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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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Shi H, Jiang X, Wen X, Hou C, Chen D, Mu Y, Shen J. Enhanced azo dye reduction at semiconductor-microbe interface: The key role of semiconductor band structure. WATER RESEARCH 2024; 248:120846. [PMID: 37952328 DOI: 10.1016/j.watres.2023.120846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Low-energy environmental remediation could be achieved by biocatalysis with assistance of light-excited semiconductor, in which the energy band structure of semiconductor has a significant influence on the metabolic process and electron transfer of microbes. In this study, direct Z-scheme and type II heterojunction semiconductor with different energy band structure were successfully synthesized for constructing semiconductor-microbe interface with Shewanella oneidensis MR-1 to achieve acid orange7 (AO7) biodegradation. UV-vis diffuse reflection spectroscopy, photoluminescence spectra and photoelectrochemical analysis revealed that the direct Z-scheme heterojunction semiconductor had stronger reduction power and faster separation of photoelectron-hole, which was beneficial for the AO7 biodegradation at semiconductor-microbe interface. Riboflavin was also involved in electron transfer between the semiconductor and microbes during AO7 reduction. Transcriptome results illustrated that functional gene expression of Shewanella oneidensis MR-1 was upregulated significantly with photo-stimulation of direct Z-scheme semiconductor, and Mtr pathway and conductive pili played the important roles in the photoelectron utilization by Shewanella oneidensis MR-1. This work is expected to provide alternative ideas for designing semiconductor-microbial interface with efficient electron transfer and broadening their applications in bioremediation.
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Affiliation(s)
- Hefei Shi
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; School of Resources and Environmental Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Xinbai Jiang
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Xiaojiao Wen
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Cheng Hou
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Dan Chen
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yang Mu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
| | - Jinyou Shen
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
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Wei B, Chen W, Ren X, Wang L, Zhao X. Enhanced Biodegradation of Methyl Orange Through Immobilization of Shewanella oneidensis MR-1 by Polyvinyl Alcohol and Sodium Alginate. Curr Microbiol 2023; 80:272. [PMID: 37410197 DOI: 10.1007/s00284-023-03387-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/26/2023] [Indexed: 07/07/2023]
Abstract
Shewanella oneidensis MR-1 has great potential for use in remediating azo dye pollution. Here, a new high-efficiency biodegradation method was developed utilizing S. oneidensis MR-1 immobilized by polyvinyl alcohol (PVA) and sodium alginate (SA). After determining the optimal immobilization conditions, the effects of various environmental factors on methyl orange (MO) degradation were analyzed. The biodegradation activity of the immobilized pellets was evaluated by analyzing the MO removal efficiency, and characterization was performed using scanning electron microscopy. The MO adsorption kinetics can be described using pseudo-second-order kinetics. Compared with free bacteria, the MO degradation rate of the immobilized S. oneidensis MR-1 increased from 41% to 92.6% after 21 days, suggesting that the immobilized bacteria performed substantially better and had more stable removal rates. These factors indicate the superiority of bacteria entrapment in addition to its easy application. This study demonstrates that the application of immobilized S. oneidensis MR-1 entrapped by PVA-SA can be used to establish a reactor with stable and high MO removal rates.
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Affiliation(s)
- Buyun Wei
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Wenwen Chen
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Xiaoyuan Ren
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Lei Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Xueqin Zhao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
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Cong J, Xie X, Liu Y, Qin Y, Fan J, Fang Y, Liu N, Zhang Q, Song X, Sand W. Biochemical characterization of a novel azo reductase named BVU5 from the bacterial flora DDMZ1: application for decolorization of azo dyes. RSC Adv 2022; 12:1968-1981. [PMID: 35425265 PMCID: PMC8979046 DOI: 10.1039/d1ra08090c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/09/2021] [Indexed: 12/07/2022] Open
Abstract
One of the main mechanisms of bacterial decolorization and degradation of azo dyes is the use of biological enzymes to catalyze the breaking of azo bonds. This paper shows the expression and properties of a novel azo reductase (hybrid-cluster NAD(P)-dependent oxidoreductase, accession no. A0A1S1BVU5, named BVU5) from the bacterial flora DDMZ1 for degradation of azo dyes. The molecular weight of BVU5 is about 40.1 kDa, and it contains the prosthetic group flavin mononucleotide (FMN). It has the decolorization ability of 80.1 ± 2.5% within 3 min for a dye concentration of 20 mg L−1, and 53.5 ± 1.8% even for a dye concentration of 200 mg L−1 after 30 min. The optimum temperature of enzyme BVU5 is 30 °C and the optimum pH is 6. It is insensitive to salt concentration up to a salinity level of 10%. Furthermore, enzyme BVU5 has good tolerance toward some metal ions (2 mM) such as Mn2+, Ca2+, Mg2+ and Cu2+ and some organic solvents (20%) such as DMSO, methanol, isopentyl, ethylene glycol and N-hexane. However, the enzyme BVU5 has a low tolerance to high concentrations of denaturants. In particular, it is sensitive to the denaturants guanidine hydrochloride (GdmCl) (2 M) and urea (2 M). Analysis of the dye substrate specificity shows that enzyme BVU5 decolorizes most azo dyes, which is indicating that the enzyme is not strictly substrate specific, it is a functional enzyme for breaking the azo structure. Liquid chromatography/time-of-flight/mass spectrometry (LC-TOF-MS) revealed after the action of enzyme BVU5 that some intermediate products with relatively large molecular weights were produced; this illustrates a symmetric or an asymmetric rapid cleavage of the azo bonds by this enzyme. The potential degradation pathways and the enzyme-catalyzed degradation mechanism are deduced in the end of this paper. The results give insight into the potential of a rapid bio-pretreatment by enzyme BVU5 for processing azo dye wastewater. The combination of BVU5 enzyme and coenzyme NADH can quickly degrade the azo dye RB5.![]()
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Affiliation(s)
- Junhao Cong
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Key Laboratory of Pollution Control and Emission Reduction Technology for Textile Industry, Donghua University Shanghai 201620 China
| | - Xuehui Xie
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Key Laboratory of Pollution Control and Emission Reduction Technology for Textile Industry, Donghua University Shanghai 201620 China.,Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092 P. R. China
| | - Yanbiao Liu
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Key Laboratory of Pollution Control and Emission Reduction Technology for Textile Industry, Donghua University Shanghai 201620 China
| | - Yan Qin
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Key Laboratory of Pollution Control and Emission Reduction Technology for Textile Industry, Donghua University Shanghai 201620 China
| | - Jiao Fan
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Key Laboratory of Pollution Control and Emission Reduction Technology for Textile Industry, Donghua University Shanghai 201620 China
| | - Yingrong Fang
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Key Laboratory of Pollution Control and Emission Reduction Technology for Textile Industry, Donghua University Shanghai 201620 China
| | - Na Liu
- School of Environment and Surveying Engineering, Suzhou University Suzhou Anhui 234000 China
| | - Qingyun Zhang
- School of Chemical and Environmental Engineering, Anhui Polytechnic University Wuhu Anhui 241000 China
| | - Xinshan Song
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Key Laboratory of Pollution Control and Emission Reduction Technology for Textile Industry, Donghua University Shanghai 201620 China.,Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092 P. R. China
| | - Wolfgang Sand
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Key Laboratory of Pollution Control and Emission Reduction Technology for Textile Industry, Donghua University Shanghai 201620 China.,Institute of Biosciences, Freiberg University of Mining and Technology Freiberg 09599 Germany
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Wang Y, Cai X, Mao Y. The first complete genome sequence of species Shewanella decolorationis, from a bioremediation competent strain Ni1-3. G3-GENES GENOMES GENETICS 2021; 11:6326802. [PMID: 34568919 PMCID: PMC8473976 DOI: 10.1093/g3journal/jkab261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/06/2021] [Indexed: 11/12/2022]
Abstract
Shewanella decolorationis are Gram-negative γ-Proteobacteria with environmental bioremediation potential because they can perform anaerobic respiration using various types of pollutants as terminal electron acceptors. So far, three isolated and cultured strains of S. decolorationis have been reported. However, no complete S. decolorationis genome has been published yet, which limited exploring their metabolism and feasibility in application. Here, S. decolorationis Ni1-3 isolated from an electroplating wastewater treatment plant showed strong reduction capabilities on azo dyes and oxidized metals. In order to construct the complete genome, high-quality whole-genome sequencing of strain Ni1-3 were performed by using both Nanopore MinION and Illumina NovaSeq platforms, from which the first complete genome of S. decolorationis was obtained by hybrid assembly. The genome of strain Ni1-3 contains a megaplasmid and a circular chromosome which encodes more proteins than that of the strains LDS1 and S12 belonging to the same species. In addition, more Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are identified in strain Ni1-3 genome. Importantly, 32 cytochrome-c and AzoR azoreductase coding genes are identified in the genome, which make strain Ni1-3 competent to degrade the azo dyes and versatile to bioremediate some other environmental pollution. The complete genome sequence of strain Ni1-3 can expand our knowledge toward its metabolic capabilities and potential, meanwhile, provide a reference to reassemble genomes of other S. decolorationis strains.
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Affiliation(s)
- Yicheng Wang
- Department of Environmental Engineering, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518071, P.R. China
| | - Xunchao Cai
- Department of Environmental Engineering, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518071, P.R. China.,Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen 518071, P.R. China
| | - Yanping Mao
- Department of Environmental Engineering, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518071, P.R. China
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6
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Min D, Cheng L, Liu DF, Li WW, Yu HQ. Electron transfer via the non-Mtr respiratory pathway from Shewanella putrefaciens CN-32 for methyl orange bioreduction. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Biochemical characterization of a novel azoreductase from Streptomyces sp.: Application in eco-friendly decolorization of azo dye wastewater. Int J Biol Macromol 2019; 140:1037-1046. [PMID: 31449862 DOI: 10.1016/j.ijbiomac.2019.08.196] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 01/07/2023]
Abstract
Azo dyes are the most widely applied chemical dyes that have also raised great concerns for environmental contamination and human health issues. There has been a growing interest in discovering bioremediation methods to degrade azo dyes for environmental and economic purposes. Azoreductases are key enzymes evolved in nature capable of degrading azo dyes. The current work reports the identification, expression, and properties of a novel azoreductase (AzoRed2) from Streptomyces sp. S27 which shows an excellent stability against pH change and organic solvents. To overcome the requirements of coenzyme while degrading azo dyes, we introduced a coenzyme regeneration enzyme, Bacillus subtilis glucose 1-dehydrogenase (BsGDH), to construct a recycling system in living cells. The whole-cell biocatalyst containing AzoRed2 and BsGDH was used to degrade a representative azo dye methyl red. The degradation rate of methyl red was up to 99% in 120 min with high substrate concentration (250 μM) and no external coenzyme added. The degradation rate was still 98% in the third batch trial. To sum up, a novel azoreductase with good properties was found, which was applied to construct whole-cell biocatalyst. Both the enzymes and whole-cell biocatalysts are good candidates for the industrial wastewater treatment and environmental restoration.
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8
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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: 25] [Impact Index Per Article: 5.0] [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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9
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Li Q, Feng X, Lu X, Li T, Han X, Xiao X, Wu X, Liu Z, Yang M, Feng Y. Combined intra- and extracellular reduction involved in the anaerobic biodecolorization of cationic azo dye by Shewanella oneidensis MR-1. CHEMOSPHERE 2018; 211:701-708. [PMID: 30098566 DOI: 10.1016/j.chemosphere.2018.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 07/13/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
Microbial reduction decolorization is a promising strategy for cationic azo dye pollution remediation, but the reduction mechanism is unclear yet. In this work, the anaerobic reduction decolorization mechanism of cationic red X-GRL (X-GRL) by Shewanella oneidensis MR-1 (MR-1) was investigated from both intracellular and extracellular aspects. The exogenous additional riboflavin treatment test was used to analyze the extracellular reduction mechanism of X-GRL, and the actual role of riboflavin during the reduction of X-GRL was identified by three-dimensional fluorescence analysis for the first time. The proteinase K and the electron competitor treatment tests were used to analyze the intracellular reduction mechanism of X-GRL. Moreover, the effect of external environment on the reduction mechanism of X-GRL was elucidated by the decolorization performance of MR-1 wild type and its mutants, ΔomcA/mtrC, ΔmtrA, ΔmtrB and ΔcymA, under different external pH conditions. The results indicated that X-GRL could be decolorized by MR-1 in both extracellular and intracellular spaces. The extracellular decolorization of X-GRL could be caused by Mtr respiratory pathway or the indirect reduction of riboflavin, while the intracellular decolorization might occur due to the intracellular reduction depending on CymA pathway and a NADH-dependent reduction catalyzed by intracellular azoreductases. Furthermore, the proportion of extracellular decolorization decreased, whereas that of intracellular decolorization increased as the environmental pH rose.
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Affiliation(s)
- Qian Li
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Xiaoli Feng
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Xuerong Lu
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Tingting Li
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Xue Han
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Xiang Xiao
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Xiangyang Wu
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Zhaoying Liu
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Mingfeng Yang
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yujie Feng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China.
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Suzuki H, Abe T, Doi K, Ohshima T. Azoreductase from alkaliphilic Bacillus sp. AO1 catalyzes indigo reduction. Appl Microbiol Biotechnol 2018; 102:9171-9181. [PMID: 30105570 DOI: 10.1007/s00253-018-9284-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 10/28/2022]
Abstract
Indigo is an insoluble blue dye historically used for dyeing textiles. A traditional approach for indigo dyeing involves microbial reduction of polygonum indigo to solubilize it under alkaline conditions; however, the mechanism by which microorganisms reduce indigo remains poorly understood. Here, we aimed to identify an enzyme that catalyzes indigo reduction; for this purpose, from alkaline liquor that performed microbial reduction of polygonum indigo, we isolated indigo carmine-reducing microorganisms. All isolates were facultative anaerobic and alkali-tolerant Bacillus spp. An isolate termed AO1 was found to be an alkaliphile that preferentially grows at pH 9.0-11.0 and at 30-35 °C. We focused on flavin-dependent azoreductase as a possible enzyme for indigo carmine reduction and identified its gene (azoA) in Bacillus sp. AO1 using homology-based strategies. azoA was monocistronic but clustered with ABC transporter genes. Primary sequence identities were < 50% between the azoA product (AzoA) and previously characterized flavin-dependent azoreductases. AzoA was heterologously produced as a flavoprotein tolerant to alkaline and organic solvents. The enzyme efficiently reduced indigo carmine in an NADH-dependent manner and showed strict specificity for electron acceptors. Notably, AzoA oxidized NADH in the presence, but not the absence, of indigo. The reaction rate was enhanced by adding organic solvents to solubilize indigo. Absorption spectrum analysis showed that indigo absorption decreased during the reaction. These observations suggest that AzoA can reduce indigo in vitro and potentially in Bacillus sp. AO1. This is the first study that identified an indigo reductase, providing a new insight into a traditional approach for indigo dyeing.
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Affiliation(s)
- Hirokazu Suzuki
- Functional Genomics of Extremophiles, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, 812-8581, Japan. .,Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8550, Japan. .,Centre for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8550, Japan.
| | - Tomoaki Abe
- Microbial Genetic Division, Institute of Genetic Resources, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, 812-8581, Japan
| | - Katsumi Doi
- Microbial Genetic Division, Institute of Genetic Resources, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, 812-8581, Japan
| | - Toshihisa Ohshima
- Microbial Genetic Division, Institute of Genetic Resources, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, 812-8581, Japan.,Faculty of Engineering, Osaka Institute of Technology, Osaka, 535-8585, Japan
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11
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12
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Xiao X, Li TT, Lu XR, Feng XL, Han X, Li WW, Li Q, Yu HQ. A simple method for assaying anaerobic biodegradation of dyes. BIORESOURCE TECHNOLOGY 2018; 251:204-209. [PMID: 29277051 DOI: 10.1016/j.biortech.2017.12.052] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/14/2017] [Accepted: 12/17/2017] [Indexed: 06/07/2023]
Abstract
Anaerobic dye degradation is usually assayed using serum vials, which is time-consuming and costly. In this work, a simple method was established for real-time nondestructive assay of dye biodegradation using 96-well microtiter plates with petrolatum oil to avoid the volatilization and high transmittance transparent tape to prevent the permeation of oxygen. With the anaerobic degradation of methyl red and amaranth by Shewanella oneidensis MR-1, this assay method was verified. Further experiments revealed that blocking Mtr pathway had no substantial effect on the degradation of methyl red and dose of riboflavin also failed to promote the degradation of methyl red. On the contrary, the anaerobic degradation of amaranth depended mainly on the electron transmembrane transfer through Mtr pathway. Our work clearly indicates that Mtr pathway had different effects on intra- and extra-cellular degradation of azo dyes by S. oneidensis MR-1. Such a developed method is helpful for investigating anaerobic dye decolorization.
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Affiliation(s)
- Xiang Xiao
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Ting-Ting Li
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xue-Rong Lu
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xiao-Li Feng
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xue Han
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China
| | - Qian Li
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science & Technology of China, Hefei 230026, China.
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13
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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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Cao X, Qi Y, Xu C, Yang Y, Wang J. Transcriptome and metabolome responses of Shewanella oneidensis MR-1 to methyl orange under microaerophilic and aerobic conditions. Appl Microbiol Biotechnol 2017; 101:3463-3472. [PMID: 28070664 DOI: 10.1007/s00253-016-8087-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 02/08/2023]
Abstract
Shewanella oneidensis MR-1 degrades various azo dyes under microaerophilic and anaerobic conditions, but this process is inhibited under aerobic conditions. The mechanisms underlying azo dye biodegradation and inhibition remain unknown. Therefore, we investigated metabolic and transcriptional changes in strain MR-1, which was cultured under different conditions, to elucidate these mechanisms. At the transcriptional level, genes involved in certain metabolic processes, particularly the tricarboxylic acid (TCA) cycle, amino acid biodegradation, and the electron transfer system, were significantly altered (M ≧ 2, p > 0.8 ) in the presence of methyl orange (MO). Moreover, a high concentration of dissolved oxygen heavily impacted the expression levels of genes involved in fatty acid biodegradation. Metabolome analysis revealed significant alteration (p < 0.05) in the concentrations of nine metabolites when strain MR-1 was cultured under aerobic conditions; the majority of these metabolites were closely associated with amino acid metabolism and DNA replication. Accordingly, we propose a possible pathway for MO biodegradation and discuss the most likely causes of biodegradation inhibition due to dissolved oxygen.
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Affiliation(s)
- Xinhua Cao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yueling Qi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Xu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Jun Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
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15
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Zhang X, Ng IS, Chang JS. Cloning and characterization of a robust recombinant azoreductase from Shewanella xiamenensis BC01. J Taiwan Inst Chem Eng 2016. [DOI: 10.1016/j.jtice.2016.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Fang Y, Xu M, Wu WM, Chen X, Sun G, Guo J, Liu X. Characterization of the enhancement of zero valent iron on microbial azo reduction. BMC Microbiol 2015; 15:85. [PMID: 25888062 PMCID: PMC4428006 DOI: 10.1186/s12866-015-0419-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 03/27/2015] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The microbial method for the treatment of azo dye is promising, but the reduction of azo dye is the rate-limiting step. Zero valent iron (Fe(0)) can enhance microbial azo reduction, but the interactions between microbes and Fe(0) and the potential mechanisms of enhancement remain unclear. Here, Shewanella decolorationis S12, a typical azo-reducing bacterium, was used to characterize the enhancement of Fe(0) on microbial decolorization. RESULTS The results indicated that anaerobic iron corrosion was a key inorganic chemical process for the enhancement of Fe(0) on microbial azo reduction, in which OH(-), H2, and Fe(2+) were produced. Once Fe(0) was added to the microbial azo reduction system, the proper pH for microbial azo reduction was maintained by OH(-), and H2 served as the favored electron donor for azo respiration. Subsequently, the bacterial biomass yield and viability significantly increased. Following the corrosion of Fe(0), nanometer-scale Fe precipitates were adsorbed onto cell surfaces and even accumulated inside cells as observed by transmission electron microscope energy dispersive spectroscopy (TEM-EDS). CONCLUSIONS A conceptual model for Fe(0)-assisted azo dye reduction by strain S12 was established to explain the interactions between microbes and Fe(0) and the potential mechanisms of enhancement. This model indicates that the enhancement of microbial azo reduction in the presence of Fe(0) is mainly due to the stimulation of microbial growth and activity by supplementation with elemental iron and H2 as an additional electron donor. This study has expanded our knowledge of the enhancement of microbial azo reduction by Fe(0) and laid a foundation for the development of Fe(0)-microbial integrated azo dye wastewater treatment technology.
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Affiliation(s)
- Yun Fang
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China.
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 510070, Guangzhou, China.
- State Key Laboratory of Applied Microbiology Southern China, 510070, Guangzhou, China.
- Key Laboratory of Biometallurgy of Ministry of Education, 410083, Changsha, China.
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 510070, Guangzhou, China.
- State Key Laboratory of Applied Microbiology Southern China, 510070, Guangzhou, China.
| | - Wei-Min Wu
- Department of Civil and Environmental Engineering, Center for Sustainable Development and Global Competitiveness, Codiga Resource Recovery Center, Stanford University, Stanford, CA, 94305, USA.
| | - Xingjuan Chen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 510070, Guangzhou, China.
- State Key Laboratory of Applied Microbiology Southern China, 510070, Guangzhou, China.
| | - Guoping Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 510070, Guangzhou, China.
- State Key Laboratory of Applied Microbiology Southern China, 510070, Guangzhou, China.
| | - Jun Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 510070, Guangzhou, China.
- State Key Laboratory of Applied Microbiology Southern China, 510070, Guangzhou, China.
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China.
- Key Laboratory of Biometallurgy of Ministry of Education, 410083, Changsha, China.
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17
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Mahmood S, Khalid A, Arshad M, Mahmood T, Crowley DE. Detoxification of azo dyes by bacterial oxidoreductase enzymes. Crit Rev Biotechnol 2015; 36:639-51. [DOI: 10.3109/07388551.2015.1004518] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Shahid Mahmood
- Department of Environmental Sciences, PMAS Arid Agriculture University, Rawalpindi, Pakistan,
| | - Azeem Khalid
- Department of Environmental Sciences, PMAS Arid Agriculture University, Rawalpindi, Pakistan,
| | - Muhammad Arshad
- Institute of Soil & Environmental Sciences, University of Agriculture, Faisalabad, Pakistan, and
| | - Tariq Mahmood
- Department of Environmental Sciences, PMAS Arid Agriculture University, Rawalpindi, Pakistan,
| | - David E. Crowley
- Department of Environmental Sciences, University of California, Riverside, CA, USA
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18
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Feng J, Han T, Zhang MQ, Zhou Y, Wu QQ. Application of 2D fluorescence correlation method to investigate the dilution-induced heterogeneous distribution of the bound FMN in azoreductase. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2014.11.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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