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

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 Periphery Design Allows Control of the New Nitrofurans Antimicrobial Selectivity

A series of 13 new 3-substituted 5-(5-nitro-2-furyl)-1,2,4-oxadiazoles was synthesized from different aminonitriles. All compounds were screened in the disc diffusion test at a 100 μg/mL concentration to determine the bacterial growth inhibition zone presence and diameter, and then the minimum inhibitory concentrations (MICs) were determined for the most active compounds by serial dilution. The compounds showed antibacterial activity against ESKAPE bacteria, predominantly suppressing the growth of 5 species out of the panel. Some compounds had similar or lower MICs against ESKAPE pathogens compared to ciprofloxacin, nitrofurantoin, and furazidin. In particular, 3-azetidin-3-yl-5-(5-nitro-2-furyl)-1,2,4-oxadiazole (2h) inhibited S. aureus at a concentration lower than all comparators. Compound 2e (5-(5-nitro-2-furyl)-3-[4-(pyrrolidin-3-yloxy)phenyl]-1,2,4-oxadiazole) was active against Gram-positive ESKAPE pathogens as well as M. tuberculosis. Differences in the molecular periphery led to high selectivity for the compounds. The induced-fit docking (IFD) modeling technique was applied to in silico research. Molecular docking results indicated the targeting of compounds against various nitrofuran-associated biological targets.

Sequence similarity network analysis of drug- and dye-modifying azoreductase enzymes found in the human gut microbiome

Drug metabolism by human gut microbes is often exemplified by azo bond reduction in the anticolitic prodrug sulfasalazine. Azoreductase activity is often found in incubations with cell cultures or ex vivo gut microbiome samples and contributes to the xenobiotic metabolism of drugs and food additives. Applying metagenomic studies to personalized medicine requires knowledge of the genes responsible for sulfasalazine and other drug metabolism, and candidate genes and proteins for drug modifications are understudied. A representative gut-abundant azoreductase from Anaerotignum lactatifermentan DSM 14214 efficiently reduces sulfasalazine and another drug, phenazopyridine, but could not reduce all azo-bonded drugs in this class. We used enzyme kinetics to characterize this enzyme for its NADH-dependent reduction of these drugs and food additives and performed computational docking to provide the groundwork for understanding substrate specificity in this family. We performed an analysis of the Flavodoxin-like fold InterPro family (IPR003680) by computing a sequence similarity network to classify distinct subgroups of the family and then performed chemically-guided functional profiling to identify proteins that are abundant in the NIH Human Microbiome Project dataset. This strategy aims to reduce the number of unique azoreductases needed to characterize one protein family in the diverse set of potential drug- and dye-modifying activities found in the human gut microbiome.

The colon targeting efficacies of mesalazine medications and their impacts on the gut microbiome

Successful treatment of ulcerative colitis (UC) is highly dependent on several parameters, including dosing regimen and the ability to deliver drugs to the disease site. In this study two strategies for delivering mesalazine (5-aminosalicylic acid, 5-ASA) to the colon were compared in an advanced in vitro model of the human gastrointestinal (GI) tract, the SHIME® system. Herein, a prodrug strategy employing bacteria-mediated drug release (sulfasalazine, Azulfidine®) was evaluated alongside a formulation strategy that utilised pH and bacteria-mediated release (5-ASA, Octasa® 1600 mg). SHIME® experiments were performed simulating both the GI physiology and colonic microbiota under healthy and inflammatory bowel disease (IBD) conditions, to study the impact of the disease state and ileal pH variability on colonic 5-ASA delivery. In addition, the effects of the products on the colonic microbiome were investigated by monitoring bacterial growth and metabolites. Results demonstrated that both the prodrug and formulation approaches resulted in a similar percentage of 5-ASA recovery under healthy conditions. On the contrary, during experiments simulating the GI physiology and microbiome of IBD patients (the target population) the formulation strategy resulted in a higher proportion of 5-ASA delivery to the colonic region as compared to the prodrug approach (P < 0.0001). Interestingly, the two products had distinct effects on the synthesis of key bacterial metabolites, such as lactate and short chain fatty acids, which varied according to disease state and ileal pH variability. Further, both 5-ASA and sulfasalazine significantly reduced the growth of the faecal microbiota sourced from six healthy humans. The findings support that the approach selected for colonic drug delivery could significantly influence the effectiveness of UC treatment, and highlight that drugs licensed for UC may differentially impact the growth and functioning of the colonic microbiota.

Molecular mechanisms of selenite reduction by Lactiplantibacillus plantarum BSe: An integrated genomic and transcriptomic analysis

The reduction of selenite [Se(Ⅳ)] by microorganisms is a green and efficient detoxification strategy. We found that Se(Ⅳ) inhibited exopolysaccharide and protein secretion by Lactiplantibacillus plantarum BSe and compromised cell integrity. In this study, L. plantarum BSe reduced Se(Ⅳ) by increasing related enzyme activity and electron transfer. Genomic analysis demonstrated that L. plantarum BSe should be able to reduce Se(Ⅳ). Further transcriptome analysis showed that L. plantarum BSe enhanced its tolerance to Se(Ⅳ) by upregulating the expression of surface proteins and transporters, thus reducing the extracellular Se(Ⅳ) concentration through related enzymatic reactions and siderophore-mediated pathways. Lactiplantibacillus plantarum BSe was able to regulate the expression of related genes involved in quorum sensing and a two-component system and then select appropriate strategies for Se(Ⅳ) transformation in response to varying environmental Se(Ⅳ) concentrations. In addition, azo reductase was linked to the reduction of Se(Ⅳ) for the first time. The present study established a multipath model for the reduction of Se(Ⅳ) by L. plantarum, providing new insights into the biological reduction of Se(Ⅳ) and the biogeochemical cycle of selenium.

Preparation, analysis and toxicity characterisation of the redox metabolites of the azo food dye tartrazine

Tartrazine (E102, FD&C Yellow 5) is a vibrant yellow azo dye added to many processed foods. The safety of this ubiquitous chemical has not been fully elucidated, and it has been linked to allergic reactions and ADHD in some individuals. In our study, bacterial species isolated from human stool decolourised tartrazine and, upon exposure to air, a purple compound formed. Tartrazine is known to undergo reduction in the gut to sulfanilic acid and 4-amino-3-carboxy-5-hydroxy-1-(4-sulfophenyl)pyrazole (SCAP). These metabolites and their derivatives are relevant to the toxicology of tartrazine. The toxicity of sulfanilic acid has been studied before, but the oxidative instability of SCAP has previously prevented full characterisation. We have verified the chemical identity of SCAP and confirmed that the purple-coloured oxidation derivative is 4-(3-carboxy-5-hydroxy-1-(4-sulfophenyl)-1H-pyrazol-4-yl)imino-5-oxo-1-(4-sulfophenyl)-4,5-dihydro-1H-pyrazole-3-carboxylic acid (purpurazoic acid, PPA), as proposed by Westöö in 1965. A yellow derivative of SCAP is proposed to be the hydrolysed oxidation product, 4,5-dioxo-1-(4-sulfophenyl)-4,5-dihydro-1H-pyrazole-3-carboxylic acid. SCAP and PPA are moderately toxic to human cells (IC50 89 and 78 μM against HEK-293, respectively), but had no apparent effect on Escherichia coli and Bacillus subtilis bacteria. These results prompt further analyses of the toxicology of tartrazine and its derivatives.

Investigating Bio-Inspired Degradation of Toxic Dyes Using Potential Multi-Enzyme Producing Extremophiles

Biological treatment methods overcome many of the drawbacks of physicochemical strategies and play a significant role in removing dye contamination for environmental sustainability. Numerous microorganisms have been investigated as promising dye-degrading candidates because of their high metabolic potential. However, few can be applied on a large scale because of the extremely harsh conditions in effluents polluted with multiple dyes, such as alkaline pH, high salinity/heavy metals/dye concentration, high temperature, and oxidative stress. Therefore, extremophilic microorganisms offer enormous opportunities for practical biodegradation processes as they are naturally adapted to multi-stress conditions due to the special structure of their cell wall, capsule, S-layer proteins, extracellular polymer substances (EPS), and siderophores structural and functional properties such as poly-enzymes produced. This review provides scientific information for a broader understanding of general dyes, their toxicity, and their harmful effects. The advantages and disadvantages of physicochemical methods are also highlighted and compared to those of microbial strategies. New techniques and methodologies used in recent studies are briefly summarized and discussed. In particular, this study addresses the key adaptation mechanisms, whole-cell, enzymatic degradation, and non-enzymatic pathways in aerobic, anaerobic, and combination conditions of extremophiles in dye degradation and decolorization. Furthermore, they have special metabolic pathways and protein frameworks that contribute significantly to the complete mineralization and decolorization of the dye when all functions are turned on. The high potential efficiency of microbial degradation by unculturable and multi-enzyme-producing extremophiles remains a question that needs to be answered in practical research.

Gut Microbiome-Wide Search for Bacterial Azoreductases Reveals Potentially Uncharacterized Azoreductases Encoded in the Human Gut Microbiome

The human gut is home to trillions of microorganisms that are responsible for the modification of many orally administered drugs, leading to a wide range of therapeutic outcomes. Prodrugs bearing an azo bond are designed to treat inflammatory bowel disease and colorectal cancer via microbial azo reduction, allowing for topical application of therapeutic moieties to the diseased tissue in the intestines. Despite the inextricable link between microbial azo reduction and the efficacy of azo prodrugs, the prevalence, abundance, and distribution of azoreductases have not been systematically examined across the gut microbiome. Here, we curated and clustered amino acid sequences of experimentally confirmed bacterial azoreductases and conducted a hidden Markov model-driven homolog search for these enzymes across 4644 genome sequences present in the representative Unified Human Gastrointestinal Genomes collection. We identified 1958 putative azo-reducing species, corroborating previous findings that azo reduction appears to be a ubiquitous function of the gut microbiome. However, through a systematic comparison of predicted and confirmed azo-reducing strains, we hypothesize the presence of uncharacterized azoreductases in 25 prominent strains of the human gut microbiome. Finally, we confirmed the azo reduction of Acid Orange 7 by multiple strains of Fusobacterium nucleatum, Bacteroides fragilis, and Clostridium clostridioforme Together, these results suggest the presence and activity of many uncharacterized azoreductases in the human gut microbiome and motivate future studies aimed at characterizing azoreductase genes in prominent members of the human gut microbiome. SIGNIFICANCE STATEMENT: This work systematically examined the prevalence, abundance, and distribution of azoreductases across the healthy and inflammatory bowel disease human gut microbiome, revealing potentially uncharacterized azoreductase genes. It also confirmed the reduction of Acid Orange 7 by strains of Fusobacterium nucleatum, Bacteroides fragilis, and Clostridium clostridioforme.

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.

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.

Complete genome sequence of Shewanella algae strain 2NE11, a decolorizing bacterium isolated from industrial effluent in Peru

Shewanella is a microbial group with high potential to be applied in textile effluents bioremediation due to its ability to use a wide variety of substrates as a final electron acceptor in respiration. The present research aimed to describe a new strain, Shewanella algae 2NE11, a decolorizing bacterium isolated from industrial effluent in Peru. S. algae 2NE11 showed an optimal growth under pH 6-9, temperature between 30-40 °C, and 0-4 % NaCl. It can tolerate high concentrations of NaCl until 10% and low temperatures as 4 °C. It decolorizes azo and anthraquinone dyes with a decolorization rate of 89-97%. We performed next-generation sequencing (Pacific Bioscience®) and achieved its complete genome sequence with a length of 5,030,813bp and a GC content of 52.98%. Genomic characterization revealed the presence of protein-coding genes related to decolorization like azoreductase, dyp-peroxidase, oxidoreductases, and the complete Mtr respiratory pathway. Likewise, we identified other properties such as the presence of metal resistant genes, and genes related to lactate and N-acetylglucosamine metabolism. These results highlight its potential to be applied in the bioremediation of textile effluents and guide future research on decolorization metabolic pathways.

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).

Biochemical characterization of a novel azo reductase named BVU5 from the bacterial flora DDMZ1: application for decolorization of azo dyes

One of the main mechanisms of bacterial decolorization and degradation of azo dyes is the use of biological enzymes to catalyze the breaking of azo bonds. This paper shows the expression and properties of a novel azo reductase (hybrid-cluster NAD(P)-dependent oxidoreductase, accession no. A0A1S1BVU5, named BVU5) from the bacterial flora DDMZ1 for degradation of azo dyes. The molecular weight of BVU5 is about 40.1 kDa, and it contains the prosthetic group flavin mononucleotide (FMN). It has the decolorization ability of 80.1 ± 2.5% within 3 min for a dye concentration of 20 mg L⁻¹, and 53.5 ± 1.8% even for a dye concentration of 200 mg L⁻¹ after 30 min. The optimum temperature of enzyme BVU5 is 30 °C and the optimum pH is 6. It is insensitive to salt concentration up to a salinity level of 10%. Furthermore, enzyme BVU5 has good tolerance toward some metal ions (2 mM) such as Mn²⁺, Ca²⁺, Mg²⁺ and Cu²⁺ and some organic solvents (20%) such as DMSO, methanol, isopentyl, ethylene glycol and N-hexane. However, the enzyme BVU5 has a low tolerance to high concentrations of denaturants. In particular, it is sensitive to the denaturants guanidine hydrochloride (GdmCl) (2 M) and urea (2 M). Analysis of the dye substrate specificity shows that enzyme BVU5 decolorizes most azo dyes, which is indicating that the enzyme is not strictly substrate specific, it is a functional enzyme for breaking the azo structure. Liquid chromatography/time-of-flight/mass spectrometry (LC-TOF-MS) revealed after the action of enzyme BVU5 that some intermediate products with relatively large molecular weights were produced; this illustrates a symmetric or an asymmetric rapid cleavage of the azo bonds by this enzyme. The potential degradation pathways and the enzyme-catalyzed degradation mechanism are deduced in the end of this paper. The results give insight into the potential of a rapid bio-pretreatment by enzyme BVU5 for processing azo dye wastewater.

The combination of BVU5 enzyme and coenzyme NADH can quickly degrade the azo dye RB5.

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.

Biocatalytic Reduction Reactions from a Chemist's Perspective

Reductions play a key role in organic synthesis, producing chiral products with new functionalities. Enzymes can catalyse such reactions with exquisite stereo-, regio- and chemoselectivity, leading the way to alternative shorter classical synthetic routes towards not only high-added-value compounds but also bulk chemicals. In this review we describe the synthetic state-of-the-art and potential of enzymes that catalyse reductions, ranging from carbonyl, enone and aromatic reductions to reductive aminations.

Bio-Decolorization of Synthetic Dyes by a Halophilic Bacterium Salinivibrio sp

Synthetic dyes, extensively used in various industries, act as pollutants in the aquatic environment, and pose a significant threat to living beings. In the present study, we assessed the potential of a halophilic bacterium Salinivibrio kushneri HTSP isolated from a saltpan for decolorization and bioremediation of synthetic dyes. The genomic assessment of this strain revealed the presence of genes encoding the enzymes involved in decolorization mechanisms including FMN-dependent NADH azoreductase Clade III, which cleave the azo bond of the dye, and the enzymes involved in deamination and isomerization of intermediate compounds. The dye decolorization assay was performed using this bacterial strain on three water-soluble dyes in different concentrations: Coomassie brilliant blue (CBB) G-250 (500–3,000 mg/L), Safranin, and Congo red (50–800 mg/L). Within 48 h, more than 80% of decolorization was observed in all tested concentrations of CBB G-250 and Congo red dyes. The rate of decolorization was the highest for Congo red followed by CBB G-250 and then Safranin. Using UV-Visible spectrometer and Fourier Transform Infrared (FTIR) analysis, peaks were observed in the colored and decolorized solutions. The results indicated a breakdown of dyes upon decolorization, as some peaks were shifted and lost for different vibrations of aromatic rings, aliphatic groups (–CH₂, –CH₃) and functional groups (–NH, –SO₃H, and –SO₃⁻) in decolorized solutions. This study has shown the potential of S. kushneri HTSP to decolorize dyes in higher concentrations at a faster pace than previously reported bacterial strains. Thus, we propose that our isolated strain can be utilized as a potential dye decolorizer and biodegradative for wastewater treatment.

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.

Gut microbiota in reductive drug metabolism

Gut bacteria are predominant microorganisms in the gut microbiota and have been recognized to mediate a variety of biotransformations of xenobiotic compounds in the gut. This review is focused on one of the gut bacterial xenobiotic metabolisms, reduction. Xenobiotics undergo different types of reductive metabolisms depending on chemically distinct groups: azo (-NN-), nitro (-NO₂), alkene (-CC-), ketone (-CO), N-oxide (-NO), and sulfoxide (-SO). In this review, we have provided select examples of drugs in six chemically distinct groups that are known or suspected to be subjected to the reduction by gut bacteria. For some drugs, responsible enzymes in specific gut bacteria have been identified and characterized, but for many drugs, only circumstantial evidence is available that indicates gut bacteria-mediated reductive metabolism. The physiological roles of even known gut bacterial enzymes have not been well defined.

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.

Mechanistic and Crystallographic Studies of Azoreductase AzoA from Bacillus wakoensis A01

The azoreductase AzoA from the alkali-tolerant Bacillus wakoensis A01 has been studied to reveal its structural and mechanistic details. For this, a recombinant expression system was developed which yields impressive amounts of fully active enzyme. The purified holo enzyme is remarkably solvent-tolerant and thermostable with an apparent melting temperature of 71 °C. The dimeric enzyme contains FMN as a prosthetic group and is strictly NADH dependent. While AzoA shows a negligible ability to use molecular oxygen as an electron acceptor, it is efficient in reducing various azo dyes and quinones. The kinetic and catalytic mechanism has been studied in detail using steady state kinetic analyses and stopped-flow studies. The data show that AzoA performs quinone and azo dye reductions via a two-electron transfer. Moreover, quinones were shown to be much better substrates (kcat values of 100-400 s-1 for several naphtoquinones) when compared with azo dyes. This suggests that the physiological role of AzoA and sequence-related microbial reductases is linked to quinone reductions and that they can better be annotated as quinone reductases. The structure of AzoA has been determined in complex with FMN at 1.8 Å resolution. AzoA displays unique features in the active site providing clues for explaining its catalytic and thermostability features. An uncommon loop, when compared with sequence-related reductases, forms an active site lid with Trp60 acting as an anchor. Several Trp60 mutants have been analyzed disclosing an important role of this residue in the stability of AzoA, while they retained activity. Structural details are discussed in relation to other azo and quinone reductases. This study provides new insights into the molecular functioning of AzoA and sequence-related reductases.

Reduction of Organoarsenical Herbicides and Antimicrobial Growth Promoters by the Legume Symbiont Sinorhizobium meliloti

Massive amounts of methyl [e.g., methylarsenate, MAs(V)] and aromatic arsenicals [e.g., roxarsone (4-hydroxy-3-nitrophenylarsonate, Rox(V)] have been utilized as herbicides for weed control and growth promotors for poultry and swine, respectively. The majority of these organoarsenicals degrade into more toxic inorganic species. Here, we demonstrate that the legume symbiont Sinorhizobium meliloti both reduces MAs(V) to MAs(III) and catalyzes sequential two-step reduction of nitro and arsenate groups in Rox(V), producing the highly toxic trivalent amino aromatic derivative 4-hydroxy-3-aminophenylarsenite (HAPA(III)). The existence of this process suggests that S. meliloti possesses the ability to transform pentavalent methyl and aromatic arsenicals into antibiotics to provide a competitive advantage over other microbes, which would be a critical process for the synthetic aromatic arsenicals to function as antimicrobial growth promoters. The activated trivalent aromatic arsenicals are degraded into less-toxic inorganic species by an MAs(III)-demethylating aerobe, suggesting that environmental aromatic arsenicals also undergo a multiple-step degradation pathway, in analogy with the previously reported demethylation pathway of the methylarsenate herbicide. We further show that an FAD-NADPH-dependent nitroreductase encoded by mdaB gene catalyzes nitroreduction of roxarsone both in vivo and in vitro. Our results demonstrate that environmental organoarsenicals trigger competition between members of microbial communities, resulting in gradual degradation of organoarsenicals and contamination by inorganic arsenic.