Isolation and biochemical characterization of two soluble iron(III) reductases from Paracoccus denitrificans

Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans

The Pden_5119 protein oxidizes NADH with oxygen under mediation by the bound flavin mononucleotide (FMN) and may be involved in the maintenance of the cellular redox pool. In biochemical characterization, the curve of the pH-rate dependence was bell-shaped with pK_a1 = 6.6 and pK_a2 = 9.2 at 2 μM FMN while it contained only a descending limb pK_a of 9.7 at 50 μM FMN. The enzyme was found to undergo inactivation by reagents reactive with histidine, lysine, tyrosine, and arginine. In the first three cases, FMN exerted a protective effect against the inactivation. X-ray structural analysis coupled with site-directed mutagenesis identified three amino acid residues important to the catalysis. Structural and kinetic data suggest that His-117 plays a role in the binding and positioning of the isoalloxazine ring of FMN, Lys-82 fixes the nicotinamide ring of NADH to support the proS-hydride transfer, and Arg-116 with its positive charge promotes the reaction between dioxygen and reduced flavin.

The Magnetosome Protein, Mms6 from Magnetospirillum magneticum Strain AMB-1, Is a Lipid-Activated Ferric Reductase

Magnetosomes of magnetotactic bacteria consist of magnetic nanocrystals with defined morphologies enclosed in vesicles originated from cytoplasmic membrane invaginations. Although many proteins are involved in creating magnetosomes, a single magnetosome protein, Mms6 from Magnetospirillum magneticum strain AMB-1, can direct the crystallization of magnetite nanoparticles in vitro. The in vivo role of Mms6 in magnetosome formation is debated, and the observation that Mms6 binds Fe³⁺ more tightly than Fe²⁺ raises the question of how, in a magnetosome environment dominated by Fe³⁺, Mms6 promotes the crystallization of magnetite, which contains both Fe³⁺ and Fe²⁺. Here we show that Mms6 is a ferric reductase that reduces Fe³⁺ to Fe²⁺ using NADH and FAD as electron donor and cofactor, respectively. Reductase activity is elevated when Mms6 is integrated into either liposomes or bicelles. Analysis of Mms6 mutants suggests that the C-terminal domain binds iron and the N-terminal domain contains the catalytic site. Although Mms6 forms multimers that involve C-terminal and N-terminal domain interactions, a fusion protein with ubiquitin remains a monomer and displays reductase activity, which suggests that the catalytic site is fully in the monomer. However, the quaternary structure of Mms6 appears to alter the iron binding characteristics of the C-terminal domain. These results are consistent with a hypothesis that Mms6, a membrane protein, promotes the formation of magnetite in vivo by a mechanism that involves reducing iron.

The ArsH Protein Product of the Paracoccus denitrificans ars Operon Has an Activity of Organoarsenic Reductase and Is Regulated by a Redox-Responsive Repressor

Paracoccus denitrificans ArsH is encoded by two identical genes located in two distinct putative arsenic resistance (ars) operons. Escherichia coli-produced recombinant N-His₆-ArsH was characterized both structurally and kinetically. The X-ray structure of ArsH revealed a flavodoxin-like domain and motifs for the binding of flavin mononucleotide (FMN) and reduced nicotinamide adenine dinucleotide phosphate (NADPH). The protein catalyzed FMN reduction by NADPH via ternary complex mechanism. At a fixed saturating FMN concentration, it acted as an NADPH-dependent organoarsenic reductase displaying ping-pong kinetics. A 1:1 enzymatic reaction of phenylarsonic acid with the reduced form of FMN (FMNH₂) and formation of phenylarsonous acid were observed. Growth experiments with P. denitrificans and E. coli revealed increased toxicity of phenylarsonic acid to cells expressing arsH, which may be related to in vivo conversion of pentavalent As to more toxic trivalent form. ArsH expression was upregulated not only by arsenite, but also by redox-active agents paraquat, tert-butyl hydroperoxide and diamide. A crucial role is played by the homodimeric transcriptional repressor ArsR, which was shown in in vitro experiments to monomerize and release from the DNA-target site. Collectively, our results establish ArsH as responsible for enhancement of organo-As(V) toxicity and demonstrate redox control of ars operon.

Microbial Cd(II) and Cr(VI) resistance mechanisms and application in bioremediation

The heavy metals cadmium (Cd) and chromium (Cr) are extensively used in industry and result in water and soil contamination. The highly toxic Cd(II) and Cr(VI) are the most common soluble forms of Cd and Cr, respectively. They enter the human body through the food chain and drinking water and then cause serious illnesses. Microorganisms can adsorb metals or transform Cd(II) and Cr(VI) into insoluble or less bioavailable forms, and such strategies are applicable in Cd and Cr bioremediation. This review focuses on the highlighting of novel achievements on microbial Cd(II) and Cr(VI) resistance mechanisms and their bioremediation applications. In addition, the knowledge gaps and research perspectives are also discussed in order to build a bridge between the theoretical breakthrough and the resolution of Cd(II) and Cr(VI) contamination problems.

Tibet plateau probiotic mitigates chromate toxicity in mice by alleviating oxidative stress in gut microbiota

Heavy metal contamination in food endangers human health. Probiotics can protect animals and human against heavy metals, but the detoxification mechanism has not been fully clarified. Here, mice were supplemented with Pediococcus acidilactici strain BT36 isolated from Tibetan plateau yogurt, with strong antioxidant activity but no chromate reduction ability for 20 days to ensure gut colonization. Strain BT36 decreased chromate accumulation, reduced oxidative stress, and attenuated histological damage in the liver of mice. 16S rRNA and metatranscriptome sequencing analysis of fecal microbiota showed that BT36 reversed Cr(VI)-induced changes in gut microbial composition and metabolic activity. Specifically, BT36 recovered the expressions of 788 genes, including 34 inherent Cr remediation-relevant genes. Functional analysis of 10 unannotated genes regulated by BT36 suggested the existence of a new Cr(VI)-reduction gene in the gut microbiota. Thus, BT36 can modulate the gut microbiota in response to Cr(VI) induced oxidative stress and protect against Cr toxicity.

Free flavins accelerate release of ferrous iron from iron storage proteins by both free flavin-dependent and -independent ferric reductases in Escherichia coli

Ferredoxin NADP⁺ oxidoreductase (Fpr) and oxygen-insensitive NAD(P)H nitroreductase (NfnB) are purified from Escherichia coli JM109 (E. coli JM109) as a predominant free flavin-independent ferric reductase. In the present study, we prepared natural iron storage proteins, E. coli ferritin A (FtnA) and bacterioferritin (Bfr), to show the effective ferrous iron release from these proteins by Fpr and NfnB in the presence of free flavins. Fpr and NfnB showed flavin reductase activity for flavin adenine dinucleotide (FAD), flavin mononucleotide (FMN) and riboflavin, and their ferrous iron release activities were positively associated with the catalytic efficiencies (k_cat/K_m) for individual flavins. The ferrous iron release activity of E. coli cell-free extracts was affected by flavin reductase activity of the extracts. The Butyl TOYOPEARL column chromatography of the extracts, on the basis of NAD(P)H-dependent flavin reductase activity, resulted in the separation of six active fractions containing Fpr, NfnB, NAD(P)H-quinone oxidoreductase (QOR), flavin reductase (Fre) or alkyl hydroperoxide reductase subunit F (AhpF) as major components. Like Fpr and NfnB, recombinant QOR, Fre, and AhpF showed flavin reductase activity and ferrous iron release activity in the presence of free flavins, indicating an association of flavin reductase activity with ferrous iron releasing activity. Taken together, both free flavin-dependent and free flavin-independent ferric reductases in E. coli require free flavins to mediate an electron transfer from NAD(P)H to ferric iron in the iron storage proteins for the effective ferrous iron release.

Functional and mechanistic characterization of an atypical flavin reductase encoded by the pden_5119 gene in Paracoccus denitrificans

Pden_5119, annotated as an NADPH-dependent FMN reductase, shows homology to proteins assisting in utilization of alkanesulfonates in other bacteria. Here, we report that inactivation of the pden_5119 gene increased susceptibility to oxidative stress, decreased growth rate and increased growth yield; growth on lower alkanesulfonates as sulfur sources was not specifically influenced. Pden_5119 transcript rose in response to oxidative stressors, respiratory chain inhibitors and terminal oxidase downregulation. Kinetic analysis of a fusion protein suggested a sequential mechanism in which FMN binds first, followed by NADH. The affinity of flavin toward the protein decreased only slightly upon reduction. The observed strong viscosity dependence of k_cat demonstrated that reduced FMN formed tends to remain bound to the enzyme where it can be re-oxidized by oxygen or, less efficiently, by various artificial electron acceptors. Stopped flow data were consistent with the enzyme-FMN complex being a functional oxidase that conducts the reduction of oxygen by NADH. Hydrogen peroxide was identified as the main product. As shown by isotope effects, hydride transfer occurs from the pro-S C4 position of the nicotinamide ring and partially limits the overall turnover rate. Collectively, our results point to a role for the Pden_5119 protein in maintaining the cellular redox state.

Arginine-95 is important for recruiting superoxide to the active site of the FerB flavoenzyme of Paracoccus denitrificans

Ferric reductase B (FerB) is a flavin mononucleotide (FMN)-containing NAD(P)H:acceptor oxidoreductase structurally close to the Gluconacetobacter hansenii chromate reductase (ChrR). The crystal structure of ChrR was previously determined with a chloride bound proximal to FMN in the vicinity of Arg101, and the authors suggested that the anionic electron acceptors, chromate and uranyl tricarbonate, bind similarly. Here, we identify the corresponding arginine residue in FerB (Arg95) as being important for the reaction of FerB with superoxide. Four mutants at position 95 were prepared and found kinetically to have impaired capacity for superoxide binding. Stopped-flow data for the flavin cofactor showed that the oxidative step is rate limiting for catalytic turnover. The findings are consistent with a role for FerB as a superoxide scavenging contributor.

Cr(VI) reduction by an extracellular polymeric substance (EPS) produced from a strain of Pseudochrobactrum saccharolyticum

A better understanding of the Cr(VI) reduction position and mechanisms by a Cr(VI)-reducing strain is important for the bioremediation of Cr pollution in the environment. In the present study, we were interested in figuring out the role of extracellular polymeric substances (EPS) as the main area for Cr(VI) reduction in the newly reported strain of Pseudochrobactrum saccharolyticum LY10. We investigated the subcellular distribution and reduction capability of each cellular component as the main area of Cr(VI) reduction by scanning electron microscopy and soft X-ray spectromicroscopy. The results suggested that most of Cr was presented in the supernatants as Cr(III) after reduction. In the cells, Cr was mostly distributed in the EPS and cell wall, while the EPS had the maximum Cr(VI) reduction rate (81.5%) as compared with the cell wall (30.1%). Soft X-ray spectromicroscopy analysis indicated that Cr accumulated more in the EPS. Therefore, the results suggested that the EPS were the main area for Cr(VI) reduction in the bacteria of P. saccharolyticum LY10.

Hydrogen ions and organic acids secreted by ectomycorrhizal fungi, Pisolithus sp1, are involved in the efficient removal of hexavalent chromium from waste water

Pisolithus sp1 is an ectomycorrhizal (ECM) fungi that was chosen during a screening test of six strains of ECM fungi due to its ability to tolerate and remove hexavalent chromium (Cr(VI)). The physiological responses of Pisolithus sp1 to Cr(VI) exposure, the relationship between Pisolithus sp1 and exogenously added organic acids (EAOAs) or Na₃VO₄ (H⁺-ATPase inhibitor) and the ability of Pisolithus sp1 to reduce Cr(VI) in liquid culture were also investigated. Hydrogen ions (H⁺), which were produced directly by Pisolithus sp1, reduced the pH of the medium and played an important role in Cr(VI) reduction; however, Na₃VO₄ significantly inhibited this process and resulted in a decrease in the Cr(VI) reduction rates. Organic acids were secreted after the reduction in Cr(VI) by Pisolithus sp1, and EAOAs did not significantly affect Cr(VI) reduction; those results revealed the secondary role of organic acids in Cr(VI) reduction. The Cr(VI) removal rate of Pisolithus sp1 approached 99% after Cr(VI) treatment for 12 days. Overall, 75% of the Cr(VI) removal was due to extracellular reduction and 24% was due to adsorption. The results of this study provide a strong basis for using Cr(VI)-tolerant and Cr(VI)-reducing fungi, as well as ectomycorrhiza, in the remediation of Cr(VI)-contaminated sites.

Overview on the Bacterial Iron-Riboflavin Metabolic Axis

Redox reactions are ubiquitous in biological processes. Enzymes involved in redox metabolism often use cofactors in order to facilitate electron-transfer reactions. Common redox cofactors include micronutrients such as vitamins and metals. By far, while iron is the main metal cofactor, riboflavin is the most important organic cofactor. Notably, the metabolism of iron and riboflavin seem to be intrinsically related across life kingdoms. In bacteria, iron availability influences expression of riboflavin biosynthetic genes. There is documented evidence for riboflavin involvement in surpassing iron-restrictive conditions in some species. This is probably achieved through increase in iron bioavailability by reduction of extracellular iron, improvement of iron uptake pathways and boosting hemolytic activity. In some cases, riboflavin may also work as replacement of iron as enzyme cofactor. In addition, riboflavin is involved in dissimilatory iron reduction during extracellular respiration by some species. The main direct metabolic relationships between riboflavin and iron in bacterial physiology are reviewed here.

Novel bacterial selenite reductase CsrF responsible for Se(IV) and Cr(VI) reduction that produces nanoparticles in Alishewanella sp. WH16-1

Alishewanella sp. WH16-1 is a facultative anaerobic bacterium isolated from mining soil. Under aerobic conditions, this bacterium efficiently reduces selenite and chromate. A flavoprotein showing 37% amino acid identity to E. coli chromate reductase ChrR was identified from the genome (named CsrF). Gene mutation and complementation along with heterologous expression revealed the ability of CsrF to reduce selenite and chromate in vivo. The purified CsrF was yellow and showed an absorption spectra similar to that of FMN. The molecular weight of CsrF was 23,906 for the monomer and 47,960 for the dimer. In vitro, CsrF catalyzes the reduction of Se(IV) and Cr(VI) using NAD(P)H as cofactors with optimal condition of pH 7.0 and temperature of 30-37°C. This enzyme also catalyze the reduction of sulfate and ferric iron but not arsenate and nitrate. Using NADPH as its electron donor, the Km for the reduction of Se(IV) and Cr(VI) was 204.1±27.91 and 250.6±23.46μmol/L, respectively. Site-directed mutagenesis showed that Arg13 and Gly113 were essential for the reduction of Se(IV) and Cr(VI). The products of the reduction of Se(IV) and Cr(VI) were Se(0)- and Cr(III)-nanoparticles, respectively. To our knowledge, CsrF is a novel and well-characterized bacterial aerobic selenite reductase.

Alleviation of toxic hexavalent chromium using indigenous aerobic bacteria isolated from contaminated tannery industry sites

In the last decade, much attention has been paid to bioremediation of Cr(VI) using various bacterial species. Cr(VI) remediation by indegeneous bacteria isolated from contaminated sites of a tannery industry located in Tamil Nadu, India, was investigated in this study. Three Cr(VI) resistant bacterial strains (TES-1, TEf-1, and TES-2) were isolated and selected based on their Cr(VI) reduction ability in minimal salt medium. Among these three bacterial strains, TES-1 was found to be most efficient in bioreduction, while TES-2 was only found to be Cr(VI) resistant and showed negligible bioreduction, whereas TEf-1 was observed to be most Cr(VI) tolerant. Potential for bioremediation of TES-1 and TEf-1 was further investigated at different concentrations of Cr(VI) in the range of 50 to 350 mg L(-1). TEf-1 showed prominent synchronous growth throughout the experiment, whereas TES-1 took a longer acclimatization time. Minimum inhibitory concentrations (MIC) of Cr(VI) for TES-1 and TEf-1 were approximated as 600 mg L(-1) and 750 mg L(-1), respectively. The kinetic behavior of Cr(VI) reduction by TES-1 and TEf-1 exhibited zero- and first-order removal kinetics for Cr(VI), respectively. The most efficient strain TES-1 was identified as Streptomyces sp. by gene sequencing of 16S rRNA.

Biochemical properties and crystal structure of the flavin reductase FerA from Paracoccus denitrificans

The Pden_2689 gene encoding FerA, an NADH:flavin oxidoreductase required for growth of Paracoccus denitrificans under iron limitation, was cloned and overexpressed as a C-terminally His6-tagged derivative. The binding of substrates and products was detected and quantified by isothermal titration calorimetry and fluorometric titration. FerA binds FMN and FAD with comparable affinity in an enthalpically driven, entropically opposed process. The reduced flavin is bound more loosely than the oxidized one, which was confirmed by a negative shift in the redox potential of FMN after addition of FerA. Initial velocity and substrate analogs inhibition studies showed that FerA follows a random-ordered sequence of substrate (NADH and FMN) binding. The primary kinetic isotope effects from stereospecifically deuterated nicotinamide nucleotides demonstrated that hydride transfer occurs from the pro-S position and contributes to rate limitation for the overall reaction. The crystal structure of FerA revealed a twisted seven-stranded antiparallel β-barrel similar to that of other short chain flavin reductases. Only minor structural changes around Arg106 took place upon FMN binding. The solution structure FerA derived from small angle X-ray scattering (SAXS) matched the dimer assembly predicted from the crystal structure. Site-directed mutagenesis pinpointed a role of Arg106 and His146 in binding of flavin and NADH, respectively. Pull down experiments performed with cytoplasmic extracts resulted in a negative outcome indicating that FerA might physiologically act without association with other proteins. Rapid kinetics experiments provided evidence for a stabilizing effect of another P. denitrificans protein, the

NAD(P)H

acceptor oxidoreducase FerB, against spontaneous oxidation of the FerA-produced dihydroflavin.

Responses in Micro-Mineral Metabolism in Rainbow Trout to Change in Dietary Ingredient Composition and Inclusion of a Micro-Mineral Premix

Responses in micro-mineral metabolism to changes in dietary ingredient composition and inclusion of a micro-mineral premix (Fe, Cu, Mn, Zn and Se) were studied in rainbow trout. In a 2 x 2 factorial design, triplicate groups of rainbow trout (initial weight: 20 g) were fed over 12 weeks at 17°C a fishmeal-based diet (M) or a plant-ingredient based diet (V), with or without inclusion of a mineral premix. Trout fed the V vs. M diet had lower feed intake, growth, hepato-somatic index, apparent availability coefficient (AAC) of Fe, Cu, Mn and Zn and also lower whole body Se and Zn concentration, whereas whole body Fe and Cu and plasma Fe concentrations were higher. Feeding the V diet increased intestinal ferric reductase activity; at transcriptional level, hepatic hepcidin expression was down-regulated and ferroportin 1 was up-regulated. Transcription of intestinal Cu-transporting ATPases and hepatic copper transporter1 were higher in V0 compared to other groups. Among the hepatic metalo-enzyme activities assayed, only Se-dependent glutathione peroxidase was affected, being lower in V fed fish. Premix inclusion reduced the AAC of Fe, Cu and Zn; increased the whole body concentration of all micro- minerals; up-regulated hepatic hepcidin and down-regulated intestinal ferroportin 1 transcription; and reduced the transcription of Cu-transporting ATPases in the intestine. Overall, the regulation of micro-mineral metabolism in rainbow trout, especially Fe and Cu, was affected both by a change in ingredient composition and micro-mineral premix inclusion.

Performances of microbial fuel cells fed with rejected wastewater from BioCH4 and BioH2 processes treating molasses wastewater

An integrated process involving conventional anaerobic digestion and microbial fuel cells (MFCs) has attracted attention recently to produce sustainable energy and to treat wastewater efficiently. To evaluate the possibility of CH4-producing process (BioCH4)-MFC or H2-producing process (BioH2)-MFC integrating systems, the MFC performances were investigated using rejected wastewater from a BioCH4 reactor (RWCH4) or BioH2 reactor (RWH2) treating molasses wastewater. When RWCH4 or RWH2 was fed into a single-chamber MFC reactor (designated as AC-MFCCH4 and AC-MFCH2, respectively) at different hydraulic retention times (HRT) of 1-7 d, both MFC systems showed maximum electricity production efficiencies at a HRT of 3 d. In the AC-MFCCH4 reactor, the average current density and average power density were 60.5 mA·m(-2) and 8.8 mW·m(-2), respectively. The AC-MFCH2 reactor generated an average current density of 71.4 mA·m(-2) and an average power density of 12.0 mW·m(-2). The COD removal rates were 45.7% in the AC-MFCCH4 reactor and 90.3% in the AC-MFCH2 reactor. There were no significant differences of the eubacterial community structures between the MFC systems, where Proteobacteria was remarkably dominant in both MFC systems. However, the archaeal community structures were significantly different where Methanothrix (89.3%) was remarkably dominant in the AC-MFCCH4 system, while Methanothrix (52.5%) and Methanosarcina (33.5%) were abundant in the AC-MFCH2 system. These findings demonstrate that the utilization of MFCs after the BioCH4 or BioH2 process is advantageous for energy recovery as well as COD removal from molasses wastewater.

Identification of proteins capable of metal reduction from the proteome of the Gram-positive bacterium Desulfotomaculum reducens MI-1 using an NADH-based activity assay

Understanding of microbial metal reduction is based almost solely on studies of Gram-negative organisms. In this study, we focus on Desulfotomaculum reducens MI-1, a Gram-positive metal reducer whose genome lacks genes with similarity to any characterized metal reductase. Using non-denaturing separations and mass spectrometry identification, in combination with a colorimetric screen for chelated Fe(III)-NTA reduction with NADH as electron donor, we have identified proteins from the D. reducens proteome not previously characterized as iron reductases. Their function was confirmed by heterologous expression in Escherichia coli. Furthermore, we show that these proteins have the capability to reduce soluble Cr(VI) and U(VI) with NADH as electron donor. The proteins identified are NADH : flavin oxidoreductase (Dred_2421) and a protein complex composed of oxidoreductase flavin adenine dinucleotide/NAD(P)-binding subunit (Dred_1685) and dihydroorotate dehydrogenase 1B (Dred_1686). Dred_2421 was identified in the soluble proteome and is predicted to be a cytoplasmic protein. Dred_1685 and Dred_1686 were identified in both the soluble as well as the insoluble protein fraction, suggesting a type of membrane association, although PSORTb predicts both proteins are cytoplasmic. This study is the first functional proteomic analysis of D. reducens and one of the first analyses of metal and radionuclide reduction in an environmentally relevant Gram-positive bacterium.

Identification of Multiple Soluble Fe(III) Reductases in Gram-Positive Thermophilic Bacterium Thermoanaerobacter indiensis BSB-33

Thermoanaerobacter indiensis BSB-33 has been earlier shown to reduce Fe(III) and Cr(VI) anaerobically at 60°C optimally. Further, the Gram-positive thermophilic bacterium contains Cr(VI) reduction activity in both the membrane and cytoplasm. The soluble fraction prepared from T. indiensis cells grown at 60°C was found to contain the majority of Fe(III) reduction activity of the microorganism and produced four distinct bands in nondenaturing Fe(III) reductase activity gel. Proteins from each of these bands were partially purified by chromatography and identified by mass spectrometry (MS) with the help of T. indiensis proteome sequences. Two paralogous dihydrolipoamide dehydrogenases (LPDs), thioredoxin reductase (Trx), NADP(H)-nitrite reductase (Ntr), and thioredoxin disulfide reductase (Tdr) were determined to be responsible for Fe(III) reductase activity. Amino acid sequence and three-dimensional (3D) structural similarity analyses of the T. indiensis Fe(III) reductases were carried out with Cr(VI) reducing proteins from other bacteria. The two LPDs and Tdr showed very significant sequence and structural identity, respectively, with Cr(VI) reducing dihydrolipoamide dehydrogenase from Thermus scotoductus and thioredoxin disulfide reductase from Desulfovibrio desulfuricans. It appears that in addition to their iron reducing activity T. indiensis LPDs and Tdr are possibly involved in Cr(VI) reduction as well.

The structural and functional basis of catalysis mediated by NAD(P)H:acceptor Oxidoreductase (FerB) of Paracoccus denitrificans

FerB from Paracoccus denitrificans is a soluble cytoplasmic flavoprotein that accepts redox equivalents from NADH or NADPH and transfers them to various acceptors such as quinones, ferric complexes and chromate. The crystal structure and small-angle X-ray scattering measurements in solution reported here reveal a head-to-tail dimer with two flavin mononucleotide groups bound at the opposite sides of the subunit interface. The dimers tend to self-associate to a tetrameric form at higher protein concentrations. Amino acid residues important for the binding of FMN and NADH and for the catalytic activity are identified and verified by site-directed mutagenesis. In particular, we show that Glu77 anchors a conserved water molecule in close proximity to the O2 of FMN, with the probable role of facilitating flavin reduction. Hydride transfer is shown to occur from the 4-pro-S position of NADH to the solvent-accessible si side of the flavin ring. When using deuterated NADH, this process exhibits a kinetic isotope effect of about 6 just as does the NADH-dependent quinone reductase activity of FerB; the first, reductive half-reaction of flavin cofactor is thus rate-limiting. Replacing the bulky Arg95 in the vicinity of the active site with alanine substantially enhances the activity towards external flavins that obeys the standard bi-bi ping-pong reaction mechanism. The new evidence for a cryptic flavin reductase activity of FerB justifies the previous inclusion of this enzyme in the protein family of NADPH-dependent FMN reductases.

Bacterial mechanisms for Cr(VI) resistance and reduction: an overview and recent advances

Chromium pollution is increasing incessantly due to continuing industrialization. Of various oxidation states, Cr(6+) is very toxic due to its carcinogenic and mutagenic nature. It also has deleterious effects on different microorganisms as well as on plants. Many species of bacteria thriving in the Cr(6+)-contaminated environments have evolved novel strategies to cope with Cr(6+) toxicity. Generally, decreased uptake or exclusion of Cr(6+) compounds through the membranes, biosorption, and the upregulation of genes associated with oxidative stress response are some of the resistance mechanisms in bacterial cells to overcome the Cr(6+) stress. In addition, bacterial Cr(6+) reduction into Cr(3+) is also a mechanism of specific significance as it transforms toxic and mobile chromium derivatives into reduced species which are innocuous and immobile. Ecologically, the bacterial trait of reductive immobilization of Cr(6+) derivatives is of great advantage in bioremediation. The present review is an effort to underline the bacterial resistance and reducing mechanisms to Cr(6+) compounds with recent development in order to garner a broad perspective.

Molecular mechanisms of Cr(VI) resistance in bacteria and fungi

Hexavalent chromium [Cr(VI)] contamination is one of the main problems of environmental protection because the Cr(VI) is a hazard to human health. The Cr(VI) form is highly toxic, mutagenic, and carcinogenic, and it spreads widely beyond the site of initial contamination because of its mobility. Cr(VI), crossing the cellular membrane via the sulfate uptake pathway, generates active intermediates Cr(V) and/or Cr(IV), free radicals, and Cr(III) as the final product. Cr(III) affects DNA replication, causes mutagenesis, and alters the structure and activity of enzymes, reacting with their carboxyl and thiol groups. To persist in Cr(VI)-contaminated environments, microorganisms must have efficient systems to neutralize the negative effects of this form of chromium. The systems involve detoxification or repair strategies such as Cr(VI) efflux pumps, Cr(VI) reduction to Cr(III), and activation of enzymes involved in the ROS detoxifying processes, repair of DNA lesions, sulfur metabolism, and iron homeostasis. This review provides an overview of the processes involved in bacterial and fungal Cr(VI) resistance that have been identified through 'omics' studies. A comparative analysis of the described molecular mechanisms is offered and compared with the cellular evidences obtained using classical microbiological approaches.

Genomic and physiological characterization of the chromate-reducing, aquifer-derived Firmicute Pelosinus sp. strain HCF1

Pelosinus spp. are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in Pelosinus sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI)-reducing columns constructed with aquifer sediment. Strain HCF1 ferments lactate to propionate and acetate (the methylmalonyl-coenzyme A [CoA] pathway was identified in the genome), and its genome encodes two [NiFe]- and four [FeFe]-hydrogenases for H(2) cycling. The reduction of Cr(VI) and Fe(III) may be catalyzed by a flavoprotein with 42 to 51% sequence identity to both ChrR and FerB. This bacterium has unexpected capabilities and gene content associated with reduction of nitrogen oxides, including dissimilatory reduction of nitrate to ammonium (two copies of NrfH and NrfA were identified along with NarGHI) and a nitric oxide reductase (NorCB). In this strain, either H(2) or lactate can act as a sole electron donor for nitrate, Cr(VI), and Fe(III) reduction. Transcriptional studies demonstrated differential expression of hydrogenases and nitrate and nitrite reductases. Overall, the unexpected metabolic capabilities and gene content reported here broaden our perspective on what biogeochemical and ecological roles this species might play as a prominent member of microbial communities in subsurface environments.

Extracytoplasmic function (ECF) sigma factor σF is involved in Caulobacter crescentus response to heavy metal stress

Background

The α-proteobacterium Caulobacter crescentus inhabits low-nutrient environments and can tolerate certain levels of heavy metals in these sites. It has been reported that C. crescentus responds to exposure to various heavy metals by altering the expression of a large number of genes.

Results

In this work, we show that the ECF sigma factor σ^F is one of the regulatory proteins involved in the control of the transcriptional response to chromium and cadmium. Microarray experiments indicate that σ^F controls eight genes during chromium stress, most of which were previously described as induced by heavy metals. Surprisingly, σ^F itself is not strongly auto-regulated under metal stress conditions. Interestingly, σ^F-dependent genes are not induced in the presence of agents that generate reactive oxygen species. Promoter analyses revealed that a conserved σ^F-dependent sequence is located upstream of all genes of the σ^F regulon. In addition, we show that the second gene in the sigF operon acts as a negative regulator of σ^F function, and the encoded protein has been named NrsF (Negative regulator of sigma F). Substitution of two conserved cysteine residues (C131 and C181) in NrsF affects its ability to maintain the expression of σ^F-dependent genes at basal levels. Furthermore, we show that σ^F is released into the cytoplasm during chromium stress and in cells carrying point mutations in both conserved cysteines of the protein NrsF.

Conclusion

A possible mechanism for induction of the σ^F-dependent genes by chromium and cadmium is the inactivation of the putative anti-sigma factor NrsF, leading to the release of σ^F to bind RNA polymerase core and drive transcription of its regulon.

Reduction of Fe(III)EDTA in a NOx scrubber liquor by a denitrifying bacterium and the effects of inorganic sulfur compounds on this process

Biological reduction of Fe(III)EDTA is one of the key steps in nitrogen oxides removal in the integrated approach of metal chelate absorption combined with microbial reduction. Paracoccus denitrificans ZGL1 was used as a model bacterium to evaluate the process of Fe(III)EDTA reduction by such microorganisms that could carry out the simultaneous reduction of NO chelated by Fe(II)EDTA (Fe(II)EDTA-NO) and Fe(III)EDTA. Enzymes analysis indicated Fe(III)EDTA reductase of ZGL1 was located both in the membrane and cytoplasmic fractions. Glucose was identified as the most efficient electron donor for Fe(III)EDTA reduction. Better reduction performance was obtained with higher initial cell concentration corresponding to a specific reduction rate of 8.7 μmol h(-1) mg protein(-1). The presence of sulfate and thiosulfate had no influences on both cell growth and Fe(III)EDTA reduction. Fe(III)EDTA reduction rate and cell growth could be inhibited by addition of sulfite mainly due to its direct and indirect toxic effects.

Removal efficiency of Cr6+ by indigenous Pichia sp. isolated from textile factory effluent

Resistance of the indigenous strains P. jadinii M9 and P. anomala M10, to high Cr⁶⁺ concentrations and their ability to reduce chromium in culture medium was studied. The isolates were able to tolerate chromium concentrations up to 104 μg mL⁻¹. Growth and reduction of Cr⁶⁺ were dependent on incubation temperature, agitation, Cr⁶⁺ concentration, and pH. Thus, in both studied strains the chromium removal was increased at 30°C with agitation. The optimum pH was different, with values of pH 3.0 and pH 7.0 in the case of P. anomala M10 and pH 7.0 using P. jadinii M9. Chromate reduction occurred both in intact cells (grown in culture medium) as well as in cell-free extracts. Chromate reductase activity could be related to cytosolic or membrane-associated proteins. The presence of a chromate reductase activity points out a possible role of an enzyme in Cr⁶⁺ reduction.

Reduction of hexavalent chromium by Ochrobactrum intermedium BCR400 isolated from a chromium-contaminated soil

Hexavalent chromium-resistant Ochrobactrum intermedium BCR400 was isolated from chromium contaminated soil collected from Vadodara, Gujarat. It reduced 100 mg Cr(VI)/L completely in 52 h with initial Cr(VI) reduction rate of 1.98 mg/L/h. The Cr(VI) reduction rate decreased with increase in Cr(VI) concentration from 100 to 500 mg/L. The addition of anthraquinone-2-sulphonic acid (AQS) to culture O. intermedium BCR400 significantly enhanced its chromium reduction rate. The activation energy of AQS-mediated Cr(VI) reduction (120.69 KJ/mol) was 1.1-fold lower than non-mediated Cr(VI) reduction. An increase in the activities of quinone reductase and chromate reductase in cells grown in presence of AQS/AQS + Cr(VI) suggests their role in reduction of Cr(VI) by O. intermedium. Both chromate reductase and quinone reductase activities were FAD independent, required NADH as reductant, displayed maximum activity at pH (7.0) and temperature (30 °C). Thus Cr(VI) bioremediation potential of O. intermedium can be enhanced by augmentation of system with AQS as redox mediator.

Removal, accumulation and resistance to chromium in heterotrophic Euglena gracilis

The removal, uptake and toxicity of chromium in Euglena gracilis cultured in absence and presence of malate with Cr(VI) or Cr(III) was evaluated. The malate extrusion and the extra- and intracellular Cr(VI) reduction capacity were determined and the contents of molecules with thiol group and ascorbate were also evaluated. Absence of malate in the medium decreased cell growth, increased Cr(III) toxicity, induced faster Cr(VI) disappearance from medium, and increased intracellular and intramitochondrial chromium accumulation. Both chromium species induced soluble and particulate ascorbate-dependent chromate reductase activities. Cells also secreted large amounts of malate and increased intracellular contents of thiol-molecules to bind extracellular and intracellular Cr(III), respectively. The former process was supported by significant increase in malate-producing enzyme activities and the assessment of the Cr-complexes indicated the in situ formation with thiol-molecules. The present results establish new paradigms regarding chromium stress on algae-like microorganisms: (i) Cr(III) may be more toxic than Cr(VI), depending on the culture (or environmental) conditions; (ii) several simultaneous mechanisms are turned on to inactivate chromium species and their toxic effects. These mechanisms, now well understood may further optimize, by genetically modifying E. gracilis, and facilitate the development of strategies for using this protist as potential bio-remediator of chromium-polluted water systems.

Chromate reductase activity of the Paracoccus denitrificans ferric reductase B (FerB) protein and its physiological relevance

The homodimeric flavoprotein FerB of Paracoccus denitrificans catalyzed the reduction of chromate with NADH as electron donor. When present, oxygen was reduced concomitantly with chromate. The recombinant enzyme had a maximum activity at pH 5.0. The stoichiometric ratio of NADH oxidized to chromate reduced was found to be 1.53 ± 0.09 (O(2) absent) or > 2 (O(2) present), the apparent K (M) value for chromate amounted to 70 ± 10 μM with the maximum rate of 2.9 ± 0.3 μmol NADH s(-1) (mg protein)(-1). Diode-array spectrophotometry and experiments with one-electron acceptors provided evidence for oxygen consumption being due to a flavin semiquinone, formed transiently during the interaction of FerB with chromate. At the whole-cell level, a ferB mutant strain displayed only slightly diminished rate of chromate reduction when compared to the wild-type parental strain. Anaerobically grown cells were more active than cells grown aerobically. The activity could be partly inhibited by antimycin, suggesting an involvement of the respiratory chain. Chromate concentrations above ten micromolars transiently slowed or halted culture growth, with the effect being more pronounced for the mutant strain. It appears, therefore, that, rather than directly reducing chromate, FerB confers a protection of cells against the oxidative stress accompanying chromate reduction. With a strain carrying the chromosomally integrated ferB promoter-lacZ fusion, it was shown that the ferB gene is not inducible by chromate.

Chlorella vulgaris aldehyde reductase is capable of functioning as ferric reductase and of driving the fenton reaction in the presence of free flavin

The free flavin-dependent Fenton reaction was detected in cell-free extracts of Chlorella. The corresponding enzyme was purified to homogeneity, and its N-terminal sequence was highly homologous to those of aldo-keto reductase family enzymes. The purified enzyme displayed aldehyde reductase activity in the presence of NADPH. Additionally, it showed ferric reductase activity and drove the Fenton reaction in the presence of free FAD and NADH.

Functional diversity of bacteria in a ferruginous hydrothermal sediment

A microbial community showing diverse respiratory processes was identified within an arsenic-rich, ferruginous shallow marine hydrothermal sediment (20-40 degrees C, pH 6.0-6.3) in Santorini, Greece. Analyses showed that ferric iron reduction with depth was broadly accompanied by manganese and arsenic reduction and FeS accumulation. Clone library analyses indicated the suboxic-anoxic transition zone sediment contained abundant Fe(III)- and sulfate-reducing Deltaproteobacteria, whereas the overlying surface sediment was dominated by clones related to the Fe(II)-oxidizing zetaproteobacterium, Mariprofundus ferroxydans. Cultures obtained from the transition zone were enriched in bacteria that reduced Fe(III), nitrate, sulfate and As(V) using acetate or lactate as electron donors. In the absence of added organic carbon, bacteria were enriched that oxidized Fe(II) anaerobically or microaerobically, sulfide microaerobically and aerobically and As(III) aerobically. According to 16S rRNA gene analyses, enriched bacteria represented a phylogenetically wide distribution. Most probable number counts indicated an abundance of nitrate-, As(V)- and Fe(III)((s,aq))-reducers, and dissolved sulfide-oxidizers over sulfate-reducers, and FeS-, As(III)- and nitrate-dependent Fe(II)-oxidisers in the transition zone. It is noteworthy that the combined community and geochemical data imply near-surface microbial iron and arsenic redox cycling were dominant biogeochemical processes.

Escherichia coli ferredoxin-NADP+ reductase and oxygen-insensitive nitroreductase are capable of functioning as ferric reductase and of driving the Fenton reaction

Two free flavin-independent enzymes were purified by detecting the NAD(P)H oxidation in the presence of Fe(III)-EDTA and t-butyl hydroperoxide from E. coli. The enzyme that requires NADH or NADPH as an electron donor was a 28 kDa protein, and N-terminal sequencing revealed it to be oxygen-insensitive nitroreductase (NfnB). The second enzyme that requires NADPH as an electron donor was a 30 kDa protein, and N-terminal sequencing revealed it to be ferredoxin-NADP(+) reductase (Fpr). The chemical stoichiometry of the Fenton activities of both NfnB and Fpr in the presence of Fe(III)-EDTA, NAD(P)H and hydrogen peroxide was investigated. Both enzymes showed a one-electron reduction in the reaction forming hydroxyl radical from hydrogen peroxide. Also, the observed Fenton activities of both enzymes in the presence of synthetic chelate iron compounds were higher than their activities in the presence of natural chelate iron compounds. When the Fenton reaction occurs, the ferric iron must be reduced to ferrous iron. The ferric reductase activities of both NfnB and Fpr occurred with synthetic chelate iron compounds. Unlike NfnB, Fpr also showed the ferric reductase activity on an iron storage protein, ferritin, and various natural iron chelate compounds including siderophore. The Fenton and ferric reductase reactions of both NfnB and Fpr occurred in the absence of free flavin. Although the k(cat)/K(m) value of NfnB for Fe(III)-EDTA was not affected by free flavin, the k(cat)/K(m) value of Fpr for Fe(III)-EDTA was 12-times greater in the presence of free FAD than in the absence of free FAD.

Crystallization and initial X-ray diffraction studies of the flavoenzyme NAD(P)H:(acceptor) oxidoreductase (FerB) from the soil bacterium Paracoccus denitrificans

The flavin-dependent enzyme FerB from Paracoccus denitrificans reduces a broad range of compounds, including ferric complexes, chromate and most notably quinones, at the expense of the reduced nicotinamide adenine dinucleotide cofactors NADH or NADPH. Recombinant unmodified and SeMet-substituted FerB were crystallized under similar conditions by the hanging-drop vapour-diffusion method with microseeding using PEG 4000 as the precipitant. FerB crystallized in several different crystal forms, some of which diffracted to approximately 1.8 A resolution. The crystals of native FerB belonged to space group P2(1), with unit-cell parameters a = 61.6, b = 110.1, c = 65.2 A, beta = 118.2 degrees and four protein molecules in the asymmetric unit, whilst the SeMet-substituted form crystallized in space group P2(1)2(1)2, with unit-cell parameters a = 61.2, b = 89.2, c = 71.5 A and two protein molecules in the asymmetric unit. Structure determination by the three-wavelength MAD/MRSAD method is now in progress.

Remediation of chromium(VI) by a methane-oxidizing bacterium

Methane-oxidizing bacteria are ubiquitous in the environment and are globally important in oxidizing the potent greenhouse gas methane. It is also well recognized that they have wide potential for bioremediation of organic and chlorinated organic pollutants, thanks to the wide substrate ranges of the methane monooxygenase enzymes that they produce. Here we have demonstrated that the well characterized model methanotroph Methylococcus capsulatus (Bath) is able to bioremediate chromium(VI) pollution over a wide range of concentrations (1.4-1000 mg L(-1) of Cr(6+)), thus extending the bioremediation potential of this major group of microorganisms to include an important heavy-metal pollutant. The chromium(VI) reduction reaction was dependent on the availability of reducing equivalents from the growth substrate methane and was partially inhibited by the metabolic poison sodium azide. X-ray spectroscopy showed that the cell-associated chromium was predominantly in the +3 oxidation state and associated with cell- or medium-derived moieties that were most likely phosphate groups. The genome sequence of Mc. capsulatus (Bath) suggests at least five candidate genes for the chromium(VI) reductase activity in this organism.

Heterologous expression and molecular characterization of the NAD(P)H:acceptor oxidoreductase (FerB) of Paracoccus denitrificans

FerB is a flavoenzyme capable of reducing quinones, ferric complexes and chromate. Its expression in Escherichia coli as a hexahistidine fusion resulted in a functional product only when the tag was placed on the C-terminus. The molecular mass values estimated by gel permeation chromatography were compatible with the existence of either dimer or trimer, whereas the light scattering data, together with cross-linking experiments that yielded exclusively monomer and dimer bands on dodecyl sulfate-polyacrylamide gels, strongly supported a dimeric nature of both native and tagged form of FerB. These two proteins also exhibited almost identical secondary structure as judged by Fourier transform infra red spectrometry. The presence of tag, however, shifted the temperature of thermal inactivation as well as the thermal denaturation curve towards lower temperatures. Despite somewhat lower thermal stability, the fusion protein is considered a better candidate for crystallization than the wild-type one due to a more negative value of its second optical viral coefficient.

Iron trafficking as an antimicrobial target

Iron is essential for the survival of most organisms. Microbial iron acquisition depends on multiple, sometimes complex steps, many of which are not shared by higher eukaryotes. Depriving pathogenic microbes of iron is therefore a potential antimicrobial strategy. The following minireview briefly describes general elements in microbial iron uptake pathways and summarizes some of the current work aiming at their medicinal inhibition.

Ferric reductase A is essential for effective iron acquisition in Paracoccus denitrificans

Based on N-terminal sequences obtained from the purified cytoplasmic ferric reductases FerA and FerB, their corresponding genes were identified in the published genome sequence of Paracoccus denitrificans Pd1222. The ferA and ferB genes were cloned and individually inactivated by insertion of a kanamycin resistance marker, and then returned to P. denitrificans for exchange with their wild-type copies. The resulting ferA and ferB mutant strains showed normal growth in brain heart infusion broth. Unlike the ferB mutant, the strain lacking FerA did not grow on succinate minimal medium with ferric 2,3-dihydroxybenzoate as the iron source, and grew only poorly in the presence of ferric sulfate, chloride, citrate, NTA, EDTA and EGTA. Moreover, the ferA mutant strain was unable to produce catechols, which are normally detectable in supernatants from iron-limited wild-type cultures. Complementation of the ferA mutation using a derivative of the conjugative broad-host-range plasmid pEG400 that contained the whole ferA gene and its putative promoter region largely restored the wild-type phenotype. Partial, though significant, restoration could also be achieved with 1 mM chorismate added to the growth medium. The purified FerA protein acted as an NADH : FMN oxidoreductase and catalysed the FMN-mediated reductive release of iron from the ferric complex of parabactin, the major catecholate siderophore of P. denitrificans. The deduced amino acid sequence of the FerA protein has closest similarity to flavin reductases that form part of the flavin-dependent two-component monooxygenases. Taken together, our results demonstrate an essential role of reduced flavins in the utilization of exogenous ferric iron. These flavins not only provide the electrons for Fe(III) reduction but most probably also affect the rate of siderophore production.

Ferredoxin-NADP+ reductase from Pseudomonas putida functions as a ferric reductase

Pseudomonas putida harbors two ferredoxin-NADP(+) reductases (Fprs) on its chromosome, and their functions remain largely unknown. Ferric reductase is structurally contained within the Fpr superfamily. Interestingly, ferric reductase is not annotated on the chromosome of P. putida. In an effort to elucidate the function of the Fpr as a ferric reductase, we used a variety of biochemical and physiological methods using the wild-type and mutant strains. In both the ferric reductase and flavin reductase assays, FprA and FprB preferentially used NADPH and NADH as electron donors, respectively. Two Fprs prefer a native ferric chelator to a synthetic ferric chelator and utilize free flavin mononucleotide (FMN) as an electron carrier. FprB has a higher k(cat)/K(m) value for reducing the ferric complex with free FMN. The growth rate of the fprB mutant was reduced more profoundly than that of the fprA mutant, the growth rate of which is also lower than the wild type in ferric iron-containing minimal media. Flavin reductase activity was diminished completely when the cell extracts of the fprB mutant plus NADH were utilized, but not the fprA mutant with NADPH. This indicates that other NADPH-dependent flavin reductases may exist. Interestingly, the structure of the NAD(P) region of FprB, but not of FprA, resembled the ferric reductase (Fre) of Escherichia coli in the homology modeling. This study demonstrates, for the first time, the functions of Fprs in P. putida as flavin and ferric reductases. Furthermore, our results indicated that FprB may perform a crucial role as a NADH-dependent ferric/flavin reductase under iron stress conditions.

Azo Dye Reduction by Mesophilic and Thermophilic Anaerobic Consortia

The reduction of the azo dye model compounds Reactive Red 2 (RR2) and Reactive Orange 14 (RO14) by mesophilic (30 degrees C) and thermophilic (55 degrees C) anaerobic consortia was studied in batch assays. The contribution of fermentative and methanogenic microorganisms in both temperatures was evaluated in the presence of the fermentative substrate glucose and the methanogenic substrates acetate, H2/CO2, methanol, and formate. Additionally, the effect of the redox mediator riboflavin on electron shuttling was assessed. We concluded that the application of thermophilic anaerobic treatment is an interesting option for the reductive decolorization of azo dyes compared to mesophilic conditions. The use of high temperature may decrease or even take the place of the need for continuous redox mediator dosage in bioreactors, contrarily to the evident effect of those compounds on dye reduction under mesophilic conditions. Both fermenters and methanogens may play an important role during reductive decolorization of dyes, in which mediators are important not only for allowing the different microbes to participate more effectively in this complex reductive biochemistry but also for assisting in the competition for electrons between dyes and other organic and inorganic electron acceptors.