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Long AR, Mortara EL, Mendoza BN, Fink EC, Sacco FX, Ciesla MJ, Stack TMM. Sequence similarity network analysis of drug- and dye-modifying azoreductase enzymes found in the human gut microbiome. Arch Biochem Biophys 2024; 757:110025. [PMID: 38740275 PMCID: PMC11295148 DOI: 10.1016/j.abb.2024.110025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/06/2024] [Accepted: 05/04/2024] [Indexed: 05/16/2024]
Abstract
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.
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Affiliation(s)
- Audrey R Long
- Department of Chemistry and Biochemistry, Providence College, 1 Cunningham Square, Providence, RI, 02918, United States
| | - Emma L Mortara
- Department of Chemistry and Biochemistry, Providence College, 1 Cunningham Square, Providence, RI, 02918, United States
| | - Brisa N Mendoza
- Department of Chemistry and Biochemistry, Providence College, 1 Cunningham Square, Providence, RI, 02918, United States
| | - Emma C Fink
- Department of Chemistry and Biochemistry, Providence College, 1 Cunningham Square, Providence, RI, 02918, United States
| | - Francis X Sacco
- Department of Chemistry and Biochemistry, Providence College, 1 Cunningham Square, Providence, RI, 02918, United States
| | - Matthew J Ciesla
- Department of Chemistry and Biochemistry, Providence College, 1 Cunningham Square, Providence, RI, 02918, United States
| | - Tyler M M Stack
- Department of Chemistry and Biochemistry, Providence College, 1 Cunningham Square, Providence, RI, 02918, United States.
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2
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Neettiyath A, Chung K, Liu W, Lee LP. Nanoplasmonic sensors for extracellular vesicles and bacterial membrane vesicles. NANO CONVERGENCE 2024; 11:23. [PMID: 38918255 PMCID: PMC11199476 DOI: 10.1186/s40580-024-00431-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/03/2024] [Indexed: 06/27/2024]
Abstract
Extracellular vesicles (EVs) are promising tools for the early diagnosis of diseases, and bacterial membrane vesicles (MVs) are especially important in health and environment monitoring. However, detecting EVs or bacterial MVs presents significant challenges for the clinical translation of EV-based diagnostics. In this Review, we provide a comprehensive discussion on the basics of nanoplasmonic sensing and emphasize recent developments in nanoplasmonics-based optical sensors to effectively identify EVs or bacterial MVs. We explore various nanoplasmonic sensors tailored for EV or bacterial MV detection, emphasizing the application of localized surface plasmon resonance through gold nanoparticles and their multimers. Additionally, we highlight advanced EV detection techniques based on surface plasmon polaritons using plasmonic thin film and nanopatterned structures. Furthermore, we evaluate the improved detection capability of surface-enhanced Raman spectroscopy in identifying and classifying these vesicles, aided by plasmonic nanostructures. Nanoplasmonic sensing techniques have remarkable precision and sensitivity, making them a potential tool for accurate EV detection in clinical applications, facilitating point-of-care molecular diagnostics. Finally, we summarize the challenges associated with nanoplasmonic EV or bacterial MV sensors and offer insights into potential future directions for this evolving field.
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Affiliation(s)
- Aparna Neettiyath
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Kyungwha Chung
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon 16419, Korea
| | - Wenpeng Liu
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Luke P Lee
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
- Harvard Medical School, Harvard University, Boston, MA 02115, USA.
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA.
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA 94720, USA.
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon 16419, Korea.
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea.
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3
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Pieper LM, Spanogiannopoulos P, Volk RF, Miller CJ, Wright AT, Turnbaugh PJ. The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli. mBio 2023; 14:e0157323. [PMID: 37642463 PMCID: PMC10653809 DOI: 10.1128/mbio.01573-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/06/2023] [Indexed: 08/31/2023] Open
Abstract
IMPORTANCE This work has broad relevance due to the ubiquity of dyes containing azo bonds in food and drugs. We report that azo dyes can be degraded by human gut bacteria through both enzymatic and nonenzymatic mechanisms, even from a single gut bacterial species. Furthermore, we revealed that environmental factors, oxygen, and L-Cysteine control the ability of E. coli to degrade azo dyes due to their impacts on bacterial transcription and metabolism. These results open up new opportunities to manipulate the azoreductase activity of the gut microbiome through the manipulation of host diet, suggest that azoreductase potential may be altered in patients suffering from gastrointestinal disease, and highlight the importance of studying bacterial enzymes for drug metabolism in their natural cellular and ecological context.
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Affiliation(s)
- Lindsey M. Pieper
- Department of Microbiology & Immunology, University of California, San Francisco, California, USA
| | - Peter Spanogiannopoulos
- Department of Microbiology & Immunology, University of California, San Francisco, California, USA
| | - Regan F. Volk
- Department of Microbiology & Immunology, University of California, San Francisco, California, USA
| | - Carson J. Miller
- Biological Sciences Group, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aaron T. Wright
- Biological Sciences Group, Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Biology, Baylor University, Waco, Texas, USA
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Peter J. Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, California, USA
- Chan Zuckerberg Biohub-San Francisco, San Francisco, California, USA
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4
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Simpson JB, Sekela JJ, Carry BS, Beaty V, Patel S, Redinbo MR. Diverse but desolate landscape of gut microbial azoreductases: A rationale for idiopathic IBD drug response. Gut Microbes 2023; 15:2203963. [PMID: 37122075 PMCID: PMC10132220 DOI: 10.1080/19490976.2023.2203963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/01/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
Prodrugs reliant on microbial activation are widely used but exhibit a range of efficacies that remain poorly understood. The anti-inflammatory compound 5-aminosalicylic acid (5-ASA), which is packaged in a variety of azo-linked prodrugs provided to most Ulcerative Colitis (UC) patients, shows confounding inter-individual variabilities in response. Such prodrugs must be activated by azo-bond reduction to form 5-ASA, a process that has been attributed to both enzymatic and non-enzymatic catalysis. Gut microbial azoreductases (AzoRs) are the first catalysts shown to activate azo-linked drugs and to metabolize toxic azo-chemicals. Here, we chart the scope of the structural and functional diversity of AzoRs in health and in patients with the inflammatory bowel diseases (IBDs) UC and Crohn's Disease (CD). Using structural metagenomics, we define the landscape of gut microbial AzoRs in 413 healthy donor and 1059 IBD patient fecal samples. Firmicutes encode a significantly higher number of unique AzoRs compared to other phyla. However, structural and biochemical analyses of distinct AzoRs from the human microbiome reveal significant differences between prevalent orthologs in the processing of toxic azo-dyes, and their generally poor activation of IBD prodrugs. Furthermore, while individuals with IBD show higher abundances of AzoR-encoding gut microbial taxa than healthy controls, the overall abundance of AzoR-encoding microbes is markedly low in both disease and health. Together, these results establish that gut microbial AzoRs are functionally diverse but sparse in both health and disease, factors that may contribute to non-optimal processing of azo-linked prodrugs and idiopathic IBD drug responses.
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Affiliation(s)
- Joshua B. Simpson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Josh J. Sekela
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Benjamin S. Carry
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Violet Beaty
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shakshi Patel
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Matthew. R. Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, Department of Microbiology and Immunology, and the Integrated Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Comparative Genomic Analysis of Antarctic Pseudomonas Isolates with 2,4,6-Trinitrotoluene Transformation Capabilities Reveals Their Unique Features for Xenobiotics Degradation. Genes (Basel) 2022; 13:genes13081354. [PMID: 36011267 PMCID: PMC9407559 DOI: 10.3390/genes13081354] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 12/04/2022] Open
Abstract
The nitroaromatic explosive 2,4,6-trinitrotoluene (TNT) is a highly toxic and persistent environmental pollutant. Since physicochemical methods for remediation are poorly effective, the use of microorganisms has gained interest as an alternative to restore TNT-contaminated sites. We previously demonstrated the high TNT-transforming capability of three novel Pseudomonas spp. isolated from Deception Island, Antarctica, which exceeded that of the well-characterized TNT-degrading bacterium Pseudomonas putida KT2440. In this study, a comparative genomic analysis was performed to search for the metabolic functions encoded in the genomes of these isolates that might explain their TNT-transforming phenotype, and also to look for differences with 21 other selected pseudomonads, including xenobiotics-degrading species. Comparative analysis of xenobiotic degradation pathways revealed that our isolates have the highest abundance of key enzymes related to the degradation of fluorobenzoate, TNT, and bisphenol A. Further comparisons considering only TNT-transforming pseudomonads revealed the presence of unique genes in these isolates that would likely participate directly in TNT-transformation, and others involved in the β-ketoadipate pathway for aromatic compound degradation. Lastly, the phylogenomic analysis suggested that these Antarctic isolates likely represent novel species of the genus Pseudomonas, which emphasizes their relevance as potential agents for the bioremediation of TNT and other xenobiotics.
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Pant A, Maiti TK, Mahajan D, Das B. Human Gut Microbiota and Drug Metabolism. MICROBIAL ECOLOGY 2022:1-15. [PMID: 35869999 PMCID: PMC9308113 DOI: 10.1007/s00248-022-02081-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 07/18/2022] [Indexed: 05/31/2023]
Abstract
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.
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Affiliation(s)
- Archana Pant
- Molecular Genetics Lab, National Institute of Immunology, New Delhi, Delhi-110067, India
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-121001, India
- Molecular Genetics Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, PO box, Gurgaon Expressway, #04 Faridabad-121001, Haryana, India
| | - Tushar K Maiti
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad-121001, India
| | - Dinesh Mahajan
- Chemistry and Pharmacology Lab, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Bhabatosh Das
- Molecular Genetics Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, PO box, Gurgaon Expressway, #04 Faridabad-121001, Haryana, India.
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Rolf J, Ngo ACR, Tischler D, Lütz S, Rosenthal K. Cell-free protein synthesis for the screening of novel azoreductases and their preferred electron donor. Chembiochem 2022; 23:e202200121. [PMID: 35593146 PMCID: PMC9401864 DOI: 10.1002/cbic.202200121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/19/2022] [Indexed: 11/26/2022]
Abstract
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.
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Affiliation(s)
- Jascha Rolf
- TU Dortmund University: Technische Universitat Dortmund, Biochemical & Chemical Engineering, Emil-Figge-Str. 66, 44227, Dortmund, GERMANY
| | - Anna Christina Reyes Ngo
- Ruhr-Universität Bochum: Ruhr-Universitat Bochum, Microbial Biotechnology, Faculty of Biology and Biotechnology, GERMANY
| | - Dirk Tischler
- Ruhr-Universität Bochum: Ruhr-Universitat Bochum, Microbial Biotechnology, Faculty of Biology and Biotechnology, GERMANY
| | - Stephan Lütz
- TU Dortmund University: Technische Universitat Dortmund, Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, GERMANY
| | - Katrin Rosenthal
- TU Dortmund university, Bioprocessengineering, Emil-Figge-Str. 66, 44227, Dortmund, GERMANY
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8
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Ngo ACR, Qi J, Juric C, Bento I, Tischler D. Identification of molecular basis that underlie enzymatic specificity of AzoRo from Rhodococcus opacus 1CP: A potential NADH:quinone oxidoreductase. Arch Biochem Biophys 2022; 717:109123. [PMID: 35051387 DOI: 10.1016/j.abb.2022.109123] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/22/2021] [Accepted: 01/15/2022] [Indexed: 12/15/2022]
Abstract
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).
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Affiliation(s)
- Anna Christina R Ngo
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Jingxian Qi
- Environmental Microbiology, Faculty of Chemistry and Physics, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Cindy Juric
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Isabel Bento
- European Molecular Biology Laboratory, EMBL c/o DESY, Building 25A, Notkestr. 85, 22607, Hamburg, Germany
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
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Patel JS, Norambuena J, Al-Tameemi H, Ahn YM, Perryman AL, Wang X, Daher SS, Occi J, Russo R, Park S, Zimmerman M, Ho HP, Perlin DS, Dartois V, Ekins S, Kumar P, Connell N, Boyd JM, Freundlich JS. Bayesian Modeling and Intrabacterial Drug Metabolism Applied to Drug-Resistant Staphylococcus aureus. ACS Infect Dis 2021; 7:2508-2521. [PMID: 34342426 DOI: 10.1021/acsinfecdis.1c00265] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the application of Bayesian modeling to identify chemical tools and/or drug discovery entities pertinent to drug-resistant Staphylococcus aureus infections. The quinoline JSF-3151 was predicted by modeling and then empirically demonstrated to be active against in vitro cultured clinical methicillin- and vancomycin-resistant strains while also exhibiting efficacy in a mouse peritonitis model of methicillin-resistant S. aureus infection. We highlight the utility of an intrabacterial drug metabolism (IBDM) approach to probe the mechanism by which JSF-3151 is transformed within the bacteria. We also identify and then validate two mechanisms of resistance in S. aureus: one mechanism involves increased expression of a lipocalin protein, and the other arises from the loss of function of an azoreductase. The computational and experimental approaches, discovery of an antibacterial agent, and elucidated resistance mechanisms collectively hold promise to advance our understanding of therapeutic regimens for drug-resistant S. aureus.
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Affiliation(s)
- Jimmy S. Patel
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
| | - Javiera Norambuena
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Hassan Al-Tameemi
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Yong-Mo Ahn
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
| | - Alexander L. Perryman
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
| | - Xin Wang
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
| | - Samer S. Daher
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
| | - James Occi
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Riccardo Russo
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Steven Park
- Public Health Research Institute, Rutgers University − New Jersey Medical School, 225 Warren St, Newark, New Jersey 07103, United States
| | - Matthew Zimmerman
- Public Health Research Institute, Rutgers University − New Jersey Medical School, 225 Warren St, Newark, New Jersey 07103, United States
| | - Hsin-Pin Ho
- Public Health Research Institute, Rutgers University − New Jersey Medical School, 225 Warren St, Newark, New Jersey 07103, United States
| | - David S. Perlin
- Public Health Research Institute, Rutgers University − New Jersey Medical School, 225 Warren St, Newark, New Jersey 07103, United States
| | - Véronique Dartois
- Public Health Research Institute, Rutgers University − New Jersey Medical School, 225 Warren St, Newark, New Jersey 07103, United States
| | - Sean Ekins
- Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay-Varina, North Carolina 27526, United States
| | - Pradeep Kumar
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Nancy Connell
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Jeffrey M. Boyd
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Joel S. Freundlich
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University − New Jersey Medical School, 185 South Orange Ave, Newark, New Jersey 07103, United States
- Department of Medicine, Center for Emerging and Re-emerging Pathogens, Rutgers University − New Jersey Medical School, Newark, New Jersey 07103, United States
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10
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Cerón-Carrasco JP, Jacquemin D. Using Theory To Extend the Scope of Azobenzene Drugs in Chemotherapy: Novel Combinations for a Specific Delivery. ChemMedChem 2021; 16:1764-1774. [PMID: 33619857 DOI: 10.1002/cmdc.202100046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/18/2021] [Indexed: 12/12/2022]
Abstract
Gut microorganisms metabolize azobenzene compounds (Ph1 -N=N-Ph2 ) into free aniline products (Ph1 -NH2 +H2 N-Ph2 ), a process that has been largely investigated to reduce dyes residues in the textile industry. However, the action of bacterial core enzymes such as azoreductases (AzoR) might also help to deliver prodrugs that become active when they reach the colonic region, a mechanism with potential applications for the treatment of inflammatory bowel disease (IBD) and colorectal cancer. So far, three azo-bonded prodrugs of 5-aminosalicylic acid (5-ASA), for example, sulfasalazine, olsalazine and balsalazide, have been used for colon-targeted delivery. The present contribution describes the first rational design of a novel azobenzene prodrug thanks to a computational approach, with a focus on linking 5-ASA to another approved anti-inflammatory drug. The resulting prodrugs were assessed for their degradation upon AzoR action. Replacing the original carriers by irsogladine is found to improve action.
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Affiliation(s)
- José P Cerón-Carrasco
- Reconocimiento y Encapsulación Molecular, Universidad Católica San Antonio de Murcia (UCAM) Campus los Jerónimos, 30107, Murcia, Spain
| | - Denis Jacquemin
- CEISAM UMR CNRS 6230, Université de Nantes, 44000, Nantes, France
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11
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Dixit S, Garg S. Enzymatic degradation of sulphonated azo dye using purified azoreductase from facultative Klebsiella pneumoniae. Folia Microbiol (Praha) 2020; 66:79-85. [PMID: 32946071 DOI: 10.1007/s12223-020-00824-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/15/2020] [Indexed: 11/29/2022]
Abstract
Heterologously expressed and purified azoreductase enzyme from facultative Klebsiella pneumoniae was used to degrade sulphonated azo dye. Methyl orange (MO) was used as the model dye to study the azo dye decolorization potential of the purified enzyme at different conditions. The enzyme had maximum activity at 40 °C and pH 8.0. The enzyme was observed to be thermo-stable as some enzyme activity was retained even at 80 °C. The apparent kinetic parameters, i.e., appKm and appVmax, for azoreductase using MO as a substrate were found to be 17.18 μM and 0.08/min, respectively. The purified enzyme was able to decolorize approximately 83% of MO (20 μM) within 10 min in the presence of NADH. Thus, efficient decolorization of MO was observed by the purified enzyme. The recombinant enzyme was purified approximately 18-fold with 46% yield at the end of four steps of the purification process. Enzyme was present in a tetrameric structure as confirmed by the volume at which protein was eluted in gel filtration chromatography, and the monomeric molecular mass of enzyme was found to be 23 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The dye degradation efficiency of azoreductase cloned from Klebsiella pneumoniae and purified from recombinant Escherichia coli was observed to be much higher as compared with the efficiencies of the reported azoreductases from other bacterial strains. In the present study, we report the purification and characterization of the azoreductase cloned from Klebsiella pneumoniae and expressed in Escherichia coli.
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Affiliation(s)
- Shweta Dixit
- Department of Chemical Engineering, IIT Kanpur, Kanpur, UP, 208016, India
| | - Sanjeev Garg
- Department of Chemical Engineering, IIT Kanpur, Kanpur, UP, 208016, India.
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12
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Zou L, Spanogiannopoulos P, Pieper LM, Chien HC, Cai W, Khuri N, Pottel J, Vora B, Ni Z, Tsakalozou E, Zhang W, Shoichet BK, Giacomini KM, Turnbaugh PJ. Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives. Proc Natl Acad Sci U S A 2020; 117:16009-16018. [PMID: 32571913 PMCID: PMC7355017 DOI: 10.1073/pnas.1920483117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Food and drug products contain diverse and abundant small-molecule additives (excipients) with unclear impacts on human physiology, drug safety, and response. Here, we evaluate their potential impact on intestinal drug absorption. By screening 136 unique compounds for inhibition of the key intestinal transporter OATP2B1 we identified and validated 24 potent OATP2B1 inhibitors, characterized by higher molecular weight and hydrophobicity compared to poor or noninhibitors. OATP2B1 inhibitors were also enriched for dyes, including 8 azo (R-N=N-R') dyes. Pharmacokinetic studies in mice confirmed that FD&C Red No. 40, a common azo dye excipient and a potent inhibitor of OATP2B1, decreased the plasma level of the OATP2B1 substrate fexofenadine, suggesting that FD&C Red No. 40 has the potential to block drug absorption through OATP2B1 inhibition in vivo. However, the gut microbiomes of multiple unrelated healthy individuals as well as diverse human gut bacterial isolates were capable of inactivating the identified azo dye excipients, producing metabolites that no longer inhibit OATP2B1 transport. These results support a beneficial role for the microbiome in limiting the unintended effects of food and drug additives in the intestine and provide a framework for the data-driven selection of excipients. Furthermore, the ubiquity and genetic diversity of gut bacterial azoreductases coupled to experiments in conventionally raised and gnotobiotic mice suggest that variations in gut microbial community structure may be less important to consider relative to the high concentrations of azo dyes in food products, which have the potential to saturate gut bacterial enzymatic activity.
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Affiliation(s)
- Ling Zou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Peter Spanogiannopoulos
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, CA 94143
| | - Lindsey M Pieper
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, CA 94143
| | - Huan-Chieh Chien
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - Natalia Khuri
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Joshua Pottel
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
- QB3 Institute, University of California, San Francisco, CA 94158
| | - Bianca Vora
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Zhanglin Ni
- Division of Quantitative Methods and Modeling, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993
| | - Eleftheria Tsakalozou
- Division of Quantitative Methods and Modeling, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
- QB3 Institute, University of California, San Francisco, CA 94158
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158;
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, CA 94143;
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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13
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Cyanobacteria as a bioreactor for synthesis of silver nanoparticles-an effect of different reaction conditions on the size of nanoparticles and their dye decolorization ability. J Microbiol Methods 2019; 162:77-82. [PMID: 31132377 DOI: 10.1016/j.mimet.2019.05.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 11/23/2022]
Abstract
The green synthesis of metallic nanoparticles has paved the way for improving and protecting the environment by decreasing the use of toxic chemicals and eliminating biological risks in biomedical applications. Biological synthesis of metal nanoparticles is gaining more importance due to simplicity, rapid rate of synthesis and eco-friendliness. In the present investigation cyanobacterial (Microchaete NCCU-342) cell free aqueous extract has been used for optimizing biosynthesis of silver nanoparticles (AgNP). The optimized reaction parameters for efficient synthesis of AgNP were: biomass quantity of 80 μg/ml, pH 5.5, 60 °C temperature, duration of 60 min UV light exposure and 1 mM AgNO3 concentration. AgNP was characterized by UV-Visible Spectrophotometery, Transmission Electron Microscopy and Dynamic light scattering. The smallest nanoparticles (obtained from biomass parameter were spherical, polydisperessed and in the range of 60-80 nm) were characterized further in a degradation study of azo dye methyl red. Degradation of methyl red within 2 h was more with AgNP (84.60%) as compared to cyanobacterial extract (49.80%).
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Suzuki H. Remarkable diversification of bacterial azoreductases: primary sequences, structures, substrates, physiological roles, and biotechnological applications. Appl Microbiol Biotechnol 2019; 103:3965-3978. [PMID: 30941462 DOI: 10.1007/s00253-019-09775-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 12/12/2022]
Abstract
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.
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Affiliation(s)
- Hirokazu Suzuki
- Faculty of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan. .,Center for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan.
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15
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Nakhaee N, Asad S, Khajeh K, Arab SS, Amoozegar MA. Improving the thermal stability of azoreductase from Halomonas elongata by introducing a disulfide bond via site-directed mutagenesis. Biotechnol Appl Biochem 2018; 65:883-891. [PMID: 30132989 DOI: 10.1002/bab.1688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/11/2018] [Indexed: 11/06/2022]
Abstract
Azoreductases mainly reduce azo dyes, the largest class of colorants, to colorless aromatic amines. AzoH, a new azoreductase from the halophilic bacterium, Halomonas elongata, has been recently cloned and expressed in Escherichia coli. The aim of this study was to improve thermal stability of this enzyme by introducing new disulfide bonds. Since X-ray crystallography was not available, homology modeling and molecular dynamics was used to construct the enzyme three-dimensional structure. Potential disulfide bonds for increasing thermal stability were found using DIScover online software. Appropriate mutations (L49C/D108C) to form a disulfide bond were introduced by the Quik-Change method. Mutant protein expressed in E. coli showed increased thermal stability at 50 °C (increased half-life from 12.6 Min in AzoH to 26.66 Min in a mutated enzyme). The mutated enzyme could also tolerate 5% (w/v) NaCl and retained 30% of original activity after 24 H incubation, whereas the wild-type enzyme was completely inactivated. According to circular dichroism studies, the secondary structure was not altered by this mutation; however, a blue shift in intrinsic florescent graph revealed changes in the tertiary structure. This is the first study to improve thermal stability and salt tolerance of a halophilic azoreductase.
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Affiliation(s)
- Narjes Nakhaee
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Sedigheh Asad
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
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Sun J, Kweon O, Jin J, He GX, Li X, Cerniglia CE, Chen H. Mutation network-based understanding of pleiotropic and epistatic mutational behavior of Enterococcus faecalis FMN-dependent azoreductase. Biochem Biophys Rep 2017; 12:240-244. [PMID: 29214224 PMCID: PMC5704035 DOI: 10.1016/j.bbrep.2017.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 10/30/2017] [Indexed: 11/15/2022] Open
Abstract
We previously identified a highly active homodimeric FMN-dependent NADH-preferred azoreductase (AzoA) from Enterococcus faecalis, which cleaves the azo bonds (R-N˭N-R) of diverse azo dyes, and determined its crystal structure. The preliminary network-based mutational analysis suggested that the two residues, Arg-21 and Asn-121, have an apparent mutational potential for fine-tuning of AzoA, based on their beneficial pleiotropic feedbacks. However, epistasis between the two promising mutational spots in AzoA has not been obtained in terms of substrate binding and azoreductase activity. In this study, we further quantified, visualized, and described the pleiotropic and/or epistatic behavior of six single or double mutations at the positions, Arg-21 and Asn-121, as a further research endeavor for beneficial fine-tuning of AzoA. Based on this network-based mutational analysis, we showed that pleiotropy and epistasis are common, sensitive, and complex mutational behaviors, depending mainly on the structural and functional responsibility and the physicochemical properties of the residue(s) in AzoA.
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Affiliation(s)
- Jinyan Sun
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ohgew Kweon
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Jinshan Jin
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Gui-Xin He
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Xiyu Li
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Carl E. Cerniglia
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Huizhong Chen
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
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Expansion of the active site of the azoreductase from Shewanella oneidensis MR-1. J Mol Graph Model 2017; 78:213-220. [DOI: 10.1016/j.jmgm.2017.10.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/27/2017] [Accepted: 10/27/2017] [Indexed: 11/19/2022]
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19
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Ingavat N, Kavran JM, Sun Z, Rokita SE. Active Site Binding Is Not Sufficient for Reductive Deiodination by Iodotyrosine Deiodinase. Biochemistry 2017; 56:1130-1139. [PMID: 28157283 PMCID: PMC5330855 DOI: 10.1021/acs.biochem.6b01308] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The minimal requirements for substrate recognition and turnover by iodotyrosine deiodinase were examined to learn the basis for its catalytic specificity. This enzyme is crucial for iodide homeostasis and the generation of thyroid hormone in chordates. 2-Iodophenol binds only very weakly to the human enzyme and is dehalogenated with a kcat/Km that is more than 4 orders of magnitude lower than that for iodotyrosine. This discrimination likely protects against a futile cycle of iodinating and deiodinating precursors of thyroid hormone biosynthesis. Surprisingly, a very similar catalytic selectivity was expressed by a bacterial homologue from Haliscomenobacter hydrossis. In this example, discrimination was not based on affinity since 4-cyano-2-iodophenol bound to the bacterial deiodinase with a Kd lower than that of iodotyrosine and yet was not detectably deiodinated. Other phenols including 2-iodophenol were deiodinated but only very inefficiently. Crystal structures of the bacterial enzyme with and without bound iodotyrosine are nearly superimposable and quite similar to the corresponding structures of the human enzyme. Likewise, the bacterial enzyme is activated for single electron transfer after binding to the substrate analogue fluorotyrosine as previously observed with the human enzyme. A cocrystal structure of bacterial deiodinase and 2-iodophenol indicates that this ligand stacks on the active site flavin mononucleotide (FMN) in a orientation analogous to that of bound iodotyrosine. However, 2-iodophenol association is not sufficient to activate the FMN chemistry required for catalysis, and thus the bacterial enzyme appears to share a similar specificity for halotyrosines even though their physiological roles are likely very different from those in humans.
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Affiliation(s)
- Nattha Ingavat
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218 United States
| | - Jennifer M. Kavran
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street Baltimore, Maryland 21205 United States,Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, 925 North Wolfe Street Baltimore, Maryland, 21205 United States
| | - Zuodong Sun
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218 United States
| | - Steven E. Rokita
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218 United States,Corresponding Author:
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Chung KT. Azo dyes and human health: A review. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2016; 34:233-261. [PMID: 27635691 DOI: 10.1080/10590501.2016.1236602] [Citation(s) in RCA: 304] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Synthetic azo dyes are widely used in industries. Gerhardt Domagk discovered that the antimicrobial effect of red azo dye Prontosil was caused by the reductively cleaved (azo reduction) product sulfanilamide. The significance of azo reduction is thus revealed. Azo reduction can be accomplished by human intestinal microflora, skin microflora, environmental microorganisms, to a lesser extent by human liver azoreductase, and by nonbiological means. Some azo dyes can be carcinogenic without being cleaved into aromatic amines. However, the carcinogenicity of many azo dyes is due to their cleaved product such as benzidine. Benzidine induces various human and animal tumors. Another azo dye component, p-phenylenediamine, is a contact allergen. Many azo dyes and their reductively cleaved products as well as chemically related aromatic amines are reported to affect human health, causing allergies and other human maladies.
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Affiliation(s)
- King-Thom Chung
- a Department of Biological Sciences , The University of Memphis , Memphis , Tennessee , USA
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21
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Ryan A. Azoreductases in drug metabolism. Br J Pharmacol 2016; 174:2161-2173. [PMID: 27487252 DOI: 10.1111/bph.13571] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 02/06/2023] Open
Abstract
Azoreductases are flavoenzymes that have been characterized in a range of prokaryotes and eukaryotes. Bacterial azoreductases are associated with the activation of two classes of drug, azo drugs for the treatment of inflammatory bowel disease and nitrofuran antibiotics. The mechanism of reduction of azo compounds is presented; it requires tautomerisation of the azo compound to a quinoneimine and provides a unifying mechanism for the reduction of azo and quinone substrates by azoreductases. The importance of further work in the characterization of azoreductases from enteric bacteria is highlighted to aid in the development of novel drugs for the treatment of colon related disorders. Human azoreductases are known to play a crucial role in the metabolism of a number of quinone-containing cancer chemotherapeutic drugs. The mechanism of hydride transfer to quinones, which is shared not only between eukaryotic and prokaryotic azoreductases but also the wider family of NAD(P)H quinone oxidoreductases, is outlined. The importance of common single nucleotide polymorphisms (SNPs) in human azoreductases is described not only in cancer prognosis but also with regard to their effects on the efficacy of quinone drug-based cancer chemotherapeutic regimens. This highlights the need to screen patients for azoreductase SNPs ahead of treatment with these regimens. LINKED ARTICLES This article is part of a themed section on Drug Metabolism and Antibiotic Resistance in Micro-organisms. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.14/issuetoc.
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Affiliation(s)
- Ali Ryan
- Faculty of Science, Engineering and Computing, Kingston University, Kingston upon Thames, UK
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22
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Qi J, Schlömann M, Tischler D. Biochemical characterization of an azoreductase from Rhodococcus opacus 1CP possessing methyl red degradation ability. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.04.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Eslami M, Amoozegar MA, Asad S. Isolation, cloning and characterization of an azoreductase from the halophilic bacterium Halomonas elongata. Int J Biol Macromol 2016; 85:111-6. [DOI: 10.1016/j.ijbiomac.2015.12.065] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 12/18/2015] [Accepted: 12/19/2015] [Indexed: 10/22/2022]
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Identification of novel members of the bacterial azoreductase family in Pseudomonas aeruginosa. Biochem J 2015; 473:549-58. [PMID: 26621870 DOI: 10.1042/bj20150856] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/30/2015] [Indexed: 11/17/2022]
Abstract
Azoreductases are a family of diverse enzymes found in many pathogenic bacteria as well as distant homologues being present in eukarya. In addition to having azoreductase activity, these enzymes are also suggested to have NAD(P)H quinone oxidoreductase (NQO) activity which leads to a proposed role in plant pathogenesis. Azoreductases have also been suggested to play a role in the mammalian pathogenesis of Pseudomonas aeruginosa. In view of the importance of P. aeruginosa as a pathogen, we therefore characterized recombinant enzymes following expression of a group of putative azoreductase genes from P. aeruginosa expressed in Escherichia coli. The enzymes include members of the arsenic-resistance protein H (ArsH), tryptophan repressor-binding protein A (WrbA), modulator of drug activity B (MdaB) and YieF families. The ArsH, MdaB and YieF family members all show azoreductase and NQO activities. In contrast, WrbA is the first enzyme to show NQO activity but does not reduce any of the 11 azo compounds tested under a wide range of conditions. These studies will allow further investigation of the possible role of these enzymes in the pathogenesis of P. aeruginosa.
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25
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Bacterial Enzymes and Multi-enzymatic Systems for Cleaning-up Dyes from the Environment. MICROBIAL DEGRADATION OF SYNTHETIC DYES IN WASTEWATERS 2015. [DOI: 10.1007/978-3-319-10942-8_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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26
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Sim E, Abuhammad A, Ryan A. Arylamine N-acetyltransferases: from drug metabolism and pharmacogenetics to drug discovery. Br J Pharmacol 2014; 171:2705-25. [PMID: 24467436 PMCID: PMC4158862 DOI: 10.1111/bph.12598] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 08/15/2013] [Accepted: 08/26/2013] [Indexed: 12/12/2022] Open
Abstract
Arylamine N-acetyltransferases (NATs) are polymorphic drug-metabolizing enzymes, acetylating arylamine carcinogens and drugs including hydralazine and sulphonamides. The slow NAT phenotype increases susceptibility to hydralazine and isoniazid toxicity and to occupational bladder cancer. The two polymorphic human NAT loci show linkage disequilibrium. All mammalian Nat genes have an intronless open reading frame and non-coding exons. The human gene products NAT1 and NAT2 have distinct substrate specificities: NAT2 acetylates hydralazine and human NAT1 acetylates p-aminosalicylate (p-AS) and the folate catabolite para-aminobenzoylglutamate (p-abaglu). Human NAT2 is mainly in liver and gut. Human NAT1 and its murine homologue are in many adult tissues and in early embryos. Human NAT1 is strongly expressed in oestrogen receptor-positive breast cancer and may contribute to folate and acetyl CoA homeostasis. NAT enzymes act through a catalytic triad of Cys, His and Asp with the architecture of the active site-modulating specificity. Polymorphisms may cause unfolded protein. The C-terminus helps bind acetyl CoA and differs among NATs including prokaryotic homologues. NAT in Salmonella typhimurium supports carcinogen activation and NAT in mycobacteria metabolizes isoniazid with polymorphism a minor factor in isoniazid resistance. Importantly, nat is in a gene cluster essential for Mycobacterium tuberculosis survival inside macrophages. NAT inhibitors are a starting point for novel anti-tuberculosis drugs. Human NAT1-specific inhibitors may act in biomarker detection in breast cancer and in cancer therapy. NAT inhibitors for co-administration with 5-aminosalicylate (5-AS) in inflammatory bowel disease has prompted ongoing investigations of azoreductases in gut bacteria which release 5-AS from prodrugs including balsalazide.
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Affiliation(s)
- E Sim
- Faculty of Science Engineering and Computing, Kingston University, Kingston, UK; Department of Pharmacology, Oxford University, Oxford, UK
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27
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Ryan A, Kaplan E, Nebel JC, Polycarpou E, Crescente V, Lowe E, Preston GM, Sim E. Identification of NAD(P)H quinone oxidoreductase activity in azoreductases from P. aeruginosa: azoreductases and NAD(P)H quinone oxidoreductases belong to the same FMN-dependent superfamily of enzymes. PLoS One 2014; 9:e98551. [PMID: 24915188 PMCID: PMC4051601 DOI: 10.1371/journal.pone.0098551] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 05/05/2014] [Indexed: 01/15/2023] Open
Abstract
Water soluble quinones are a group of cytotoxic anti-bacterial compounds that are secreted by many species of plants, invertebrates, fungi and bacteria. Studies in a number of species have shown the importance of quinones in response to pathogenic bacteria of the genus Pseudomonas. Two electron reduction is an important mechanism of quinone detoxification as it generates the less toxic quinol. In most organisms this reaction is carried out by a group of flavoenzymes known as NAD(P)H quinone oxidoreductases. Azoreductases have previously been separate from this group, however using azoreductases from Pseudomonas aeruginosa we show that they can rapidly reduce quinones. Azoreductases from the same organism are also shown to have distinct substrate specificity profiles allowing them to reduce a wide range of quinones. The azoreductase family is also shown to be more extensive than originally thought, due to the large sequence divergence amongst its members. As both NAD(P)H quinone oxidoreductases and azoreductases have related reaction mechanisms it is proposed that they form an enzyme superfamily. The ubiquitous and diverse nature of azoreductases alongside their broad substrate specificity, indicates they play a wide role in cellular survival under adverse conditions.
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Affiliation(s)
- Ali Ryan
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
- Faculty of Science, Engineering and Computing, Kingston University, Kingston upon Thames, United Kingdom
| | - Elise Kaplan
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Jean-Christophe Nebel
- Faculty of Science, Engineering and Computing, Kingston University, Kingston upon Thames, United Kingdom
| | - Elena Polycarpou
- Faculty of Science, Engineering and Computing, Kingston University, Kingston upon Thames, United Kingdom
| | - Vincenzo Crescente
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
- Faculty of Science, Engineering and Computing, Kingston University, Kingston upon Thames, United Kingdom
| | - Edward Lowe
- Laboratory of Molecular Biophysics, Biochemistry Department, University of Oxford, Oxford, United Kingdom
| | - Gail M. Preston
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Edith Sim
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
- Faculty of Science, Engineering and Computing, Kingston University, Kingston upon Thames, United Kingdom
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Yu J, Ogata D, Gai Z, Taguchi S, Tanaka I, Ooi T, Yao M. Structures of AzrA and of AzrC complexed with substrate or inhibitor: insight into substrate specificity and catalytic mechanism. ACTA ACUST UNITED AC 2014; 70:553-64. [PMID: 24531489 DOI: 10.1107/s1399004713030988] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 11/11/2013] [Indexed: 11/10/2022]
Abstract
Azo dyes are major synthetic dyestuffs with one or more azo bonds and are widely used for various industrial purposes. The biodegradation of residual azo dyes via azoreductase-catalyzed cleavage is very efficient as the initial step of wastewater treatment. The structures of the complexes of azoreductases with various substrates are therefore indispensable to understand their substrate specificity and catalytic mechanism. In this study, the crystal structures of AzrA and of AzrC complexed with Cibacron Blue (CB) and the azo dyes Acid Red 88 (AR88) and Orange I (OI) were determined. As an inhibitor/analogue of NAD(P)H, CB was located on top of flavin mononucleotide (FMN), suggesting a similar binding manner as NAD(P)H for direct hydride transfer to FMN. The structures of the AzrC-AR88 and AzrC-OI complexes showed two manners of binding for substrates possessing a hydroxy group at the ortho or the para position of the azo bond, respectively, while AR88 and OI were estimated to have a similar binding affinity to AzrC from ITC experiments. Although the two substrates were bound in different orientations, the hydroxy groups were located in similar positions, resulting in an arrangement of electrophilic C atoms binding with a proton/electron-donor distance of ∼3.5 Å to N5 of FMN. Catalytic mechanisms for different substrates are proposed based on the crystal structures and on site-directed mutagenesis analysis.
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Affiliation(s)
- Jian Yu
- Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Daiki Ogata
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - ZuoQi Gai
- Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Seiichi Taguchi
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Toshihiko Ooi
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
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Brissos V, Gonçalves N, Melo EP, Martins LO. Improving kinetic or thermodynamic stability of an azoreductase by directed evolution. PLoS One 2014; 9:e87209. [PMID: 24475252 PMCID: PMC3903626 DOI: 10.1371/journal.pone.0087209] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 12/20/2013] [Indexed: 12/28/2022] Open
Abstract
Protein stability arises from a combination of factors which are often difficult to rationalise. Therefore its improvement is better addressed through directed evolution than by rational design approaches. In this study, five rounds of mutagenesis/recombination followed by high-throughput screening (≈10,000 clones) yielded the hit 1B6 showing a 300-fold higher half life at 50°C than that exhibited by the homodimeric wild type PpAzoR azoreductase from Pseudomonas putida MET94. The characterization using fluorescence, calorimetry and light scattering shows that 1B6 has a folded state slightly less stable than the wild type (with lower melting and optimal temperatures) but in contrast is more resistant to irreversible denaturation. The superior kinetic stability of 1B6 variant was therefore related to an increased resistance of the unfolded monomers to aggregation through the introduction of mutations that disturbed hydrophobic patches and increased the surface net charge of the protein. Variants 2A1 and 2A1-Y179H with increased thermodynamic stability (10 to 20°C higher melting temperature than wild type) were also examined showing the distinctive nature of mutations that lead to improved structural robustness: these occur in residues that are mostly involved in strengthening the solvent-exposed loops or the inter-dimer interactions of the folded state.
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Affiliation(s)
- Vânia Brissos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Nádia Gonçalves
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Eduardo P. Melo
- Institute for Biotechnology and Bioengineering, Center for Molecular and Structural Biomedicine, Universidade do Algarve, Faro, Portugal
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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Gonçalves AMD, Mendes S, de Sanctis D, Martins LO, Bento I. The crystal structure of Pseudomonas putida azoreductase - the active site revisited. FEBS J 2013; 280:6643-57. [PMID: 24127652 DOI: 10.1111/febs.12568] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 10/03/2013] [Accepted: 10/08/2013] [Indexed: 11/28/2022]
Abstract
The enzymatic degradation of azo dyes begins with the reduction of the azo bond. In this article, we report the crystal structures of the native azoreductase from Pseudomonas putida MET94 (PpAzoR) (1.60 Å), of PpAzoR in complex with anthraquinone-2-sulfonate (1.50 Å), and of PpAzoR in complex with Reactive Black 5 dye (1.90 Å). These structures reveal the residues and subtle changes that accompany substrate binding and release. Such changes highlight the fine control of access to the catalytic site that is required by the ping-pong mechanism, and in turn the specificity offered by the enzyme towards different substrates. The topology surrounding the active site shows novel features of substrate recognition and binding that help to explain and differentiate the substrate specificity observed among different bacterial azoreductases.
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Affiliation(s)
- Ana Maria D Gonçalves
- Macromolecular Crystallography Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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31
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The non-enzymatic reduction of azo dyes by flavin and nicotinamide cofactors under varying conditions. Anaerobe 2013; 23:87-96. [DOI: 10.1016/j.anaerobe.2013.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 07/09/2013] [Accepted: 07/17/2013] [Indexed: 11/20/2022]
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32
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Yang Y, Lu L, Gao F, Zhao Y. Characterization of an efficient catalytic and organic solvent-tolerant azoreductase toward methyl red from Shewanella oneidensis MR-1. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:3232-3239. [PMID: 23089953 DOI: 10.1007/s11356-012-1221-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 09/20/2012] [Indexed: 06/01/2023]
Abstract
The acyl carrier protein (ACP) phosphodiesterase gene (SO 4396) of Shewanella oneidensis MR-1 which was analyzed to have azoreductase activity was heterologously expressed in Escherichia coli. The ACP phosphodiesterase was found to reach maximum enzyme velocity 220.59 U/mg, named azoreductase in this study. The azoreductase had highest specific activity (153.16 U/mg) at pH 6.5, which showed a preference for nicotinamide adenine dinucleotide (NADH) as electron donor. The phylogenetic tree analysis indicated that the azoreductase had preference for NADH and dependence for flavin mononucleotide (FMN). However, the azoreductase from S. oneidensis MR-1 still had high enzyme activity in the absence of FMN. The Mg(2+) had a positive influence on the enzyme activity with 25 mM concentration, whereas Cr(3+), Cd(2+) usually had significantly negative effect on enzyme activity. The purified azoreductase retained nearly 100 % activity after incubating in 30 % dimethyl sulfoxide (DMSO), 30 % acetone, 30 % methanol, 20 % ethanol, 20 % isopropanol, and 10 % propanol.
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Affiliation(s)
- Yuyi Yang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
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33
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Bacterial Decolorization and Degradation of Azo Dyes. ENVIRONMENTAL SCIENCE AND ENGINEERING 2012. [DOI: 10.1007/978-3-642-23789-8_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Ryan A, Kaplan E, Laurieri N, Lowe E, Sim E. Activation of nitrofurazone by azoreductases: multiple activities in one enzyme. Sci Rep 2011; 1:63. [PMID: 22355582 PMCID: PMC3216550 DOI: 10.1038/srep00063] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 07/28/2011] [Indexed: 11/10/2022] Open
Abstract
Azoreductases are well known for azo pro-drug activation by gut flora. We show that azoreductases have a wider role in drug metabolism than previously thought as they can also reduce and hence activate nitrofurazone. Nitrofurazone, a nitroaromatic drug, is a broad spectrum antibiotic which has until now been considered as activated in bacteria by nitroreductases. The structure of the azoreductase with nitrofurazone bound was solved at 2.08 Å and shows nitrofurazone in an active conformation. Based on the structural information, the kinetics and stoichiometry of nitrofurazone reduction by azoreductase from P. aeruginosa, we propose a mechanism of activation which accounts for the ability of azoreductases to reduce both azo and nitroaromatic drugs. This mode of activation can explain the cytotoxic side-effects of nitrofurazone through human azoreductase homologues.
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Affiliation(s)
- Ali Ryan
- Pharmacology Department, University of Oxford, OX1 3QT
- Faculty of Science, Engineering and Computing, Kingston University, KT1 2EE
| | - Elise Kaplan
- Pharmacology Department, University of Oxford, OX1 3QT
| | | | - Edward Lowe
- Laboratory of Molecular Biophysics, Biochemistry Department, University of Oxford, OX1 3QU
| | - Edith Sim
- Pharmacology Department, University of Oxford, OX1 3QT
- Faculty of Science, Engineering and Computing, Kingston University, KT1 2EE
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35
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Molecular determinants of azo reduction activity in the strain Pseudomonas putida MET94. Appl Microbiol Biotechnol 2011; 92:393-405. [DOI: 10.1007/s00253-011-3366-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 04/29/2011] [Accepted: 05/02/2011] [Indexed: 10/18/2022]
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36
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Effects of Orange II and Sudan III azo dyes and their metabolites on Staphylococcus aureus. J Ind Microbiol Biotechnol 2011; 38:1729-38. [PMID: 21451978 DOI: 10.1007/s10295-011-0962-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 03/12/2011] [Indexed: 12/25/2022]
Abstract
Azo dyes are widely used in the plastic, paper, cosmetics, food, and pharmaceutical industries. Some metabolites of these dyes are potentially genotoxic. The toxic effects of azo dyes and their potential reduction metabolites on Staphylococcus aureus ATCC BAA 1556 were studied. When the cultures were incubated with 6, 18, and 36 μg/ml of Orange II and Sudan III for 48 h, 76.3, 68.5, and 61.7% of Orange II and 97.8, 93.9, and 75.8% of Sudan III were reduced by the bacterium, respectively. In the presence of 36 μg/ml Sudan III, the cell viability of the bacterium decreased to 61.9% after 48 h of incubation, whereas the cell viability of the control culture without the dye was 71.5%. Moreover, the optical density of the bacterial cultures at 10 h decreased from 0.74 to 0.55, indicating that Sudan III is able to inhibit growth of the bacterium. However, Orange II had no significant effects on either cell growth or cell viability of the bacterium at the tested concentrations. 1-Amino-2-naphthol, a metabolite common to Orange II and Sudan III, was capable of inhibiting cell growth of the bacterium at 1 μg/ml and completely stopped bacterial cell growth at 24-48 μg/ml. On the other hand, the other metabolites of Orange II and Sudan III, namely sulfanilic acid, p-phenylenediamine, and aniline, showed no significant effects on cell growth. p-Phenylenediamine exhibited a synergistic effect with 1-amino-2-naphthol on cell growth inhibition. All of the dye metabolites had no significant effects on cell viability of the bacterium.
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37
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Saratale R, Saratale G, Chang J, Govindwar S. Bacterial decolorization and degradation of azo dyes: A review. J Taiwan Inst Chem Eng 2011. [DOI: 10.1016/j.jtice.2010.06.006] [Citation(s) in RCA: 660] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Correia B, Chen Z, Mendes S, Martins LO, Bento I. Crystallization and preliminary X-ray diffraction analysis of the azoreductase PpAzoR from Pseudomonas putida MET94. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:121-3. [PMID: 21206041 PMCID: PMC3079989 DOI: 10.1107/s1744309110048220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 11/18/2010] [Indexed: 11/10/2022]
Abstract
PpAzoR, an FMN-dependent NADPH azoreductase from Pseudomonas putida MET94, has been crystallized using the sitting-drop vapour-diffusion technique. The crystals diffracted to 1.6 Å resolution using synchrotron radiation and belonged to the orthorhombic space group F222, with unit-cell parameters a=72.1, b=95.5, c=146.1 Å. Data sets were collected from the native protein to 2.2 Å resolution using in-house equipment and to 1.6 Å resolution using synchrotron radiation and the three-dimensional structure was determined by the molecular-replacement method.
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Affiliation(s)
- Bruno Correia
- Instituto de Tecnologia Quimica e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-257 Oeiras, Portugal
| | - Zhenjia Chen
- Instituto de Tecnologia Quimica e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-257 Oeiras, Portugal
| | - Sónia Mendes
- Instituto de Tecnologia Quimica e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-257 Oeiras, Portugal
| | - Lígia O. Martins
- Instituto de Tecnologia Quimica e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-257 Oeiras, Portugal
| | - Isabel Bento
- Instituto de Tecnologia Quimica e Biológica, Universidade Nova de Lisboa, Avenida da República, 2780-257 Oeiras, Portugal
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Ryan A, Wang CJ, Laurieri N, Westwood I, Sim E. Reaction mechanism of azoreductases suggests convergent evolution with quinone oxidoreductases. Protein Cell 2010; 1:780-90. [PMID: 21203919 DOI: 10.1007/s13238-010-0090-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 06/28/2010] [Indexed: 01/17/2023] Open
Abstract
Azoreductases are involved in the bioremediation by bacteria of azo dyes found in waste water. In the gut flora, they activate azo pro-drugs, which are used for treatment of inflammatory bowel disease, releasing the active component 5-aminosalycilic acid. The bacterium P. aeruginosa has three azoreductase genes, paAzoR1, paAzoR2 and paAzoR3, which as recombinant enzymes have been shown to have different substrate specificities. The mechanism of azoreduction relies upon tautomerisation of the substrate to the hydrazone form. We report here the characterization of the P. aeruginosa azoreductase enzymes, including determining their thermostability, cofactor preference and kinetic constants against a range of their favoured substrates. The expression levels of these enzymes during growth of P. aeruginosa are altered by the presence of azo substrates. It is shown that enzymes that were originally described as azoreductases, are likely to act as NADH quinone oxidoreductases. The low sequence identities observed among NAD(P)H quinone oxidoreductase and azoreductase enzymes suggests convergent evolution.
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Affiliation(s)
- Ali Ryan
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
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40
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Feng J, Heinze TM, Xu H, Cerniglia CE, Chen H. Evidence for significantly enhancing reduction of Azo dyes in Escherichia coli by expressed cytoplasmic Azoreductase (AzoA) of Enterococcus faecalis. Protein Pept Lett 2010; 17:578-84. [PMID: 19663804 DOI: 10.2174/092986610791112701] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 08/07/2009] [Indexed: 11/22/2022]
Abstract
Although cytoplasmic azoreductases have been purified and characterized from various bacteria, little evidence demonstrating that these azoreductases are directly involved in azo dye reduction in vivo is known. In order to evaluate the contribution of the enzyme to azo dye reduction in vivo, experiments were conducted to determine the effect of a recombinant cytoplasmic azoreductase (AzoA) from Enterococcus faecalis expressed in Escherichia coli on the rate of metabolism of Methyl Red, Ponceau BS and Orange II. The intact cells that contained IPTG induced AzoA had a higher rate of dye reduction with increases of 2 (Methyl Red), 4 (Ponceau BS) and 2.6 (Orange II)-fold compared to noninduced cells, respectively. Metabolites of Methyl Red isolated from induced cultures were identified as N,N-dimethyl-p-phenylenediamine and 2-aminobenzoic acid through liquid chromatography electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) analyses. In conclusion, our data demonstrate that AzoA from Ent. faecalis is capable of increasing the reduction of azo dyes in intact E. coli cells and that cytoplasmic azoreductase is involved in bacterial dye degradation in vivo.
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Affiliation(s)
- J Feng
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079-9502, USA
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41
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Bürger S, Stolz A. Characterisation of the flavin-free oxygen-tolerant azoreductase from Xenophilus azovorans KF46F in comparison to flavin-containing azoreductases. Appl Microbiol Biotechnol 2010; 87:2067-76. [DOI: 10.1007/s00253-010-2669-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 05/05/2010] [Accepted: 05/05/2010] [Indexed: 12/01/2022]
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A novel mechanism for azoreduction. J Mol Biol 2010; 400:24-37. [PMID: 20417637 DOI: 10.1016/j.jmb.2010.04.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 04/12/2010] [Accepted: 04/13/2010] [Indexed: 11/20/2022]
Abstract
Azoreductases are important due to their ability to activate anti-inflammatory azo pro-drugs and to detoxify azo dyes. Three genes encoding azoreductases have been identified in Pseudomonas aeruginosa. We describe here a comparison of the three enzymes. The pure recombinant proteins each have a distinct substrate specificity profile against a range of azo substrates. Using the structure of P. aeruginosa azoreductase (paAzoR) 1 and the homology models of paAzoR2 and paAzoR3, we have identified residues important for substrate specificity. We have defined a novel flavin mononucleotide binding cradle, which is a recurrent motif in many flavodoxin-like proteins. A novel structure of paAzoR1 with the azo pro-drug balsalazide bound within the active site was determined by X-ray crystallography and demonstrates that the substrate is present in a hydrazone tautomer conformation. We propose that the structure with balsalazide bound represents an enzyme intermediate and, together with the flavin mononucleotide binding cradle, we propose a novel catalytic mechanism.
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Chen H, Feng J, Kweon O, Xu H, Cerniglia CE. Identification and molecular characterization of a novel flavin-free NADPH preferred azoreductase encoded by azoB in Pigmentiphaga kullae K24. BMC BIOCHEMISTRY 2010; 11:13. [PMID: 20233432 PMCID: PMC2858024 DOI: 10.1186/1471-2091-11-13] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 03/16/2010] [Indexed: 11/10/2022]
Abstract
Background Microbial degradation of azo dyes is commonly initiated by the reduction of the azo bond(s) by a group of NADH or NADPH dependant azoreductases with many requiring flavin as a cofactor. In this study, we report the identification of a novel flavin-free NADPH preferred azoreductase encoded by azoB in Pigmentiphaga kullae K24. Results The deduced amino acid sequence of azoB from P. kullae K24 showed 61% identity to a previously studied azoreductase (AzoA) from the same strain. azoB encoded a protein of 203 amino acids and heterologously expressed in Escherichia coli. The purified recombinant enzyme was a monomer with a molecular mass of 22 kDa. Both NADH and NADPH can be used as an electron donor for its activity with 4-(4-hydroxy-1-naphthylazo) benzenesulfonic acid (Orange I) as substrate. The apparent Km values for both NADH and Orange I were 170 and 8.6 μM, respectively. The Km of NADPH for the enzyme is 1.0 μM. When NADPH served as the electron donor, the activity of the enzyme is 63% higher than that when NADH was used. The pH and temperature optima for activity of the enzyme with Orange I as the substrate were at pH 6.0 and between 37 and 45°C. Phylogenetic analysis shows that AzoB belongs to the flavin-free azoreductase group which has a key fingerprint motif GXXGXXG for NAD(P)H binding at the N-terminus of the amino acid sequences. The 3D structure of AzoB was generated by comparative modeling approach. The structural combination of three conserved glycine residues (G7xxG10xxG13) in the pyrophosphate-binding loop with the Arg-32 explains the preference for NADPH of AzoB. Conclusion The biochemical and structural properties of AzoB from P. kullae K24 revealed its preference for NADPH over NADH and it is a member of the monomeric flavin-free azoreductase group. Our studies show the substrate specificity of AzoB based on structure and cofactor requirement and the phylogenetic relationship among azoreductase groups.
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Affiliation(s)
- Huizhong Chen
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079-9502, USA.
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Wang CJ, Laurieri N, Abuhammad A, Lowe E, Westwood I, Ryan A, Sim E. Role of tyrosine 131 in the active site of paAzoR1, an azoreductase with specificity for the inflammatory bowel disease prodrug balsalazide. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:2-7. [PMID: 20057057 PMCID: PMC2805523 DOI: 10.1107/s1744309109044741] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 10/27/2009] [Indexed: 11/10/2022]
Abstract
Azoreductase 1 from Pseudomonas aeruginosa strain PAO1 (paAzoR1) catalyses the activation of the prodrug balsalazide and reduces the azo dye methyl red using reduced nicotinamide adenine dinucleotide cofactor as an electron donor. To investigate the mechanism of the enzyme, a Y131F mutation was introduced and the enzymic properties of the mutant were compared with those of the wild-type enzyme. The crystallographic structure of the mutant with methyl red bound was solved at 2.1 A resolution and compared with the wild-type structure. Tyr131 is important in the architecture of the active site but is not essential for enzymic activity.
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Affiliation(s)
- Chan-Ju Wang
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, England
| | - Nicola Laurieri
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, England
| | - Areej Abuhammad
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, England
| | - Edward Lowe
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Park Road, Oxford OX1 3QU, England
| | - Isaac Westwood
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, England
| | - Ali Ryan
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, England
| | - Edith Sim
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, England
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Characterization of thermostable FMN-dependent NADH azoreductase from the moderate thermophile Geobacillus stearothermophilus. Appl Microbiol Biotechnol 2009; 86:1431-8. [PMID: 19997911 DOI: 10.1007/s00253-009-2351-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 11/06/2009] [Accepted: 11/09/2009] [Indexed: 10/20/2022]
Abstract
The gene encoding an FMN-dependent NADH azoreductase, AzrG, from thermophilic Geobacillus stearothermophilus was cloned and functionally expressed in recombinant Escherichia coli. Purified recombinant AzrG is a homodimer of 23 kDa and bore FMN as a flavin cofactor. The optimal temperature of AzrG was 85 degrees C for the degradation of Methyl Red (MR). AzrG remained active for 1 h at 65 degrees C and for 1 month at 30 degrees C, demonstrating both superior thermostability and long-term stability of the enzyme. AzrG efficiently decolorized MR, Ethyl Red at 30 degrees C. Furthermore, the enzyme exhibited a wide-range of degrading activity towards several tenacious azo dyes, such as Acid Red 88, Orange I, and Congo Red. These results suggested the sustainable utilization of G. stearothermophilus as an azo-degrading strain for AzrG carrying whole-cell wastewater treatments for azo pollutants under high temperature conditions.
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46
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The Escherichia coli azoreductase AzoR Is involved in resistance to thiol-specific stress caused by electrophilic quinones. J Bacteriol 2009; 191:6394-400. [PMID: 19666717 DOI: 10.1128/jb.00552-09] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The physiological role of Escherichia coli azoreductase AzoR was studied. It was found that AzoR was capable of reducing several benzo-, naphtho-, and anthraquinone compounds, which were better substrates for AzoR than the model azo substrate methyl red. The DeltaazoR mutant displayed reduced viability when exposed to electrophilic quinones, which are capable of depleting cellular reduced glutathione (GSH). Externally added GSH can partially restore the impaired growth of the DeltaazoR mutant caused by 2-methylhydroquinone. The transcription of azoR was induced by electrophiles, including 2-methylhydroquinone, catechol, menadione, and diamide. A transcription start point was identified 44 bp upstream from the translation start point. These data indicated that AzoR is a quinone reductase providing resistance to thiol-specific stress caused by electrophilic quinones.
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Chen H, Xu H, Kweon O, Chen S, Cerniglia CE. Functional role of Trp-105 of Enterococcus faecalis azoreductase (AzoA) as resolved by structural and mutational analysis. MICROBIOLOGY-SGM 2008; 154:2659-2667. [PMID: 18757799 DOI: 10.1099/mic.0.2008/019877-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Enterococcus faecalis azoreductase (AzoA) is a very active enzyme with a broad spectrum of substrate specificity and is capable of degrading various azo dyes. The enzyme has an absolute requirement for reduced FMN, which delivers a total of four electrons from NADH to the substrate, resulting in the cleavage of the nitrogen double bond. In this study, we report the identification of amino acid residues critical for FMN binding in AzoA. FMN is stabilized by 22 amino acid residues, eight of which, Trp-105, Asn-106, Leu-107, Gly-150, Gly-151, Tyr-153, Asn-121 and Tyr-129, are involved in binding the FMN isoalloxazine ring. In silico analysis of the amino acid residues revealed that the Trp residue at position 105 of AzoA is the most likely significant contributor to the binding of FMN to the enzyme and is involved in FMN stabilization and destabilization. Site-directed mutagenesis analysis of Trp-105 was performed to determine the role of this amino acid residue in FMN binding and azo dye reductive activity. The mutant proteins were overexpressed in Escherichia coli and purified by anion-exchange and size-exclusion chromatography. The replacement of Trp-105 by the small side-chain amino acids Ala and Gly caused complete loss of both affinity for FMN and enzyme activity. Substitution of Tyr for Trp-105 did not significantly decrease the V(max) of the enzyme (22 % reduction). Substitutions with three bulky side-chain amino acids, Gln, Phe and His, produced enzymes with lower V(max) values (decreases of 68.2, 30.6 and 8.2-fold, respectively). However, these mutated enzymes maintained K(m) values similar to the wild-type enzyme. This study provides an insight into the catalytic properties of AzoA in FMN stabilization and enzyme activity.
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Affiliation(s)
- Huizhong Chen
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079-9502, USA
| | - Haiyan Xu
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079-9502, USA
| | - Ohgew Kweon
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079-9502, USA
| | - Siwei Chen
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079-9502, USA
| | - Carl E Cerniglia
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079-9502, USA
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Liu G, Zhou J, Wang J, Yan B, Li J, Lu H, Qu Y, Jin R. Site-directed mutagenesis of substrate binding sites of azoreductase from Rhodobacter sphaeroides. Biotechnol Lett 2007; 30:869-75. [PMID: 18165868 DOI: 10.1007/s10529-007-9627-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 12/11/2007] [Accepted: 12/11/2007] [Indexed: 11/30/2022]
Abstract
Comparison of three-dimensional structures of flavin-dependent azoreductases revealed two conserved loops around the flavin mononucleotide (FMN) cofactor. Tyr74, His75 and Lys109 in the two loops of azoreductase AZR from Rhodobacter sphaeroides were replaced with Trp, Asn and Ala/His by site-directed mutagenesis, respectively. The optimal pH values of K109H and H75N were pH 6, and those of K109A and Y74W were pH 9. The optimal temperature (30 degrees C) was not affected by mutation. Positively charged residues at position 109 is critical for the binding of methyl red. K109 might only be involved in the binding of the 2'-phosphate group of NADPH and have no effect on the binding of NADH. Y74W and H75N mutations decreased the binding of methyl red/nitrofurazone and had no affect on the binding of NADPH.
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Affiliation(s)
- Guangfei Liu
- School of Environmental and Biological Science and Technology, Dalian University of Technology, 116024, Dalian, P.R. China
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