alphaC/D being formed. The structure and atomic identity of the binuclear metal center were determined by means of anomalous scattering analysis. The site contained 1.0 mol of hexacoordinate Fe, 0.80-0.87 mol of tetracoordinate Zn, and 0.73-0.88 mol of putative O(2) per monomer. The metal ions were found at exchanged positions compared to those in the Fe/Zn-containing rubrerythrin from Desulfovibrio vulgaris. The results demonstrate that the binuclear metal center of rubrerythrin-like proteins is plastic in its ability to bind metal ions.

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.