Biochemical characterization of an azoreductase from Rhodococcus opacus 1CP possessing methyl red degradation ability

Appraisal of malachite green biodegradation and detoxification potential of laccase from Trametes cubensis

The laccase from the newly isolated Trametes cubensis was investigated for its potential to degrade malachite green (MG) dye. Optimized solid-substrate fermentation enhanced laccase production by 8.8-fold, reaching an activity of 6577.0 ± 14.3 U/g. Proteomic characterization identified enzyme with 4 % sequence coverage, molecular weight of 43.1 kDa, and alignment with multicopper oxidases. Using one-factor-at-a-time optimization, MG decolorization was maximized at 89 % under optimal conditions: 20 U/mL enzyme dose, 0.1 mg/mL dye concentration, pH 5.0, and 2 h incubation at 50 °C. Crosslinking the laccase onto chitosan beads resulted in 82 % immobilization efficiency, with high recyclability and reusability, retaining over 52 % activity after 7 cycles and demonstrating similar (p < 0.05) dye degradation potential. MG degradation products exhibited significantly reduced phyto-, cyto-, and microbial toxicity. The degradation pathway was elucidated using gas chromatography-mass spectrometry analysis. Thus, both free and immobilized laccase from T. cubensis offer sustainable tool for effective MG degradation with reduced toxicity.

Breaking the Myth of Enzymatic Azoreduction

Flavin-dependent azoreductases have been applied to a wide range of tasks from decolorizing numerous azo dyes to releasing azo-conjugated prodrugs. A general narrative reiterated in much of the literature suggests that this enzyme promotes sequential reduction of both the azo-containing substrate and its corresponding hydrazo product to release the aryl amine components while consuming two equivalents of NAD(P)H. Indeed, such aryl amines can be formed by incubation of certain azo compounds with azoreductases, but the nature of the substrates capable of this apparent azo bond lysis remained unknown. We have now prepared a set of azobenzene derivatives and characterized their turnover and products after treatment with azoreductase from Escherichia coli to discover the structural basis regulating aryl amine formation. Without resonance donation by aryl substituents, reduction ceases at the hydrazo product. This indicates that azoreductases do not act on the hydrazo bond. Instead, aryl amine formation depends on a spontaneous hydrazo bond lysis that is promoted by resonance stabilization and subsequent reduction of the quinone-like intermediate by azoreductase. Experimental and computational approaches confirm the substituent dependence of this process. With knowledge of this requirement, full release of aryl amines from azo-conjugates can now be designed and applied with confidence.

Characterization and rational engineering of an alkaline-tolerant azoreductase derived from Roseibium sp. H3510 for enhanced decolorization of azo dyes

rAzoR2326, an azoreductase derived from Roseibium sp. H3510, functions as an FMN-dependent homodimer utilizing NADH as cofactor. It demonstrated maximum activity at 45 °C and retained moderate activity above 50 °C, exhibiting stability from pH 7-10. Evolution and structure guided rational design of wild-type rAzoR2326 (WT) efficiently yielded 6 single-point mutants with improved thermostability and activity from a 22-variant library. Further combinatorial mutation led to mutant M20 with substantially enhanced thermostability (15-fold longer half-life at 50 °C) and activity (3.24-fold higher kcat/Km). M20 exhibited superior catalytic properties for decolorizing Allura Red compared to WT. Specifically, its decolorization capacity at pH 10.0 was 4.26-fold higher than WT. Additionally, M20 demonstrated remarkable thermostability, retaining 76.83 % decolorization activity for Allura Red after 120 min at 50 °C, whereas WT nearly lost all catalytic activity under the same conditions. Molecular dynamics simulations revealed the structural changes in M20, such as improved hydrogen bonding and a new C-H···π interaction, led to a more compact and rigid enzyme structure. This resulted in a more stable FMN-binding pocket and substrate tunnel, thereby improving the catalytic stability and activity of M20. Given its enhanced dye decolorization ability and alkaline tolerance, M20 shows promise as a biocatalyst for treating azo dye effluents.

Selective pressure leads to an improved synthetic consortium fit for dye degradation

Microorganisms have great potential for bioremediation as they have powerful enzymes and machineries that can transform xenobiotics. The use of a microbial consortium provides more advantages in application point of view than pure cultures due to cross-feeding, adaptations, functional redundancies, and positive interactions among the organisms. In this study, we screened about 107 isolates for their ability to degrade dyes in aerobic conditions and without additional carbon source. From our screening results, we finally limited our synthetic consortium to Gordonia and Rhodococcus isolates. The synthetic consortium was trained and optimized for azo dye degradation using sequential treatment of small aromatic compounds such as phenols that act as selective pressure agents. After four rounds of optimization with different aims for each round, the consortium was able to decolorize and degrade various dyes after 48 h (80%-100% for brilliant black bn, methyl orange, and chromotrop 2b; 50-70% for orange II and reactive orange 16; 15-30% for chlorazol black e, reactive red 120, and allura red ac). Through rational approaches, we can show that treatment with phenolic compounds at micromolar dosages can significantly improve the degradation of bulky dyes and increase its substrate scope. Moreover, our selective pressure approach led to the production of various dye-degrading enzymes as azoreductase, laccase-like, and peroxidase-like activities were detected from the phenol-treated consortium. Evidence of degradation was also shown as metabolites arising from the degradation of methyl red and brilliant black bn were detected using HPLC and LC-MS analysis. Therefore, this study establishes the importance of rational and systematic screening and optimization of a consortium. Not only can this approach be applied to dye degradation, but this study also offers insights into how we can fully maximize microbial consortium activity for other applications, especially in biodegradation and biotransformation.

Molecular characterization of azoreductase and its potential for the decolorization of Remazol Red R and Acid Blue 29

Azoreductase is a reductive enzyme that efficiently biotransformed textile azo dyes. This study demonstrated the heterologous overexpression of the azoreductase gene in Escherichia coli for the effective degradation of Remazol Red-R and Acid-Blue 29 dyes. The AzK gene of Klebsiella pneumoniae encoding a ≈22 kDa azoreductase enzyme was cloned into the pET21+C expression vector. The inoculum size of 1.5%, IPTG concentration of 0.5 mM, and incubation time of 6 h were optimized by response surface methodology a statistical tool. The crude extract showed 76% and 74%, while the purified enzyme achieved 94% and 93% decolorization of RRR and AB-29, respectively in 0.3 h. The reaction kinetics showed that RRR had a Km and Vmax value of 0.058 mM and 1416 U mg-1, respectively at an NADH concentration of 10 mM. HPLC and GC-MS analyses showed that RRR was effectively bio-transformed by azoreductase to 2-[3-(hydroxy-amino) benzene-1-sulfonyl and AB-29 to aniline and 3-nitrosoaniline. This study explored the potential of recombinant azoreductase isolated from K. pneumoniae in the degradation of toxic textile azo dyes into less toxic metabolites.

Cell-Free Protein Synthesis for the Screening of Novel Azoreductases and Their Preferred Electron Donor

Azoreductases are potent biocatalysts for the cleavage of azo bonds. Various gene sequences coding for potential azoreductases are available in databases, but many of their gene products are still uncharacterized. To avoid the laborious heterologous expression in a host organism, we developed a screening approach involving cell-free protein synthesis (CFPS) combined with a colorimetric activity assay, which allows the parallel screening of putative azoreductases in a short time. First, we evaluated different CFPS systems and optimized the synthesis conditions of a model azoreductase. With the findings obtained, 10 azoreductases, half of them undescribed so far, were screened for their ability to degrade the azo dye methyl red. All novel enzymes catalyzed the degradation of methyl red and can therefore be referred to as azoreductases. In addition, all enzymes degraded the more complex and bulkier azo dye Brilliant Black and four of them also showed the ability to reduce p-benzoquinone. NADH was the preferred electron donor for the most enzymes, although the synthetic nicotinamide co-substrate analogue 1-benzyl-1,4-dihydronicotinamide (BNAH) was also accepted by all active azoreductases. This screening approach allows accelerated identification of potential biocatalysts for various applications.

Human Gut Microbiota and Drug Metabolism

The efficacy of drugs widely varies in individuals, and the gut microbiota plays an important role in this variability. The commensal microbiota living in the human gut encodes several enzymes that chemically modify systemic and orally administered drugs, and such modifications can lead to activation, inactivation, toxification, altered stability, poor bioavailability, and rapid excretion. Our knowledge of the role of the human gut microbiome in therapeutic outcomes continues to evolve. Recent studies suggest the existence of complex interactions between microbial functions and therapeutic drugs across the human body. Therapeutic drugs or xenobiotics can influence the composition of the gut microbiome and the microbial encoded functions. Both these deviations can alter the chemical transformations of the drugs and hence treatment outcomes. In this review, we provide an overview of (i) the genetic ecology of microbially encoded functions linked with xenobiotic degradation; (ii) the effect of drugs on the composition and function of the gut microbiome; and (iii) the importance of the gut microbiota in drug metabolism.

Degradation and detoxification of reactive yellow dyes by Scedosporium apiospermum: a mycoremedial approach

Textile industrial effluents have long enunciated the essentiality of ascertaining an efficient wastewater treatment for the removal of azo dyes given their potential disturbances on the ecosystem. Our study investigated the efficiency of the strain SKF2 among 14 other isolates, molecularly identified to be Scedosporium apiospermum, isolated by our research group from the textile effluent sludge in the degradation of two azo dyes, Reactive Yellow 145 and Remazol Yellow RR. Kinetic profiling of the degradation process revealed the decolourisation efficiency to be 94.8 and 86.9% for RY 145 and RYRR, respectively, during the declining growth phase. Laccase and polyphenol oxidase (RY 145-2.37 and RYRR-2.30 U/mL; RY 145-3.26 and RYRR-2.89 U/mL, respectively) were found to influence the biodegradation process in both the dyes than the other examined fungal degradative enzymes. The metabolic pathway predicted with the aid of GC-MS analysis identified the degraded metabolites to be smaller molecular weight non-toxic products. Assessment of toxicity via brine shrimp lethality assay (RY 145-23.3% and RYRR-16.7%, respectively) and seed germination assay (RY 145-96.7% and RYRR-83.3%) further solidified the detoxified status of both the dyes after biodegradation. The experimental data thus substantiated the expediency of S. apiospermum SKF2 in the degradation of textile azo dyes and its further employment in the bioremediation of textile wastewaters for agricultural applications and ecological recycling.

Microbial Degradation of Azo Dyes: Approaches and Prospects for a Hazard-Free Conversion by Microorganisms

Azo dyes have become a staple in various industries, as colors play an important role in consumer choices. However, these dyes pose various health and environmental risks. Although different wastewater treatments are available, the search for more eco-friendly options persists. Bioremediation utilizing microorganisms has been of great interest to researchers and industries, as the transition toward greener solutions has become more in demand through the years. This review tackles the health and environmental repercussions of azo dyes and its metabolites, available biological approaches to eliminate such dyes from the environment with a focus on the use of different microorganisms, enzymes that are involved in the degradation of azo dyes, and recent trends that could be applied for the treatment of azo dyes.

An Integrative Approach to Study Bacterial Enzymatic Degradation of Toxic Dyes

Synthetic dyes pose a large threat to the environment and consequently to human health. Various dyes are used in textile, cosmetics, and pharmaceutical industries, and are released into the environment without any treatment, thus adversely affecting both the environment and neighboring human populations. Several existing physical and chemical methods for dye degradation are effective but have many drawbacks. Biological methods over the years have gained importance in the decolorization and degradation of dye and have also overcome the disadvantages of physiochemical methods. Furthermore, biological methods are eco-friendly and lead to complete decolorization. The mechanism of decolorization and degradation by several bacterial enzymes are discussed in detail. For the identification of ecologically sustainable strains and their application at the field level, we have focused on bioaugmentation aspects. Furthermore, in silico studies such as molecular docking of bacterial enzymes with dyes can give a new insight into biological studies and provide an easy way to understand the interaction at the molecular level. This review mainly focuses on an integrative approach and its importance for the effective treatment and decolorization of dyes.

Improving biocatalytic properties of an azoreductase via the N-terminal fusion of formate dehydrogenase

Azoreductases require NAD(P)H to reduce azo dyes but the costly price of NAD(P)H limits its application. Formate dehydrogenase (FDH) allows NAD(P)+ recycling and therefore, the fusion of these two biocatalysts seems promising. This study investigated the changes to the fusion protein involving azoreductase (AzoRo) of Rhodococcus opacus 1CP and FDH (FDHC23S and FDHC23SD195QY196H) of Candida boidinii in different positions with His-tag as the linker. The position affected enzyme activities as AzoRo activity decreased by 20-fold when it is in the N-terminus of the fusion protein. FDHC23S+AzoRo was the most active construct and was further characterized. Enzymatic activities of FDHC23S+AzoRo decreased compared to parental enzymes but showed improved substrate scope - accepting bulkier dyes. Moreover, pH has an influence on the stability and activity of the fusion protein because at pH 6 (pH that is suboptimal for FDH), the dye reduction decreased to more than 50% and this could be attributed to the impaired NADH supply for the AzoRo part.

Identification of molecular basis that underlie enzymatic specificity of AzoRo from Rhodococcus opacus 1CP: A potential NADH:quinone oxidoreductase

Azo dyes are important to various industries such as textile industries. However, these dyes are known to comprise toxic, mutagenic, and carcinogenic representatives. Several approaches have already been employed to mitigate the problem such as the use of enzymes. Azoreductases have been well-studied in its capability to reduce azo dyes. AzoRo from Rhodococcus opacus 1CP has been found to be accepting only methyl red as a substrate, surmising that the enzyme may have a narrow active site. To determine the active site configuration of AzoRo at atomic level and identify the key residues involved in substrate binding and enzyme specificity, we have determined the crystal structure of holo-AzoRo and employed a rational design approach to generate AzoRo variants. The results reported here show that AzoRo has a different configuration of the active site when compared with other bacterial NAD(P)H azoreductases, having other key residues playing a role in the substrate binding and restricting the enzyme activity towards different azo dyes. Moreover, it was observed that AzoRo has only about 50% coupling yield to methyl red and p-benzoquinone - giving rise to the possibility that NADH oxidation still occurs even during catalysis. Results also showed that AzoRo is more active and more efficient towards quinones (about four times higher than methyl red).

In vitro and in silico analysis of Brilliant Black degradation by Actinobacteria and a Paraburkholderia sp

The soil bacteria isolated in this study, including three strains of actinobacteria and one Paraburkholderia sp., showed decolorization activity of azo dyes in the resting cell assay and were shown to use methyl red as the sole carbon source to proliferate. Therefore, their ability to degrade, bioabsorb, or a combination of both was investigated using the substrate brilliant black. The strains DP-A9 and DP-L11, within 24 h of incubation, showed complete biodegradation of 173.54 mg/L brilliant black and the strains DP-D10 and DP-P12 showed partial decolorization of 83.3 mg/L and 36.4 mg/L, respectively, by both biosorption and biodegradation. In addition, the shotgun assembled genome of strains studied included a highly diverse set of genes encoding for candidate dye degrading enzymes, providing avenues to study azo dye metabolism in more detail.

Biodegradation of Reactive Red 198 by textile effluent adapted microbial strains

A sustainable technology to eliminate the persistent reactive dyes from the textile effluents discharged indiscriminately in the environment is highly desirous given the explosive growth of textile industries. The present study investigated the potential of two different bacterial strains, Bacillus cereus SKB12 and Enterobacter hormaechei SKB16 isolated from the dye house effluent sludge in the biotransformation of Reactive Red 198 (RR 198). Process variables such as temperature, pH, shaking conditions and contact time were optimized for the successful decolourization of RR 198. Maximum decolourization of 80% and 85% of RR 198 was achieved at pH 6 and 7, and 40 °C in microaerophilic conditions on treatment with B. cereus and E. hormaechei, respectively. High-Performance Liquid Chromatography (HPLC), and Gas Chromatography-Mass Spectrometry (GC-MS) analyses conducted further affirmed that the decolourization of RR 198 was rather due to biodegradation than biosorption through shift in wavenumbers, retention time variations and the appearance of lesser molecular weight peaks. Degradative pathway for RR 198 predicted based on the enzyme assay data and dye degraded metabolite peaks acquired through GC-MS analysis highlighted the significance of azoreductase and laccase in the degradation of RR 198 into smaller non-toxic compounds. In addition, toxicity assessment through zootoxicological and phytotoxicological experiments using brine shrimp and Vigna radiata validated the detoxified status of the metabolites thus proving the promising potentials of the bacterial strains in the remediation of azo dyes.

A dendritic polyamidoamine supramolecular system composed of pillar[5]arene and azobenzene for targeting drug-resistant colon cancer

Fusobacterium nucleatum caused drug-resistant around tumor sites often leads to the failure of chemotherapy during colorectal cancer (CRC) treatment. Multifunctional cationic quaternary ammonium materials have been widely used as broad-spectrum antibacterial agents in antibacterial and anticancer fields. Herein, we design a smart supramolecular quaternary ammonium nanoparticle, namely quaternary ammonium PAMAM-AZO@CP[5]A (Q-P-A@CP[5]A), consisting of azobenzene (AZO)-conjugated dendritic cationic quaternary ammonium polyamidoamine (PAMAM) as the core and carboxylatopillar[5]arene (CP[5]A)-based switch, for antibacterial and anti-CRC therapies. The quaternary ammonium-PAMAM-AZO (Q-P-A) core endows the supramolecular system with enhanced antibacterial and anticancer properties. -N⁺CH₃ groups on the surface of Q-P-A are accommodated in the CP[5]A cavity under normal conditions, which significantly improves the biocompatibility of Q-P-A@CP[5]A. Meanwhile, the CP[5]A host can be detached from -N⁺CH₃ groups under pathological conditions, achieving efficient antibacterial and antitumor therapies. Furthermore, azoreductase in the tumor site can break the -NN- bonds of AZO in Q-P-A@CP[5]A, leading to the morphology recovery of supramolecular nanoparticles and CRC therapy through inducing cell membrane rupture. Both in vitro and in vivo experiments demonstrate that Q-P-A@CP[5]A possesses good biocompatibility, excellent antibacterial effect, and CRC treatment capability with negligible side effects. This supramolecular quaternary ammonium system provides an effective treatment method to overcome chemotherapy-resistant cancer caused by bacteria.

Characterization of Two Hydrogen Peroxide Resistant Peroxidases from Rhodococcus opacus 1CP

The dye-decolorizing peroxidases (DyP) are a family of heme-dependent enzymes present on a broad spectrum of microorganisms. While the natural function of these enzymes is not fully understood, their capacity to degrade highly contaminant pigments such as azo dyes or anthraquinones make them excellent candidates for applications in bioremediation and organic synthesis. In this work, two novel DyP peroxidases from the organism Rhodococcus opacus 1CP (DypA and DypB) were cloned and expressed in Escherichia coli. The enzymes were purified and biochemically characterized. The activities of the two DyPs via 2,2′-azino-bis [3-ethylbenzthiazoline-6-sulphonic acid] (ABTS) assay and against Reactive Blue 5 were assessed and optimized. Results showed varying trends for DypA and DypB. Remarkably, these enzymes presented a particularly high tolerance towards H2O2, retaining its activities at about 10 mM H2O2 for DypA and about 4.9 mM H2O2 for DypB.

Developing a Fluorescent Hybrid Nanobiosensor Based on Quantum Dots and Azoreductase Enzyme forMethyl Red Monitoring

Background:

Azo dyes are the most widely used synthetic colorants in the textile, food, pharmaceutical, cosmetic, and other industries, accounting for nearly 70% of all dyestuffs consumed. Recently, much research attention has been paid to efficient monitoring of these hazardous chemicals and their related metabolites because of their potentially harmful effect on environmental issues. In contrast to the complex and expensive instrumental procedures, the detection system based on the QDs with the superior optochemical properties provides a new era in the pollution sensing and prevention.

Methods:

We have developed a QD-enzyme hybrid system to probe MR in aqueous solutions using a fluorescence quenching procedure.

Results:

The azoreductase enzyme catalyzed the reduction of azo group in MR, which can efficiently decrease the FRET between the QDs and MR molecules. The correlation between the QDs photoluminescence recovery and MR enzymatic decolorization at the neutral phosphate buffer permitted the creation of a fluorescence quenching-based sensor. The synthesized biosensor can be used for the accurate detection of MR in a linear calibration over MR concentrations of 5-84 μM, with the LOD of 0.5 μM in response time of three minutes.

Conclusion:

Our findings revealed that this fluorometric sensor has the potential to be successfully applied for monitoring a wide linear range of MR concentration with the relative standard deviation of 4% rather than the other method.

Performance of Burkholderia multivorans CCA53 for ethyl red degradation

The discharge of industrial dyes and their breakdown products are often environmentally harmful. Here, we describe a biodegradation method using Burkholderia multivorans CCA53, which exhibits a capacity to degrade azo dyes, particularly ethyl red. Under the optimized culture conditions, 100 μM ethyl red was degraded more than 99% after incubation for 8 h. Real-time PCR analysis of azoR1 and azoR2, encoding two azoreductases, revealed that transcription level of these genes is enhanced at early phase under the optimized conditions. For a more practical approach, hydrolysates were prepared from eucalyptus or Japanese cedar chips or rice straw, and rice straw hydrolysate was used as the best medium for ethyl red biodegradation. Under those conditions, ethyl red was also degraded with high efficiency (>91%). We have thus constructed a potentially economical method for the biodegradation of ethyl red.

Asymmetric Reduction of (R)-Carvone through a Thermostable and Organic-Solvent-Tolerant Ene-Reductase

Ene-reductases allow regio- and stereoselective reduction of activated C=C double bonds at the expense of nicotinamide adenine dinucleotide cofactors [NAD(P)H]. Biological NAD(P)H can be replaced by synthetic mimics to facilitate enzyme screening and process optimization. The ene-reductase FOYE-1, originating from an acidophilic iron oxidizer, has been described as a promising candidate and is now being explored for applied biocatalysis. Biological and synthetic nicotinamide cofactors were evaluated to fuel FOYE-1 to produce valuable compounds. A maximum activity of (319.7±3.2) U mg-1 with NADPH or of (206.7±3.4) U mg-1 with 1-benzyl-1,4-dihydronicotinamide (BNAH) for the reduction of N-methylmaleimide was observed at 30 °C. Notably, BNAH was found to be a promising reductant but exhibits poor solubility in water. Different organic solvents were therefore assayed: FOYE-1 showed excellent performance in most systems with up to 20 vol% solvent and at temperatures up to 40 °C. Purification and application strategies were evaluated on a small scale to optimize the process. Finally, a 200 mL biotransformation of 750 mg (R)-carvone afforded 495 mg of (2R,5R)-dihydrocarvone (>95 % ee), demonstrating the simplicity of handling and application of FOYE-1.

Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium

In the present study, we report the draft genome of soil isolate DP-K7 that has the potential to degrade methyl red. The 16S rRNA gene sequencing and whole-genome analysis exposed that the bacterial strain DP-K7 belongs to the species Kocuria indica. The genome annotation of the strain DP-K7 through the bioinformatics tool “Prokka” showed that the genome contains 3,010,594 bp with 69.01% GC content. The genome comprises 57 contigs including 2 rRNA genes, 47 tRNA genes, and 2754 CDS. The plate and broth assay showed that the strain DP-K7 has the potential to utilize methyl red as the sole carbon source for growth. Indeed, the RP-HPLC analysis proved that the strain DP-K7 is capable of degrading methyl red. The genome BLAST against a characterized azoreductase (AzoB—Xenophilus azovorans KF46F) revealed the presence of two azoreductase-like genes (azoKi-1 and azoKi-2). The phylogenetic analysis of the primary amino acid sequence of characterized azoreductases suggested that AzoKi-1 and AzoKi-2 belong to members of the clade IV azoreductase, which are flavin-independent. The multiple sequence alignment of AzoKi-1 and AzoKi-2 with flavin-independent azoreductases showed the presence of NAD(P)H binding like motif (GxxGxxG). In addition, other genes coding for dye degrading enzymes (SodC, SodA, KatA, KatE, and DyP2) were also found in the genome supporting that the strain K. indica DP-K7 is a potential azo dye degrader.

Decolourization and biodegradation of azo dye methyl red by Rhodococcus strain UCC 0016

In the present study, locally isolated Rhodococcus strains were attempted as biological tools for methyl red removal, a mutagenic azo dye posing threat to the environment if left untreated. Rhodococcus strain UCC 0016 demonstrated superior methyl red-decolourizing activity of 100% after 24 h at static condition in comparison to Rhodococcus strain UCC 0008 which recorded 65% decolourization after 72 h. Optimization of physicochemical parameters at 30°C, pH 7 and supplementing glucose as the carbon source resulted in improved methyl red-decolourizing activity at static condition and reduced the time taken to achieve complete decolourization by 80%. Higher concentration of methyl red (5 g/L) was able to be decolourized completely within 10 h by adopting the technology of immobilization. The encapsulated cells of Rhodococcus strain UCC 0016 demonstrated higher substrate affinity (K_m = 0.6995 g/L) and an accelerated rate of disappearance of methyl red (V_max = 0.3203 g/L/h) compared to the free cells. Furthermore, the gellan gum beads could be reused up to nine batches without substantial loss in the catalytic activity indicating the economic importance of this protocol. Analysis of methyl red degradation products revealed no germination inhibition on Triticum aestivum and Vigna radiata demonstrating complete toxicity removal of the parent dye after biological treatment. The occurrence of new and altered peaks (UV-Vis and FTIR) further supported the notion that the removal of methyl red by Rhodococcus strain UCC 0016 was indeed through biodegradation. Therefore, this strain has a huge potential as a candidate for efficient bioremediation of wastewater containing methyl red.

Folding and stability of recombinant azoreductase enzyme from Chromobacterium violaceum

Azoreductase from Chromobacterium violaceum was characterized biophysically using experimental and computational tools. The in-silico docking and cross-linking experiments using glutaraldehyde suggest dimeric nature of the enzyme. The enzyme structure was modelled and also studied using circular dichroism (CD) spectroscopy which suggests 40% α- helix, 30% β- sheet and 30% random coils. In the modelled structure of the azoreductase, the cofactor flavin mononucleotide (FMN) binding energy was -3.8 kJ/mol. The binding of FMN affects the azoreductase-cofactor complex stability. The stability-folding studies indicate that the cofactor, FMN is required for folding, stability and activity. Overall, the data provides interesting insight into stability and biophysical parameters of the azoreductase protein.

Biochemical characterization of a novel azoreductase from Streptomyces sp.: Application in eco-friendly decolorization of azo dye wastewater

Azo dyes are the most widely applied chemical dyes that have also raised great concerns for environmental contamination and human health issues. There has been a growing interest in discovering bioremediation methods to degrade azo dyes for environmental and economic purposes. Azoreductases are key enzymes evolved in nature capable of degrading azo dyes. The current work reports the identification, expression, and properties of a novel azoreductase (AzoRed2) from Streptomyces sp. S27 which shows an excellent stability against pH change and organic solvents. To overcome the requirements of coenzyme while degrading azo dyes, we introduced a coenzyme regeneration enzyme, Bacillus subtilis glucose 1-dehydrogenase (BsGDH), to construct a recycling system in living cells. The whole-cell biocatalyst containing AzoRed2 and BsGDH was used to degrade a representative azo dye methyl red. The degradation rate of methyl red was up to 99% in 120 min with high substrate concentration (250 μM) and no external coenzyme added. The degradation rate was still 98% in the third batch trial. To sum up, a novel azoreductase with good properties was found, which was applied to construct whole-cell biocatalyst. Both the enzymes and whole-cell biocatalysts are good candidates for the industrial wastewater treatment and environmental restoration.

Remarkable diversification of bacterial azoreductases: primary sequences, structures, substrates, physiological roles, and biotechnological applications

Azoreductases reductively cleave azo linkages by using NAD(P)H as an electron donor. The enzymes are widely found in bacteria and act on numerous azo dyes, which allow various unique applications. This review describes primary amino acid sequences, structures, substrates, physiological roles, and biotechnological applications of bacterial azoreductases to discuss their remarkable diversification. According to primary sequences, azoreductases were classified phylogenetically into four main clades. Most members of clades I-III are flavoproteins, whereas clade IV members include flavin-free azoreductases. Clades I and II prefer NADPH and NADH, respectively, as electron donors, whereas other members generally use both. Several enzymes formed no clades; moreover, some bacteria produce azoreductases with longer primary structures than those hitherto identified, which implies further diversification of bacterial azoreductases. The crystal structures commonly reveal the Rossmann folds; however, ternary structures are moderately varied with different quaternary conformation. Although physiological roles are obscure, several azoreductases have been shown to act on metabolites such as flavins, quinones, and metal ions more efficiently than on azo dyes. Considering that many homologs exclusively act on these metabolites, it is possible that azoreductases are actually side activities of versatile reductases that act on various substrates with different specificities. In parallel, this idea raises the possibility that homologous enzymes, even if these are already defined as other types of reductases, widely harbor azoreductase activities. Although azoreductases for which their genes have been identified are not abundant, it may be simple to identify azoreductases of biotechnological importance that have novel substrate specificities.

Catalytic Performance of a Class III Old Yellow Enzyme and Its Cysteine Variants

Class III old yellow enzymes (OYEs) contain a conserved cysteine in their active sites. To address the role of this cysteine in OYE-mediated asymmetric synthesis, we have studied the biocatalytic properties of OYERo2a from Rhodococcus opacus 1CP (WT) as well as its engineered variants C25A, C25S and C25G. OYERo2a in its redox resting state (oxidized form) is irreversibly inactivated by N-methylmaleimide. As anticipated, inactivation does not occur with the Cys variants. Steady-state kinetics with this maleimide substrate revealed that C25S and C25G doubled the turnover frequency (k cat) while showing increased K M values compared to WT, and that C25A performed more similar to WT. Applying the substrate 2-cyclohexen-1-one, the Cys variants were less active and less efficient than WT. OYERo2a and its Cys variants showed different activities with NADPH, the natural reductant. The variants did bind NADPH less well but k cat was significantly increased. The most efficient variant was C25G. Replacement of NADPH with the cost-effective synthetic cofactor 1-benzyl-1,4-dihydronicotinamide (BNAH) drastically changed the catalytic behavior. Again C25G was most active and showed a similar efficiency as WT. Biocatalysis experiments showed that OYERo2a, C25S, and C25G converted N-phenyl-2-methylmaleimide equally well (81-84%) with an enantiomeric excess (ee) of more than 99% for the R-product. With cyclic ketones, the highest conversion (89%) and ee (>99%) was observed for the reaction of WT with R-carvone. A remarkable poor conversion of cyclic ketones occurred with C25G. In summary, we established that the generation of a cysteine-free enzyme and cofactor optimization allows the development of more robust class III OYEs.

VpStyA1/VpStyA2B of Variovorax paradoxus EPS: An Aryl Alkyl Sulfoxidase Rather than a Styrene Epoxidizing Monooxygenase

Herein we describe the first representative of an E2-type two-component styrene monooxygenase of proteobacteria. It comprises a single epoxidase protein (VpStyA1) and a two domain protein (VpStyA2B) harboring an epoxidase (A2) and a FAD-reductase (B) domain. It was annotated as VpStyA1/VpStyA2B of Variovorax paradoxus EPS. VpStyA2B serves mainly as NADH:FAD-oxidoreductase. A Km of 33.6 ± 4.0 µM for FAD and a kcat of 22.3 ± 1.1 s-1 were determined and resulted in a catalytic efficiency (kcatKm-1) of 0.64 s-1 μM-1. To investigate its NADH:FAD-oxidoreductase function the linker between A2- and B-domain (AREAV) was mutated. One mutant (AAAAA) showed 18.7-fold higher affinity for FAD (kcatKm-1 of 5.21 s-1 μM-1) while keeping wildtype NADH-affinity and -oxidation activity. Both components, VpStyA2B and VpStyA1, showed monooxygenase activity on styrene of 0.14 U mg-1 and 0.46 U mg-1, as well as on benzyl methyl sulfide of 1.62 U mg-1 and 3.11 U mg-1, respectively. The high sulfoxidase activity was the reason to test several thioanisole-like substrates in biotransformations. VpStyA1 showed high substrate conversions (up to 95% in 2 h) and produced dominantly (S)-enantiomeric sulfoxides of all tested substrates. The AAAAA-mutant showed a 1.6-fold increased monooxygenase activity. In comparison, the GQWCSQY-mutant did neither show monooxygenase nor efficient FAD-reductase activity. Hence, the linker between the two domains of VpStyA2B has effects on the reductase as well as on the monooxygenase performance. Overall, this monooxygenase represents a promising candidate for biocatalyst development and studying natural fusion proteins.

Textile dye biodecolourization and ammonium removal over nitrite in aerobic granular sludge sequencing batch reactors

Biodecolourization of azo dye and removal of ammonium by aerobic granular sludge (AGS) was investigated under different growth conditions. AGS not previously exposed to azo dye was able to effectively decolourize azo dye under anaerobic and microaerophilic conditions. Azo dye, total organic carbon and ammoniacal nitrogen removal efficiencies of 89-100%, 79-95% and 92-100%, respectively, were achieved in the AGS reactor operated for 80days under microaerophilic conditions. Removal of carbon, nitrogen and phosphorus was not impacted by azo dye loading. Azo dye, organic carbon and ammonium were majorly removed in the anoxic period wherein bulk dissolved oxygen was ranged from 0.5 and <0.08mgL^-1. Removal of 60mgL^-1 NH₄⁺-N was associated only with smaller amounts of nitrite build-up (∼5mgL^-1 NO₂^--N) and negligible nitrate concentrations. Profiles of nitrogen compounds in individual sequencing batch reactor cycles supported the occurrence of ammonium removal over nitrite pathway. Bacterial community analysis showed enrichment of specific microorganisms capable of decolourizing azo dyes in the dye-decolourizing AGS. Dye decolourization and nutrient removal by AGS under microaerophilic conditions is a novel finding and can be further developed for treating textile wastewaters onsite or after dilution with sewage.

Changing the electron donor improves azoreductase dye degrading activity at neutral pH

The oxygen-insensitive azoreductase AzoRo originating from Rhodococcus opacus 1CP was found to be most active at low pH (ca. 4) and high temperature (ca. 50°C). AzoRo is not an efficient biocatalyst when used at low pH due to stability problems. To overcome this issue, we discovered that AzoRo accepts an alternative electron donor, 1-benzyl-1,4-dihydronicotinamide (BNAH), which allows fast turnover at neutral pH. In order to screen this nicotinamide coenzyme mimic as a source of electrons, AzoRo-catalysed reactions were run under neutral conditions, under which typically slow rates are observed with NADH. For the reduction of 1 azo bond by azoreductases 2mol nicotinamide coenzyme are needed. AzoRo displayed Methyl Red (MR) reduction activities with NADH and NADPH of 5.49±0.14Umg^-1 and 4.96±0.25Umg^-1, respectively, whereas with BNAH it displayed 17.01±0.74Umg^-1 (following BNAH oxidation) and 7.16±0.06Umg^-1 (following MR reduction). Binding of BNAH to AzoRo was determined with a K_m of 18.75±2.45μM (BNAH oxidation) and 12.45±0.47μM (MR reduction). In order to show applicability of this system an upscaled reaction was performed using 78.6μg of purified AzoRo to convert 2.96μmol of MR (total reaction volume: 40ml) within a 1h reaction.