Crystal structure of ChrR--a quinone reductase with the capacity to reduce chromate

A PadR family transcriptional repressor regulates the transcription of chromate efflux transporter in Enterobacter sp. Z1

Chromium is a prevalent toxic heavy metal, and chromate [Cr(VI)] exhibits high mutagenicity and carcinogenicity. The presence of the Cr(VI) efflux protein ChrA has been identified in strains exhibiting resistance to Cr(VI). Nevertheless, certain strains of bacteria that are resistant to Cr(VI) lack the presence of ChrB, a known regulatory factor. Here, a PadR family transcriptional repressor, ChrN, has been identified as a regulator in the response of Enterobacter sp. Z1(CCTCC NO: M 2019147) to Cr(VI). The chrN gene is cotranscribed with the chrA gene, and the transcriptional expression of this operon is induced by Cr(VI). The binding capacity of the ChrN protein to Cr(VI) was demonstrated by both the tryptophan fluorescence assay and Ni-NTA purification assay. The interaction between ChrN and the chrAN operon promoter was validated by reporter gene assay and electrophoretic mobility shift assay. Mutation of the conserved histidine residues His14 and His50 resulted in loss of ChrN binding with the promoter of the chrAN operon. This observation implies that these residues are crucial for establishing a DNA-binding site. These findings demonstrate that ChrN functions as a transcriptional repressor, modulating the cellular response of strain Z1 to Cr(VI) exposure.

Deciphering the impacts of chromium contamination on soil bacterial communities: A comparative analysis across various soil types

Addressing the widespread concern of chromium (Cr) pollution, this study investigated its impacts on bacterial communities across eight soil types, alongside the potential Cr transformation-related genes. Utilizing real-time PCR, 16S rRNA gene sequencing and gene prediction, we revealed shifts in bacterial community structure and function at three Cr exposure levels. Our results showed that the bacterial abundance in all eight soil types was influenced by Cr to varying extents, with yellow‒brown soil being the most sensitive. The bacterial community composition of different soil types exhibited diverse responses to Cr, with only the relative abundance of Proteobacteria decreasing with increasing Cr concentration across all soil types. Beta diversity analysis revealed that while Cr concentration impacted the assembly process of bacterial communities to a certain extent, the influence on the compositional structure of bacterial communities was primarily driven by soil type rather than Cr concentration. The study also identified biomarkers for each soil type under three Cr levels, offering a basis for monitoring changes in Cr pollution. By predicting crucial functional genes related to Cr transformation, it was observed that the relative abundance of chrA (chromate transporter) in yellow‒brown soil significantly exceeded that in all other soil types, suggesting its potential for Cr adaptation. The study also revealed correlations among soil physicochemical properties, Cr concentration, and these functional genes, providing a foundation for future research aimed at more precise functional analysis and the development of effective soil remediation strategies.

Phenotypic and resistome analysis of antibiotic and heavy metal resistance in the Antarctic bacterium Pseudomonas sp. AU10

Resistance to antibiotics and heavy metals in Antarctic bacteria has been investigated due to anthropogenic impact on the continent. However, there is still much to learn about the genetic determinants of resistance in native bacteria. In this study, we investigated antibiotic, heavy metal, and metalloid resistance in Pseudomonas sp. AU10, isolated from King George Island (Antarctica), and analyzed its genome to look for all the associated genetic determinants (resistome). We found that AU10 displayed resistance to Cr(VI), Cu(II), Mn(II), Fe(II), and As(V), and produced an exopolysaccharide with high Cr(VI)-biosorption capacity. Additionaly, the strain showed resistance to aminopenicillins, cefotaxime, aztreonam, azithromycin, and intermediate resistance to chloramphenicol. Regarding the resistome, we did not find resistance genes in AU10's natural plasmid or in a prophage context. Only a copper resistance cluster indicated possible horizontal acquisition. The mechanisms of resistance found were mostly efflux systems, several sequestering proteins, and a few enzymes, such as an AmpC β-lactamase or a chromate reductase, which would account for the observed phenotypic profile. In contrast, the presence of a few gene clusters, including the terZABCDE operon for tellurite resistance, did not correlate with the expected phenotype. Despite the observed resistance to multiple antibiotics and heavy metals, the lack of resistance genes within evident mobile genetic elements is suggestive of the preserved nature of AU10's Antarctic habitat. As Pseudomonas species are good bioindicators of human impact in Antarctic environments, we consider that our results could help refine surveillance studies based on monitoring resistances and associated resistomes in these populations.

Arbuscular mycorrhizal fungi alter rhizosphere fungal community characteristics of Acorus calamus to improve Cr resistance

To investigate changes in fungal community characteristics under different Cr(VI) concentration stresses and the advantages of adding arbuscular mycorrhizal fungi (AMF), we used high throughput sequencing to characterize the fungal communities. Cr(VI) stress reduced rhizosphere soil SOM (soil organic matter) content and AMF addition improved this stress phenomenon. There were significant differences in fungal community changes under different Cr(VI) concentrations. The fungal community characteristics changed through inhibition of fungal metabolic ability, as fungal abundance increased after AMF addition, and the fungal diversity increased under high Cr(VI) concentration. The dominant phyla were members of the Ascomycota, Basidiomycota, Mortierellomycota, and Rozellomycota. Dominant groups relevant to Cr resistance were Ascomycota and Basidiomycota fungi. Moreover, Fungal community characteristics were analyzed using high-throughput sequencing of the cytochrome c metabolic pathway, NADH dehydrogenase, and NADH: ubiquinone reductase and all these functions were enhanced after AMF addition. Therefore, Cr(VI) stress significantly affects fungal community structure, while AMF addition could increase its SOM content, and metabolic capacity, and improve fungal community tolerance to Cr stress. This study contributed to the understanding response of rhizosphere fungal community in AMF-assisted wetland phytoremediation under Cr stress.

Cr(VI)-bioremediation mechanism of a novel strain Bacillus paramycoides Cr6 with the powerful ability to remove Cr(VI) from contaminated water

This research provided an excellent novel hexavalent chromium (Cr(VI))-removal bacterium, Bacillus paramycoides Cr6, and investigated its removal mechanism from the perspective of molecular biology. Cr6 could resist up to 2500 mg/L Cr(VI), and the removal rate of 2000 mg/L Cr(VI) reached 67.3% under the optimal culture conditions of 220 r/min, pH 8 and 31 ℃. When the initial concentration of Cr(VI) was 200 mg/L, Cr6 had a removal rate of 100% within 18 h. The differential transcriptome analysis identified two key structural genes named bcr005 and bcb765 of Cr6, which were upregulated by Cr(VI). Their functions were predicted and further confirmed by bioinformatic analyses and in vitro experiments. bcr005 encodes Cr(VI)-reductase BCR005, and bcb765 encodes Cr(VI)-binding protein BCB765. Real-time fluorescent quantitative PCRs were performed, and the data illustrated a parallel pathway (one is Cr(VI) reduction, and the other is Cr(VI) immobilisation) of Cr6 to remove Cr(VI), which relies on the synergistic expression of the genes bcr005 and bcb765 induced by different concentrations of Cr(VI). In summary, a deeper molecular mechanism of Cr(VI) microorganism removal was elaborated; Bacillus paramycoides Cr6 was an exceptional novel Cr(VI)-removed bacterial resource, while BCR005 and BCB765 were two new-found efficient enzymes that have potential practical applications for sustainable microbial remediation of Cr-contaminated water.

Draft genome of Raoultella planticola, a high lead resistance bacterium from industrial wastewater

Isolation of heavy metals-resistant bacteria from their original habitat is a crucial step in bioremediation. Six lead (Pb) resistant bacterial strains were isolated and identified utilizing 16S rRNA to be Enterobacter ludwigii FACU 4, Shigella flexneri FACU, Microbacterium paraoxydans FACU, Klebsiella pneumoniae subsp. pneumonia FACU, Raoultella planticola FACU 3 and Staphylococcus xylosus FACU. It was determined that all these strains had their Minimum inhibitory concentration (MIC) to be 2500 ppm except R. planticola FACU 3 has a higher maximum tolerance concentration (MTC) up to 2700 ppm. We evaluated the survival of all six strains on lead stress, the efficiency of biosorption and lead uptake. It was found that R. planticola FACU 3 is the highest MTC and S. xylosus FACU was the lowest MTC in this evaluation. Therefore, transmission electron microscopy (TEM) confirmed the difference between the morphological responses of these two strains to lead stress. These findings led to explore more about the genome of R. planticola FACU 3 using illumine Miseq technology. Draft genome sequence analysis revealed the genome size of 5,648,460 bp and G + C content 55.8% and identified 5526 CDS, 75 tRNA and 4 rRNA. Sequencing technology facilitated the identification of about 47 genes related to resistance to many heavy metals including lead, arsenic, zinc, mercury, nickel, silver and chromium of R. planticola FACU 3 strain. Moreover, genome sequencing identified plant growth-promoting genes (PGPGs) including indole acetic acid (IAA) production, phosphate solubilization, phenazine production, trehalose metabolism and 4-hydroxybenzoate production genes and a lot of antibiotic-resistant genes.

Cloning of Nitrate Reductase and Nitrite Reductase Genes and Their Functional Analysis in Regulating Cr(VI) Reduction in Ectomycorrhizal Fungus Pisolithus sp.1

Assimilatory-type nitrate reductase (NR) and nitrite reductase (NiR) are the key enzymes that involve in nitrate assimilation and nitrogen cycling in microorganisms. NR and NiR with NADH or NADPH and FMN or FAD domains could be coupled to the reduction process of hexavalent chromium [Cr(VI)] in microorganisms. A new assimilatory-type NR gene (named niaD) and a new assimilatory-type NiR gene (named niiA) are cloned, identified, and functionally characterized by 5′ and 3′ RACE, alignment, annotation, phylogenetic tree, and yeast mutant complementation analyses from Pisolithus sp.1, a dominant symbiotic ectomycorrhizal fungi (EMF) that can assist in phytoremediation. Assimilatory-type niaD and niiA were 2,754 bp and 3,468 bp and encode a polypeptide with 917 and 1,155 amino acid residues, respectively. The isoelectric points of NR (Pisolithus sp.1 NR) and NiR (Pisolithus sp.1 NiR) of Pisolithus sp.1 are 6.07 and 6.38, respectively. The calculated molecular mass of Pisolithus sp.1 NR and Pisolithus sp.1 NiR is 102.065 and 126.914 kDa, respectively. Yeast mutant complementation analysis, protein purification, and activities of NR and NiR under Cr treatment suggest that Pisolithus sp.1 NR is a functional NR that mediates Cr(VI) tolerance and reduction. The multiple alignment demonstrates that Pisolithus sp.1 NR is potentially a nicotinamide adenine dinucleotide phosphate-dependent flavin mononucleotide reductase and also Class II chromate reductase. Our results suggest that Pisolithus sp.1 NR plays a key role in Cr(VI) reduction in the EMF Pisolithus sp.1.

Recent Progress and Prospects in Catalytic Water Treatment

Presently, conventional technologies in water treatment are not efficient enough to completely mineralize refractory water contaminants. In this context, the implementation of catalytic processes could be an alternative. Despite the advantages provided in terms of kinetics of transformation, selectivity, and energy saving, numerous attempts have not yet led to implementation at an industrial scale. This review examines investigations at different scales for which controversies and limitations must be solved to bridge the gap between fundamentals and practical developments. Particular attention has been paid to the development of solar-driven catalytic technologies and some other emerging processes, such as microwave assisted catalysis, plasma-catalytic processes, or biocatalytic remediation, taking into account their specific advantages and the drawbacks. Challenges for which a better understanding related to the complexity of the systems and the coexistence of various solid-liquid-gas interfaces have been identified.

Genome analysis to decipher syntrophy in the bacterial consortium 'SCP' for azo dye degradation

Background

A bacterial consortium SCP comprising three bacterial members, viz. Stenotrophomonas acidaminiphila APG1, Pseudomonas stutzeri APG2 and Cellulomonas sp. APG4 was developed for degradation of the mono-azo dye, Reactive Blue 28. The genomic analysis of each member of the SCP consortium was done to elucidate the catabolic potential and role of the individual organism in dye degradation.

Results

The genes for glycerol utilization were detected in the genomes of APG2 and APG4, which corroborated with their ability to grow on a minimal medium containing glycerol as the sole co-substrate. The genes for azoreductase were identified in the genomes of APG2 and APG4, while no such trait could be determined in APG1. In addition to co-substrate oxidation and dye reduction, several other cellular functions like chemotaxis, signal transduction, stress-tolerance, repair mechanisms, aromatic degradation, and copper tolerance associated with dye degradation were also annotated. A model for azo dye degradation is postulated, representing the predominant role of APG4 and APG2 in dye metabolism while suggesting an accessory role of APG1.

Conclusions

This exploratory study is the first-ever attempt to divulge the genetic basis of azo-dye co-metabolism by cross-genome comparisons and can be harnessed as an example for demonstrating microbial syntrophy.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02236-9.

In vitro microcosm of co-cultured bacteria for the removal of hexavalent Cr and tannic acid: A mechanistic approach to study the impact of operational parameters

Industrial wastes, for instance, tannery wastes are rich soups of resistant and bioremediation-potent bacteria. In the present work, Chromium (Cr) and tannic acid (TA) resistance bacterial strains were isolated from tannery effluent and identified as Bacillus subtilis (MCC 3275) and Bacillus safensis (MCC 3283) based on its 16S Ribosomal RNA homology. Hexavalent Cr is highly toxic and mutagenic due to its high mobility and reactivity. Whereas, TA is known to inhibit enzyme activity, substrate deprivation, and interaction with membranes and matrix-metal ions. The developed In vitro co-cultured microcosm of B. subtilis and B. safensis was able to remove Cr(VI) up to 95% and TA up to 23%. The bacteria cultures separately were able to degrade Cr(VI) to 88% by B. subtilis and 91% by B. safensis and TA up to 27%. Plackett Burman design (PBD) followed by Response surface methodology (RSM) was applied for the optimization of physio-chemical parameters. The optimized conditions for co-culture development were recorded as K₂HPO₄ = 0.2 g/L, MgSO₄ = 0.2 g/L, NH₄Cl = 0.5 g/L, glucose - 0.2 g/L, TA - 5%, Cr = 200 ppm, incubation period of 96 h, agitation speed of 110 rpm, pH = 5.0, temperature= 30 °C and inoculum size = 3%. Scanning electron microscopy (SEM) and Fourier transform infrared (FTIR) revealed the thorough mechanism of cellular uptake followed by degradation of Cr(VI) and TA. The efficiency of co-culture for other heavy metals was observed as follows: Zn 65%, Pb 63%, Cd 65%, and Ni 65%. Bioremediation using bacteria is an economical and environmentally better alternative to conventional remediation methods. The isolated bacteria are useful in the effluent treatment of tannery or related industries and in metal recovery in mining processes.

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.

Draft genome sequence data of a chromium reducing bacterium, Bacillus licheniformis strain KNP

A chromium-reducing bacterium designated as strain KNP was isolated from a sample collected from a tannery effluent of Kanpur, India. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain KNP belonged to the Bacillus genus and showed 100% similarity with Bacillus licheniformis. Furthermore, average nucleotide identity and digital DNA-DNA hybridization between strain KNP and its closely related strains confirmed its affiliation with Bacillus licheniformis species. Whole-genome sequencing of Bacillus licheniformis KNP was performed using the Illumina Hiseq platform. Here, we present the draft genome sequence of Bacillus licheniformis KNP. The total size of the draft assembly was 4,280,093 bp, distributed into 21 contigs with an N50 value of 4,186,229. The genome has 45.9% G + C content, 4255 coding sequences and 86 putative RNA genes. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JACDXS000000000. The version described in this paper is version JACDXS010000000.

Purification, characterization, and crystal structure of YhdA-type azoreductase from Bacillus velezensis

Azoreductases are being extensively investigated for their ability to initiate degradation of recalcitrant azo dyes through reduction of azo bonds. There is great interest in studying their diversity, structure, and function to facilitate better understanding and effective application. Current study reports azoreductase enzyme from Bacillus velezensis, which showed 69.5% identity to the Bacillus subtilis azoreductase YhdA. The enzyme was homotetrameric and molecular weight of each subunit was 20 kDa. It decolorized azo dyes with different structures. The V_max for decolorization of congo red, methyl orange and methyl red was 14.7, 28.6, and 77.9 nmol/min/mg, respectively. The enzyme contained FMN as cofactor and used NADPH as the favored co-substrate. It was oxygen-insensitive, but the presence of reducing agents enhanced its activity, which is a new finding. The azoreductase expression in B. velezensis was found to be unaffected by addition of azo dyes, although azo dyes are known to induce azoreductase expression in few organisms. The enzyme was thermostable with melting temperature of 89.5°C and functioned in wide temperature range. Further, the enzyme was crystallized and its structure was solved. The structural basis of its functional attributes is discussed. In our knowledge, this is the first report on characterization of azoreductase enzyme from B. velezensis.

Cu(II) nonspecifically binding chromate reductase NfoR promotes Cr(VI) reduction

Cu(II)-enhanced microbial Cr(VI) reduction is common in the environment, yet its mechanism is unknown. The specific activity of chromate reductase, NfoR, from Staphylococcus aureus sp. LZ-01 was augmented 1.5-fold by Cu(II). Isothermal titration calorimetry and spectral data show that Cu(II) binds to NfoR nonspecifically. Further, Cu(II) stimulates the nitrobenzene reduction of NfoR, indicating that Cu(II) promotes electron transfer. The crystal structure of NfoR in complex with CuSO₄ (1.46 Å) was determined. The overall structure of NfoR-Cu(II) complex is a dimer that covalently binds with FMN and Cu(II)-binding pocket is located at the interface of the NfoR dimer. Structural superposition revealed that NfoR resembles the structure of class II chromate reductase. Site-directed mutagenesis revealed that Leu⁴⁶ and Phe¹²³ were involved in NADH binding, whereas Trp⁷⁰ and Ser⁴⁵ were the key residues for nitrobenzene binding. Furthermore, His¹⁰⁰ and Asp¹⁷¹ were preferential affinity sites for Cu(II) and that Cys¹⁶³ is an active site for FMN binding. Attenuation reductase activity in C163S can be partially restored to 54% wild type by increasing Cu(II) concentration. Partial restoration indicates dual-channel electron transfer of NfoR via Cu(II) and FMN. We propose a catalytic mechanism for Cu(II)-enhanced NfoR activity in which Cu(I) is formed transiently. Together, the current results provide an insight on Cu (II)-induced enhancement and benefit of Cr(VI) bioremediation.

NfoR: Chromate Reductase or Flavin Mononucleotide Reductase?

Soil bacteria can detoxify Cr(VI) ions by reduction. Within the last 2 decades, numerous reports of chromate reductase enzymes have been published. These reports describe catalytic reduction of chromate ions by specific enzymes. These enzymes each have sequence similarity to known redox-active flavoproteins. We investigated the enzyme NfoR from Staphylococcus aureus, which was reported to be upregulated in chromate-rich soils and to have chromate reductase activity (H. Han, Z. Ling, T. Zhou, R. Xu, et al., Sci Rep 7:15481, 2017, https://doi.org/10.1038/s41598-017-15588-y). We show that NfoR has structural similarity to known flavin mononucleotide (FMN) reductases and reduces FMN as a substrate. NfoR binds FMN with a dissociation constant of 0.4 μM. The enzyme then binds NADPH with a dissociation constant of 140 μM and reduces the flavin at a rate of 1,350 s^-1 Turnover of the enzyme is apparently limited by the rate of product release that occurs, with a net rate constant of 0.45 s^-1 The rate of product release limits the rate of observed chromate reduction, so the net rate of chromate reduction by NfoR is orders of magnitude lower than when this process occurs in solution. We propose that NfoR is an FMN reductase and that the criterion required to define chromate reduction as enzymatic has not been met. That NfoR expression is increased in the presence of chromate suggests that the survival adaption was to increase the net rate of chromate reduction by facile, adventitious redox processes.IMPORTANCE Chromate is a toxic by-product of multiple industrial processes. Chromate reduction is an important biological activity that ameliorates Cr(VI) toxicity. Numerous researchers have identified chromate reductase activity by observing chromate reduction. However, all identified chromate reductase enzymes have flavin as a cofactor or use a flavin as a substrate. We show here that NfoR, an enzyme claimed to be a chromate reductase, is in fact an FMN reductase. In addition, we show that reduction of a flavin is a viable way to transfer electrons to chromate but that it is unlikely to be the native function of enzymes. We propose that upregulation of a redox-active flavoprotein is a viable means to detoxify chromate that relies on adventitious reduction that is not catalyzed.

Novel Biochemical Properties and Physiological Role of the Flavin Mononucleotide Oxidoreductase YhdA from Bacillus subtilis

Cr(VI) is mutagenic and teratogenic and considered an environmental pollutant of increasing concern. The use of microbial enzymes that convert this ion into its less toxic reduced insoluble form, Cr(III), represents a valuable bioremediation strategy. In this study, we examined the Bacillus subtilis YhdA enzyme, which belongs to the family of NADPH-dependent flavin mononucleotide oxide reductases and possesses azo-reductase activity as a factor that upon overexpression confers protection on B. subtilis from the cytotoxic effects promoted by Cr(VI) and counteracts the mutagenic effects of the reactive oxygen species (ROS)-promoted lesion 8-OxoG. Further, our in vitro assays unveiled catalytic and biochemical properties of biotechnological relevance in YhdA; a pure recombinant His10-YhdA protein efficiently catalyzed the reduction of Cr(VI) employing NADPH as a cofactor. The activity of the pure oxidoreductase YhdA was optimal at 30°C and at pH 7.5 and displayed Km and Vmax values of 7.26 mM and 26.8 μmol·min-1·mg-1 for Cr(VI), respectively. Therefore, YhdA can be used for efficient bioremediation of Cr(VI) and counteracts the cytotoxic and genotoxic effects of oxygen radicals induced by intracellular factors and those generated during reduction of hexavalent chromium.IMPORTANCE Here, we report that the bacterial flavin mononucleotide/NADPH-dependent oxidoreductase YhdA, widely distributed among Gram-positive bacilli, conferred protection to cells from the cytotoxic effects of Cr(VI) and prevented the hypermutagenesis exhibited by a MutT/MutM/MutY-deficient strain. Additionally, a purified recombinant His10-YhdA protein displayed a strong NADPH-dependent chromate reductase activity. Therefore, we postulate that in bacterial cells, YhdA counteracts the cytotoxic and genotoxic effects of intracellular and extracellular inducers of oxygen radicals, including those caused by hexavalent chromium.

Chromium Pollution in European Water, Sources, Health Risk, and Remediation Strategies: An Overview

Chromium is a potentially toxic metal occurring in water and groundwater as a result of natural and anthropogenic sources. Microbial interaction with mafic and ultramafic rocks together with geogenic processes release Cr (VI) in natural environment by chromite oxidation. Moreover, Cr (VI) pollution is largely related to several Cr (VI) industrial applications in the field of energy production, manufacturing of metals and chemicals, and subsequent waste and wastewater management. Chromium discharge in European Union (EU) waters is subjected to nationwide recommendations, which vary depending on the type of industry and receiving water body. Once in water, chromium mainly occurs in two oxidation states Cr (III) and Cr (VI) and related ion forms depending on pH values, redox potential, and presence of natural reducing agents. Public concerns with chromium are primarily related to hexavalent compounds owing to their toxic effects on humans, animals, plants, and microorganisms. Risks for human health range from skin irritation to DNA damages and cancer development, depending on dose, exposure level, and duration. Remediation strategies commonly used for Cr (VI) removal include physico-chemical and biological methods. This work critically presents their advantages and disadvantages, suggesting a site-specific and accurate evaluation for choosing the best available recovering technology.

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.

Extracellular Vesicle-Mediated In Vitro Transcribed mRNA Delivery for Treatment of HER2+ Breast Cancer Xenografts in Mice by Prodrug CB1954 without General Toxicity

Prodrugs are harmless until activated by a bacterial or viral gene product; they constitute the basis of gene-delivered prodrug therapies called GDEPT, which can kill tumors without major side effects. Previously, we utilized the prodrug CNOB (C₁₆H₇CIN₂O₄; not clinically tested) and enzyme HChrR6 in GDEPT to generate the drug MCHB (C₁₆H₉CIN₂O₂) in tumors. Extracellular vesicles (EVs) were used for directed gene delivery and HChrR6 mRNA as gene. Here, the clinical transfer of this approach is enhanced by: (i) use of CB1954 (tretazicar) for which safe human dose is established; HChrR6 can activate this prodrug. (ii) EVs delivered in vitro transcribed (IVT) HChrR6 mRNA, eliminating the potentially harmful plasmid transfection of EV producer cells we utilized previously; this has not been done before. IVT mRNA loading of EVs required several steps. Naked mRNA being unstable, we ensured its prodrug activating functionality at each step. This was not possible using tretazicar itself; we relied instead on HChrR6's ability to convert CNOB into MCHB, whose fluorescence is easily visualizable. HChrR6 mRNA-translated product's ability to generate fluorescence from CNOB vicariously indicated its competence for tretazicar activation. (iii) Systemic IVT mRNA-loaded EVs displaying an anti-HER2 single-chain variable fragment ("IVT EXO-DEPTs") and tretazicar caused growth arrest of human HER2⁺ breast cancer xenografts in athymic mice. As this occurred without injury to other tissues, absence of off-target mRNA delivery is strongly indicated. Many cancer sites are not amenable for direct gene injection, but current GDEPTs require this. In circumventing this need, a major advance in GDEPT applicability has been accomplished.

Insights into the mode of flavin mononucleotide binding and catalytic mechanism of bacterial chromate reductases: A molecular dynamics simulation study

Enzymes from natural sources protect the environment via complex biological mechanisms, which aid in reductive immobilization of toxic metals including chromium. Nevertheless, progress was being made in elucidating high-resolution crystal structures of reductases and their binding with flavin mononucleotide (FMN) to understand the underlying mechanism of chromate reduction. Therefore, herein, we employed molecular dynamics (MD) simulations, principal component analysis (PCA), and binding free energy calculations to understand the dynamics behavior of these enzymes with FMN. Six representative chromate reductases in monomeric and dimeric forms were selected to study the mode, dynamics, and energetic component that drive the FMN binding process. As evidenced by MD simulation, FMN prefers to bind the cervix formed between the catalytic domain surrounded by strong conserved hydrogen bonding, electrostatic, and hydrophobic contacts. The slight movement and reorientation of FMN resulted in breakage of some crucial H-bonds and other nonbonded contacts, which were well compensated with newly formed H-bonds, electrostatic, and hydrophobic interactions. The critical residues aiding in tight anchoring of FMN within dimer were found to be strongly conserved in the bacterial system. The molecular mechanics combined with the Poisson-Boltzmann surface area binding free energy of the monomer portrayed that the van der Waals and electrostatic energy contribute significantly to the total free energy, where, the polar solvation energy opposes the binding of FMN. The proposed proximity relationships between enzyme and FMN binding site presented in this study will open up better avenues to engineer enzymes with optimized chromate reductase activity for sustainable bioremediation of heavy metals.

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.

Not as easy as π: An insertional residue does not explain the π-helix gain-of-function in two-component FMN reductases

The π-helix located at the tetramer interface of two-component FMN-dependent reductases contributes to the structural divergence from canonical FMN-bound reductases within the NADPH:FMN reductase family. The π-helix in the SsuE FMN-dependent reductase of the alkanesulfonate monooxygenase system has been proposed to be generated by the insertion of a Tyr residue in the conserved α4-helix. Variants of Tyr118 were generated, and their X-ray crystal structures determined, to evaluate how these alterations affect the structural integrity of the π-helix. The structure of the Y118A SsuE π-helix was converted to an α-helix, similar to the FMN-bound members of the NADPH:FMN reductase family. Although the π-helix was altered, the FMN binding region remained unchanged. Conversely, deletion of Tyr118 disrupted the secondary structural properties of the π-helix, generating a random coil region in the middle of helix 4. Both the Y118A and Δ118 SsuE SsuE variants crystallize as a dimer. The MsuE FMN reductase involved in the desulfonation of methanesulfonates is structurally similar to SsuE, but the π-helix contains a His insertional residue. Exchanging the π-helix insertional residue of each enzyme did not result in equivalent kinetic properties. Structure-based sequence analysis further demonstrated the presence of a similar Tyr residue in an FMN-bound reductase in the NADPH:FMN reductase family that is not sufficient to generate a π-helix. Results from the structural and functional studies of the FMN-dependent reductases suggest that the insertional residue alone is not solely responsible for generating the π-helix, and additional structural adaptions occur to provide the altered gain of function.

Discerning three novel chromate reduce and transport genes of highly efficient Pannonibacter phragmitetus BB: From genome to gene and protein

Here, Pannonibacter phragmitetus BB was investigated at genomic, genetic and protein levels to explore molecular mechanisms of chromium biotransformation, respectively. The results of Miseq sequencing uncovered that a high-qualified bacterial genome draft was achieved with 5.07 Mb in length. Three novel genes involved in chromate reduce and transport, named nitR, chrA1 and chrA2, were identified by alignment, annotation and phylogenetic tree analyses, which encode a chromate reductase (NitR) and two chromate transporters (ChrA1 and ChrA2). Reverse transcription real-time polymerase chain reaction (RT-qPCR) analyses showed that the relative quantitative transcription of the three genes as the maximum reduction rate of Cr(VI) were significantly up-regulated with the increasing initial Cr(VI) concentrations. However, at the maximum cell growth points nitR was in a low transcription level, while the transcription of chrA1 and chrA2 were hold at a relatively high level and decreased with the increasing initial Cr(VI) concentrations. The ex-situ chromate reducing activity of NitR was revealed a V_max of 34.46 µmol/min/mg enzyme and K_m of 14.55 µmol/L, suggesting feasibility of the reaction with Cr(VI) as substrate. The multiple alignment demonstrates that NitR is potentially a nicotinamide adenine dinucleotide phosphate (NADPH) dependent flavin mononucleotide (FMN) reductase of Class I chromate reductases. Our results will prompt a large-scaled bioremediation on the contaminated soils and water by Pannonibacter phragmitetus BB, taking advantage of uncovering its molecular mechanisms of chromium biotransformation.

Screening of potential bioremediation enzymes from hot spring bacteria using conventional plate assays and liquid chromatography - Tandem mass spectrometry (Lc-Ms/Ms)

The search for an eco-friendly, non-toxic, economical and efficient means of cleaning water through bioremediation is not only more favourable but critical to maintaining water quality globally especially in water-scarce countries. Thermophilic bacteria including Bacillus species are an important source of novel enzymes for biotechnology applications. In this study, 56 bacterial isolates which were cultured from five hot springs in South Africa were identified predominantly as Bacillus sp. or Bacillus-related spp by 16S rDNA gene sequencing. These isolates were screened for potentially useful enzymes for water bioremediation. Using conventional agar plate assays, 56% (n = 43), 68% (n = 38) and 16% (n = 31) were positive for amylase, protease and bromothymol blue decolorisation respectively. In liquid starch culture, three amylase-positive isolates differentially degraded starch by 34% (isolate 20S) to 98% (isolate 9T). Phenol degradation revealed that five out of thirty reduced phenol up to 42% by colorimetric assay. A thermophilic strain of Anoxybacillus rupiensis 19S (optimal growth temperature of 50 °C), which degraded starch, protein and phenol, was selected for further analysis by tandem LC-MS/MS. This newer technique identified potential enzymes for water bioremediation relating to pollutants from the food industry (amylase, proteases), polyaromatic hydrocarbons and dye pollutants (catalase peroxidase, superoxide dismutase, azoreductase, quinone oxidoreductase), antibiotic residues (ribonucleases), solubilisation of phosphates (inorganic pyrophosphatase) and reduction of chromate and lead. In addition, potential enzymes for biomonitoring of environmental pollutants were also identified. Specifically, dehydrogenases were found to decrease as the level of inorganic heavy metals and petroleum increased in soil samples. This study concludes that bacteria found in South African hot springs are a potential source of novel enzymes with tandem LC-MS/MS revealing substantially more information compared with conventional assays, which can be used for various applications of water bioremediation.

Identification of the main mechanisms involved in the tolerance and bioremediation of Cr(VI) by Bacillus sp. SFC 500-1E

Chromium pollution is a problem that affects different areas worldwide and, therefore, must be solved. Bioremediation is a promising alternative to treat environmental contamination, but finding bacterial strains able to tolerate and remove different contaminants is a major challenge, since most co-polluted sites contain mixtures of organic and inorganic substances. In the present work, Bacillus sp. SFC 500-1E, isolated from the bacterial consortium SFC 500-1 native to tannery sediments, showed tolerance to various concentrations of different phenolic compounds and heavy metals, such as Cr(VI). This strain was able to efficiently remove Cr(VI), even in the presence of phenol. The detection of the chrA gene suggested that Cr(VI) extrusion could be a mechanism that allowed this strain to tolerate the heavy metal. However, reduction through cytosolic NADH-dependent chromate reductases may be the main mechanism involved in the remediation. The information provided in this study about the mechanisms through which Bacillus sp. SFC 500-1E removes Cr(VI) should be taken into account for the future application of this strain as a possible candidate to remediate contaminated environments.

Callitriche cophocarpa (water starwort) proteome under chromate stress: evidence for induction of a quinone reductase

Chromate-induced physiological stress in a water-submerged macrophyte Callitriche cophocarpa Sendtn. (water starwort) was tested at the proteomic level. The oxidative stress status of the plant treated with 1 mM Cr(VI) for 3 days revealed stimulation of peroxidases whereas catalase and superoxide dismutase activities were similar to the control levels. Employing two-dimensional electrophoresis, comparative proteomics enabled to detect five differentiating proteins subjected to identification with mass spectrometry followed by an NCBI database search. Cr(VI) incubation led to induction of light harvesting chlorophyll a/b binding protein with a concomitant decrease of accumulation of ribulose bisphosphate carboxylase (RuBisCO). The main finding was, however, the identification of an NAD(P)H-dependent dehydrogenase FQR1, detectable only in Cr(VI)-treated plants. The FQR1 flavoenzyme is known to be responsive to oxidative stress and to act as a detoxification protein by protecting the cells against oxidative damage. It exhibits the in vitro quinone reductase activity and is capable of catalyzing two-electron transfer from NAD(P)H to several substrates, presumably including Cr(VI). The enhanced accumulation of FQR1 was chromate-specific since other stressful conditions, such as salt, temperature, and oxidative stresses, all failed to induce the protein. Zymographic analysis of chromate-treated Callitriche shoots showed a novel enzymatic protein band whose activity was attributed to the newly identified enzyme. We suggest that Cr(VI) phytoremediation with C. cophocarpa can be promoted by chromate reductase activity produced by the induced quinone oxidoreductase which might take part in Cr(VI) → Cr(III) bioreduction process and thus enable the plant to cope with the chromate-generated oxidative stress.

Anti-HER2 scFv-Directed Extracellular Vesicle-Mediated mRNA-Based Gene Delivery Inhibits Growth of HER2-Positive Human Breast Tumor Xenografts by Prodrug Activation

This paper deals with specific targeting of the prodrug/enzyme regimen, CNOB/HChrR6, to treat a serious disease, namely HER2⁺ human breast cancer with minimal off-target toxicity. HChrR6 is an improved bacterial enzyme that converts CNOB into the cytotoxic drug MCHB. Extracellular vesicles (EV) were used for mRNA-based HchrR6 gene delivery: EVs may cause minimal immune rejection, and mRNA may be superior to DNA for gene delivery. To confine HChrR6 generation and CNOB activation to the cancer, the EVHB chimeric protein was constructed. It contains high-affinity anti-HER2 scFv antibody (ML39) and is capable of latching on to EV surface. Cells transfected with EVHB-encoding plasmid generated EVs displaying this protein ("directed EVs"). Transfection of a separate batch of cells with the new plasmid, XPort/HChrR6, generated EVs containing HChrR6 mRNA; incubation with pure EVHB enabled these to target the HER2 receptor, generating "EXO-DEPT" EVs. EXO-DEPT treatment specifically enabled HER2-overexpressing BT474 cells to convert CNOB into MCHB in actinomycin D-independent manner, showing successful and specific delivery of HChrR6 mRNA. EXO-DEPTs-but not undirected EVs-plus CNOB caused near-complete growth arrest of orthotopic BT474 xenografts in vivo, demonstrating for the first time EV-mediated delivery of functional exogenous mRNA to tumors. EXO-DEPTs may be generated from patients' own dendritic cells to evade immune rejection, and without plasmids and their potentially harmful genetic material, raising the prospect of clinical use of this regimen. This approach can be used to treat any disease overexpressing a specific marker. Mol Cancer Ther; 17(5); 1133-42. ©2018 AACR.

Proteomic and enzymatic response under Cr(VI) overload in yeast isolated from textile-dye industry effluent

Cyberlindnera jadinii M9 and Wickerhamomyces anomalus M10 isolated from textile-dye liquid effluents has shown capacity for chromium detoxification via Cr(VI) biological reduction. The aim of the study was to evaluate the effect of hexavalent chromium on synthesis of novel and/or specific proteins involved in chromium tolerance and reduction in response to chromium overload in two indigenous yeasts. A study was carried out following a proteomic approach with W. anomalus M10 and Cy. jadinii M9 strains. For this, proteins extracts belonging to total cell extracts, membranes and mitochondria were analyzed. When Cr(VI) was added to culture medium there was an over-synthesis of 39 proteins involved in different metabolic pathways. In both strains, chromium supplementation changed protein biosynthesis by upregulating proteins involved in stress response, methionine metabolism, energy production, protein degradation and novel oxide-reductase enzymes. Moreover, we observed that Cy. jadinii M9 and W. anomalus M10 displayed ability to activate superoxide dismutase, catalase and chromate reductase activity. Two enzymes from the total cell extracts, type II nitroreductase (Frm2) and flavoprotein wrbA (Ycp4), were identified as possibly responsible for inducing crude chromate-reductase activity in cytoplasm of W. anomalus M10 under chromium overload. In Cy.jadinii M9, mitochondrial Ferredoxine-NADP reductase (Yah1) and membrane FAD flavoprotein (Lpd1) were identified as probably involved in Cr(VI) reduction. To our knowledge, this is the first study proposing chromate reductase activity of these four enzymes in yeast and reporting a relationship between protein synthesis, enzymatic response and chromium biospeciation in Cy. jadinii and W. anomalus.

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.

Relationship of Biodiversity with Heavy Metal Tolerance and Sorption Capacity: A Meta-Analysis Approach

Microbial remediation of metals can alleviate the concerns of metal pollution in the environment. The microbial remediation, however, can be a complex process since microbial metal resistance and biodiversity can play a direct role in the bioremediation process. This study aims to understand the relationships among microbial metal resistance, biodiversity, and metal sorption capacity. Meta-analyses based on 735 literature data points of minimum inhibitory concentrations (MIC) of Plantae, Bacteria, and Fungi exposed to As, Cd, Cr Cu, Ni, Pb, and Zn showed that metal resistance depends on the microbial Kingdom and the type of heavy metal and that consortia are significantly more resistant to heavy metals than pure cultures. A similar meta-analysis comparing 517 MIC values from different bacterial genera (Bacillus, Cupriavidus, Klebsiella, Ochrobactrum, Paenibacillus, Pseudomonas, and Ralstonia) confirmed that metal tolerance depends on the type of genus. Another meta-analysis with 195 studies showed that the maximum sorption capacity is influenced by microbial Kingdoms, the type of biosorbent (whether consortia or pure cultures), and the type of metal. This study also suggests that bioremediation using microbial consortia is a valid option to reduce environmental metal contaminations.

Copper (II) binding of NAD(P)H- flavin oxidoreductase (NfoR) enhances its Cr (VI)-reducing ability

Microbes can reduce hexavalent chromium Cr (VI) to the less toxic and soluble trivalent Cr (III). Copper stimulates microbial reduction of Cr (VI) by the Bacillus, Ochrobactrum, and Gluconobacter species; however, the mechanism remains unclear. In our study, the rate of Cr (VI) reduction by Staphylococcus aureus LZ-01 was increased by 210 % when supplemented with 60 μM Cu (II). A putative NAD(P)H-flavin oxidoreductase gene (nfoR) was upregulated under Cr (VI) stress. NfoR-knockout mutant displayed impaired reduction of Cr (VI) and Cu (II)-enhanced Cr (VI) reduction by nfoR isogenic mutant was attenuated in the presence of Cu (II). In vitro tests showed an increased V_max value of 25.22 μM min⁻¹ mg⁻¹ NfoR in the presence of Cu (II). Together, these results indicate that NfoR is responsible for Cu (II) enhancement. Isothermal titration calorimetry (ITC) assays confirmed the interaction of NfoR with Cu (II) at the dissociation constant of 85.5 μM. Site-directed mutagenesis indicates that His100, His128, and Met165 residues may be important for Cu (II) binding, while Cys163 is necessary for the FMN binding of NfoR. These findings show that Cu (II)-enhanced NfoR belongs to a new branch of Cr (VI) reductases and profoundly influences Cr (VI) reduction.

Utilizing native fluorescence imaging, modeling and simulation to examine pharmacokinetics and therapeutic regimen of a novel anticancer prodrug

Background

Success of cancer prodrugs relying on a foreign gene requires specific delivery of the gene to the cancer, and improvements such as higher level gene transfer and expression. Attaining these objectives will be facilitated in preclinical studies using our newly discovered CNOB-GDEPT, consisting of the produrg: 6-chloro-9-nitro-5-oxo-5H-benzo-(a)-phenoxazine (CNOB) and its activating enzyme ChrR6, which generates the cytotoxic product 9-amino-6-chloro-5H-benzo[a]phenoxazine-5-one (MCHB). MCHB is fluorescent and can be noninvasively imaged in mice, and here we investigated whether MCHB fluorescence quantitatively reflects its concentration, as this would enhance its reporter value in further development of the CNOB-GDEPT therapeutic regimen. PK parameters were estimated and used to predict more effective CNOB administration schedules.

Methods

CNOB (3.3 mg/kg) was injected iv in mice implanted with humanized ChrR6 (HChrR6)-expressing 4T1 tumors. Fluorescence was imaged in live mice using IVIS Spectrum, and quantified by Living Image 3.2 software. MCHB and CNOB were quantified also by LC/MS/MS analysis. We used non-compartmental model to estimate PK parameters. Phoenix WinNonlin software was used for simulations to predict a more effective CNOB dosage regimen.

Results

CNOB administration significantly prolonged mice survival. MCHB fluorescence quantitatively reflected its exposure levels to the tumor and the plasma, as verified by LC/MS/MS analysis at various time points, including at a low concentration of 2 ng/g tumor. The LC/MS/MS data were used to estimate peak plasma concentrations, exposure (AUC_0-24), volume of distribution, clearance and half-life in plasma and the tumor. Simulations suggested that the CNOB-GDEPT can be a successful therapy without large increases in the prodrug dosage.

Conclusion

MCHB fluorescence quantifies this drug, and CNOB can be effective at relatively low doses. MCHB fluorescence characteristics will expedite further development of CNOB-GDEPT by, for example, facilitating specific gene delivery to the tumor, its prolonged expression, as well as other attributes necessary for successful gene-delivered enzyme prodrug therapy.

Electronic supplementary material

The online version of this article (doi:10.1186/s12885-016-2508-6) contains supplementary material, which is available to authorized users.

WrpA Is an Atypical Flavodoxin Family Protein under Regulatory Control of the Brucella abortus General Stress Response System

The general stress response (GSR) system of the intracellular pathogen Brucella abortus controls the transcription of approximately 100 genes in response to a range of stress cues. The core genetic regulatory components of the GSR are required for B. abortus survival under nonoptimal growth conditions in vitro and for maintenance of chronic infection in an in vivo mouse model. The functions of the majority of the genes in the GSR transcriptional regulon remain undefined. bab1_1070 is among the most highly regulated genes in this regulon: its transcription is activated 20- to 30-fold by the GSR system under oxidative conditions in vitro. We have solved crystal structures of Bab1_1070 and demonstrate that it forms a homotetrameric complex that resembles those of WrbA-type NADH:quinone oxidoreductases, which are members of the flavodoxin protein family. However, B. abortus WrbA-related protein (WrpA) does not bind flavin cofactors with a high affinity and does not function as an NADH:quinone oxidoreductase in vitro. Soaking crystals with flavin mononucleotide (FMN) revealed a likely low-affinity binding site adjacent to the canonical WrbA flavin binding site. Deletion of wrpA (ΔwrpA) does not compromise cell survival under acute oxidative stress in vitro or attenuate infection in cell-based or mouse models. However, a ΔwrpA strain does elicit increased splenomegaly in a mouse model, suggesting that WrpA modulates B. abortus interaction with its mammalian host. Despite high structural homology with canonical WrbA proteins, we propose that B. abortus WrpA represents a functionally distinct member of the diverse flavodoxin family.

IMPORTANCE

Brucella abortus is an etiological agent of brucellosis, which is among the most common zoonotic diseases worldwide. The general stress response (GSR) regulatory system of B. abortus controls the transcription of approximately 100 genes and is required for maintenance of chronic infection in a murine model; the majority of GSR-regulated genes remain uncharacterized. We present in vitro and in vivo functional and structural analyses of WrpA, whose expression is strongly induced by GSR under oxidative conditions. Though WrpA is structurally related to NADH:quinone oxidoreductases, it does not bind redox cofactors in solution, nor does it exhibit oxidoreductase activity in vitro. However, WrpA does affect spleen inflammation in a murine infection model. Our data provide evidence that WrpA forms a new functional class of WrbA/flavodoxin family proteins.

H2O2 production rate in Lactobacillus johnsonii is modulated via the interplay of a heterodimeric flavin oxidoreductase with a soluble 28 Kd PAS domain containing protein

Host and commensals crosstalk, mediated by reactive oxygen species (ROS), has triggered a growing scientific interest to understand the mechanisms governing such interaction. However, the majority of the scientific studies published do not evaluate the ROS production by commensals bacteria. In this context we recently showed that Lactobacillus johnsonii N6.2, a strain of probiotic value, modulates the activity of the critical enzymes 2,3-indoleamine dioxygenase via H₂O₂ production. L. johnsonii N6.2 by decreasing IDO activity, is able to modify the tryptophan/kynurenine ratio in the host blood with further systemic consequences. Understanding the mechanisms of H₂O₂ production is critical to predict the probiotic value of these strains and to optimize bacterial biomass production in industrial processes. We performed a transcriptome analysis to identify genes differentially expressed in L. johnsonii N6.2 cells collected from cultures grown under different aeration conditions. Herein we described the biochemical characteristics of a heterodimeric FMN reductase (FRedA/B) whose in vitro activity is controlled by LjPAS protein with a typical Per-Arnst-Sim (PAS) sensor domain. Interestingly, LjPAS is fused to the FMN reductase domains in other lactobacillaceae. In L. johnsonii, LjPAS is encoded by an independent gene which expression is repressed under anaerobic conditions (>3 fold). Purified LjPAS was able to slow down the FRedA/B initial activity rate when the holoenzyme precursors (FredA, FredB, and FMN) were mixed in vitro. Altogether the results obtained suggest that LjPAS module regulates the H₂O₂ production helping the cells to minimize oxidative stress in response to environmental conditions.

Interaction of Cr(VI) reduction and denitrification by strain Pseudomonas aeruginosa PCN-2 under aerobic conditions

Inhibition of efficient denitrification in presence of toxic heavy metals is one of the current problems encountered in municipal wastewater treatment plants. This paper presents how to remove hexavalent chromium (Cr(VI)) and nitrate simultaneously by the novel strain Pseudomonas aeruginosa PCN-2 under aerobic conditions. The capability of strain PCN-2 for Cr(VI) and nitrate reduction was confirmed by PCR analysis of gene ChrR, napA, nirS, cnorB, nosZ, while Cr(VI) reduction was proved via an initial single-electron transfer through Cr(V) detection using electron paramagnetic resonance. Experimental results demonstrated that Cr(VI) and nitrate reduction by strain PCN-2 was much faster at pH 8-9 and higher initial cell concentration. However, increasing Cr(VI) concentration would inhibit aerobic denitrification process and result in an significant delay of nitrate reduction or N2O accumulation, which was attributed to competition between three electron acceptors, i.e., Cr(VI), O2 and nitrate in the electron transport chain.

Cloning and sequence analysis demonstrate the chromate reduction ability of a novel chromate reductase gene from Serratia sp

The ChrT gene encodes a chromate reductase enzyme which catalyzes the reduction of Cr(VI). The chromate reductase is also known as flavin mononucleotide (FMN) reductase (FMN_red). The aim of the present study was to clone the full-length ChrT DNA from Serratia sp. CQMUS2 and analyze the deduced amino acid sequence and three-dimensional structure. The putative ChrT gene fragment of Serratia sp. CQMUS2 was isolated by polymerase chain reaction (PCR), according to the known FMN_red gene sequence from Serratia sp. AS13. The flanking sequences of the ChrT gene were obtained by high efficiency TAIL-PCR, while the full-length gene of ChrT was cloned in Escherichia coli for subsequent sequencing. The nucleotide sequence of ChrT was submitted onto GenBank under the accession number, KF211434. Sequence analysis of the gene and amino acids was conducted using the Basic Local Alignment Search Tool, and open reading frame (ORF) analysis was performed using ORF Finder software. The ChrT gene was found to be an ORF of 567 bp that encodes a 188-amino acid enzyme with a calculated molecular weight of 20.4 kDa. In addition, the ChrT protein was hypothesized to be an NADPH-dependent FMN_red and a member of the flavodoxin-2 superfamily. The amino acid sequence of ChrT showed high sequence similarity to the FMN reductase genes of Klebsiella pneumonia and Raoultella ornithinolytica, which belong to the flavodoxin-2 superfamily. Furthermore, ChrT was shown to have a 85.6% similarity to the three-dimensional structure of Escherichia coli ChrR, sharing four common enzyme active sites for chromate reduction. Therefore, ChrT gene cloning and protein structure determination demonstrated the ability of the gene for chromate reduction. The results of the present study provide a basis for further studies on ChrT gene expression and protein function.

Bacterial chromate reductase, a potential enzyme for bioremediation of hexavalent chromium: a review

Hexavalent chromium is mobile, highly toxic and considered as a priority environmental pollutant. Chromate reductases, found in chromium resistant bacteria are known to catalyse the reduction of Cr(VI) to Cr(III) and have recently received particular attention for their potential use in bioremediation process. Different chromate reductases such as ChrR, YieF, NemA and LpDH, have been identified from bacterial sources which are located either in soluble fractions (cytoplasm) or bound to the membrane of the bacterial cell. The reducing conditions under which these enzymes are functional can either be aerobic or anaerobic or sometimes both. Enzymatic reduction of Cr(VI) to Cr(III) involves transfer of electrons from electron donors like NAD(P)H to Cr(VI) and simultaneous generation of reactive oxygen species (ROS). Based on the steps involved in electron transfer to Cr(VI) and the subsequent amount of ROS generated, two reaction mechanisms, namely, Class I "tight" and Class II "semi tight" have been proposed. The present review discusses on the types of chromate reductases found in different bacteria, their mode of action and potential applications in bioremediation of hexavalent chromium both under free and immobilize conditions. Besides, techniques used in characterization of the Cr (VI) reduced products were also discussed.

Chromium

Chromium is ubiquitous in the environment as Cr(III) and Cr(VI) oxidation states, which interconvert under environmentally and biologically relevant conditions (although Cr(III) usually predominates). While Cr(VI) is an established human carcinogen and a major occupational and environmental hazard, Cr(III) has long been regarded as an essential human micronutrient, although recent literature has cast serious doubts on the validity of this postulate. Despite five decades of research, no functional Cr-containing enzymes or cofactors have been characterized conclusively, and several hypotheses on their possible structures have been refuted. Gastrointestinal absorption pathways for both Cr(III) and Cr(VI) are apparent and whole-blood speciation can involve Cr(VI) uptake and reduction by red blood cells, as well as Cr(III) binding to both proteins and low-molecular-mass ligands in the plasma. DNA-damaging effects of Cr(VI) and anti-diabetic activities of Cr(III) are likely to arise from common mechanistic pathways that involve reactive Cr(VI/V/IV) intermediates and kinetically inert Cr(III)-protein and Cr(III)-DNA adducts. Both Cr(III) and Cr(VI) are toxic to plants and microorganisms, particularly Cr(VI) due to its higher bioavailability and redox chemistry. Some bacteria reduce Cr(VI) to Cr(III) without the formation of toxic Cr(V) intermediates and these bacteria are being considered for use in the bioremediation of Cr(VI)-polluted environments.

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.

Escherichia coli response to uranyl exposure at low pH and associated protein regulations

Better understanding of uranyl toxicity in bacteria is necessary to optimize strains for bioremediation purposes or for using bacteria as biodetectors for bioavailable uranyl. In this study, after different steps of optimization, Escherichia colicells were exposed to uranyl at low pH to minimize uranyl precipitation and to increase its bioavailability. Bacteria were adapted to mid acidic pH before exposure to 50 or 80 µM uranyl acetate for two hours at pH≈3. To evaluate the impact of uranium, growth in these conditions were compared and the same rates of cells survival were observed in control and uranyl exposed cultures. Additionally, this impact was analyzedby two-dimensional differential gel electrophoresis proteomics to discover protein actors specifically present or accumulated in contact with uranium.Exposure to uranium resulted in differential accumulation of proteins associated with oxidative stress and in the accumulation of the NADH/quinone oxidoreductase WrbA. This FMN dependent protein performs obligate two-electron reduction of quinones, and may be involved in cells response to oxidative stress. Interestingly, this WrbA protein presents similarities with the chromate reductase from E. coli, which was shown to reduce uranyl in vitro.

H(2)O(2) production in species of the Lactobacillus acidophilus group: a central role for a novel NADH-dependent flavin reductase

Hydrogen peroxide production is a well-known trait of many bacterial species associated with the human body. In the presence of oxygen, the probiotic lactic acid bacterium Lactobacillus johnsonii NCC 533 excretes up to 1 mM H(2)O(2), inducing growth stagnation and cell death. Disruption of genes commonly assumed to be involved in H(2)O(2) production (e.g., pyruvate oxidase, NADH oxidase, and lactate oxidase) did not affect this. Here we describe the purification of a novel NADH-dependent flavin reductase encoded by two highly similar genes (LJ_0548 and LJ_0549) that are conserved in lactobacilli belonging to the Lactobacillus acidophilus group. The genes are predicted to encode two 20-kDa proteins containing flavin mononucleotide (FMN) reductase conserved domains. Reductase activity requires FMN, flavin adenine dinucleotide (FAD), or riboflavin and is specific for NADH and not NADPH. The Km for FMN is 30 ± 8 μM, in accordance with its proposed in vivo role in H(2)O(2) production. Deletion of the encoding genes in L. johnsonii led to a 40-fold reduction of hydrogen peroxide formation. H(2)O(2) production in this mutant could only be restored by in trans complementation of both genes. Our work identifies a novel, conserved NADH-dependent flavin reductase that is prominently involved in H(2)O(2) production in L. johnsonii.

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.

Structure determination and functional analysis of a chromate reductase from Gluconacetobacter hansenii

Environmental protection through biological mechanisms that aid in the reductive immobilization of toxic metals (e.g., chromate and uranyl) has been identified to involve specific NADH-dependent flavoproteins that promote cell viability. To understand the enzyme mechanisms responsible for metal reduction, the enzyme kinetics of a putative chromate reductase from Gluconacetobacter hansenii (Gh-ChrR) was measured and the crystal structure of the protein determined at 2.25 Å resolution. Gh-ChrR catalyzes the NADH-dependent reduction of chromate, ferricyanide, and uranyl anions under aerobic conditions. Kinetic measurements indicate that NADH acts as a substrate inhibitor; catalysis requires chromate binding prior to NADH association. The crystal structure of Gh-ChrR shows the protein is a homotetramer with one bound flavin mononucleotide (FMN) per subunit. A bound anion is visualized proximal to the FMN at the interface between adjacent subunits within a cationic pocket, which is positioned at an optimal distance for hydride transfer. Site-directed substitutions of residues proposed to involve in both NADH and metal anion binding (N85A or R101A) result in 90–95% reductions in enzyme efficiencies for NADH-dependent chromate reduction. In comparison site-directed substitution of a residue (S118A) participating in the coordination of FMN in the active site results in only modest (50%) reductions in catalytic efficiencies, consistent with the presence of a multitude of side chains that position the FMN in the active site. The proposed proximity relationships between metal anion binding site and enzyme cofactors is discussed in terms of rational design principles for the use of enzymes in chromate and uranyl bioremediation.