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Eppinger E, Stolz A, Ferraroni M. Crystal structure of the monocupin ring-cleaving dioxygenase 5-nitrosalicylate 1,2-dioxygenase from Bradyrhizobium sp. Acta Crystallogr D Struct Biol 2023; 79:632-640. [PMID: 37326584 PMCID: PMC10306065 DOI: 10.1107/s2059798323004199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/14/2023] [Indexed: 06/17/2023] Open
Abstract
5-Nitrosalicylate 1,2-dioxygenase (5NSDO) is an iron(II)-dependent dioxygenase involved in the aerobic degradation of 5-nitroanthranilic acid by the bacterium Bradyrhizobium sp. It catalyzes the opening of the 5-nitrosalicylate aromatic ring, a key step in the degradation pathway. Besides 5-nitrosalicylate, the enzyme is also active towards 5-chlorosalicylate. The X-ray crystallographic structure of the enzyme was solved at 2.1 Å resolution by molecular replacement using a model from the AI program AlphaFold. The enzyme crystallized in the monoclinic space group P21, with unit-cell parameters a = 50.42, b = 143.17, c = 60.07 Å, β = 107.3°. 5NSDO belongs to the third class of ring-cleaving dioxygenases. Members of this family convert para-diols or hydroxylated aromatic carboxylic acids and belong to the cupin superfamily, which is one of the most functionally diverse protein classes and is named on the basis of a conserved β-barrel fold. 5NSDO is a tetramer composed of four identical subunits, each folded as a monocupin domain. The iron(II) ion in the enzyme active site is coordinated by His96, His98 and His136 and three water molecules with a distorted octahedral geometry. The residues in the active site are poorly conserved compared with other dioxygenases of the third class, such as gentisate 1,2-dioxygenase and salicylate 1,2-dioxygenase. Comparison with these other representatives of the same class and docking of the substrate into the active site of 5NSDO allowed the identification of residues which are crucial for the catalytic mechanism and enzyme selectivity.
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Affiliation(s)
- Erik Eppinger
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Andreas Stolz
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Marta Ferraroni
- Dipartimento di Chimica ‘Ugo Schiff’, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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Kurt Z, Qu Y, Spain JC. Novel catabolic pathway for 4-Nitroaniline in a Rhodococcus sp. strain JS360. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131473. [PMID: 37146325 DOI: 10.1016/j.jhazmat.2023.131473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/03/2023] [Accepted: 04/21/2023] [Indexed: 05/07/2023]
Abstract
4-Nitroaniline (4NA), the starting material for the first synthesized azo dye, is a toxic compound found in industrial wastewaters. Several bacterial strains capable of 4NA biodegradation were previously reported but the details of the catabolic pathway were not established. To search for novel metabolic diversity, we isolated a Rhodococcus sp. Strain JS360 by selective enrichment from 4NA-contaminated soil. When grown on 4NA the isolate accumulated biomass released stoichiometric amounts of nitrite and released less than stoichiometric amounts of ammonia, indicating that 4NA was used as sole carbon and nitrogen source to support growth and mineralization. Enzyme assays coupled with respirometry provided preliminary evidence that the first and second steps of 4NA degradation involve monooxygenase-catalyzed reactions followed by ring cleavage prior to deamination. Sequencing and annotation of the whole genome revealed candidate monooxygenases that were subsequently cloned and expressed in E.coli. Heterologously expressed 4NA monooxygenase (NamA) and 4-aminophenol (4AP) monooxygenase (NamB) transformed 4NA to 4AP and 4AP to 4-aminoresorcinol (4AR) respectively. The results revealed a novel pathway for nitroanilines and defined two monooxygenase mechanisms likely to be involved in the biodegradation of similar compounds.
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Affiliation(s)
- Zohre Kurt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0512, Georgia; Middle East Technical University, Ankara, Turkey; Florida State University Panamá, Panama.
| | - Yi Qu
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0512, Georgia
| | - Jim C Spain
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0512, Georgia; Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, FL 32514-5751, United States
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Nzila A, Musa MM, Afuecheta E, Al-Thukair A, Sankaran S, Xiang L, Li QX. Benzo[A]Pyrene Biodegradation by Multiple and Individual Mesophilic Bacteria under Axenic Conditions and in Soil Samples. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:1855. [PMID: 36767220 PMCID: PMC9914810 DOI: 10.3390/ijerph20031855] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
To date, only a handful of bacterial strains that can independently degrade and utilize benzo[a]pyrene (BaP) as the sole carbon source has been isolated and characterized. Here, three new bacterial strains-JBZ1A, JBZ2B, and JBZ5E-were isolated from contaminated soil and, using 16S rRNA sequencing, were identified as Brad rhizobium japonicum, Micrococcus luteus, and Bacillus cereus, respectively. The growth ability of each individual strain and a consortium of all strains in the presence of BaP (4-400 µmol·L-1, pH 7, 37 °C) was identified by the doubling time (dt). The results illustrate that dt decreased with increasing BaP concentrations for individual strains and the consortium. The optimum growth conditions of the consortium were 37 °C, 0.5% NaCl (w/v), and pH 7. Under these conditions, the degradation rate was 1.06 µmol·L-1·day-1, whereas that of individual strains ranged from 0.9 to 0.38 µmol·L-1·day-1. B. cereus had the strongest contribution to the consortium's activity, with a degradation rate of 0.9 µmol·L-1·day-1. The consortium could also remove BaP spiked with soil but at a lower rate (0.01 µmol L-1.day-1). High-performance liquid chromatography-high-resolution tandem mass spectrometry permitted the detection of the metabolites of these strains, and a biodegradation pathway is proposed.
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Affiliation(s)
- Alexis Nzila
- Department of Bioengineering, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
- Interdisciplinary Research Center for Membranes and Water Security, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
| | - Musa M. Musa
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
- Interdisciplinary Research Center for Refining and Advanced Chemicals, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
| | - Emmanuel Afuecheta
- Departments of Mathematics, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
| | - Assad Al-Thukair
- Department of Bioengineering, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
| | - Saravanan Sankaran
- Department of Bioengineering, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Qing X. Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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Cao L, Zhu G, Tao J, Zhang Y. Iron carriers promote biofilm formation and p-nitrophenol degradation. CHEMOSPHERE 2022; 293:133601. [PMID: 35033514 DOI: 10.1016/j.chemosphere.2022.133601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/14/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Vertical baffled biofilm reactors (VBBR) equipped with Plastic-carriers and Fe-carriers were employed to explore the effect of biofilm carriers on biofilm formation and p-nitrophenol (PNP) degradation. The results showed that Fe-carriers enhanced biofilm formation and PNP degradation. The maximum thickness of biofilm grown on the Fe-carriers was 1.5-fold higher than that on the Plastic-carriers. The Fe-VBBR reached a maximum rate of PNP removal at 13.02 μM L-1 h-1 with less sodium acetate addition (3 mM), while the maximum rate of PNP removal was 11.53 μM L-1 h-1 with more sodium acetate addition (6 mM) in the Plastic-based VBBR. High-throughput sequencing suggested that the Fe-VBBR had a higher biodiversity of the bacterial community in evenness, and the Achromobacter genus and Xanthobacteraceae family were as main PNP degraders. Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology analysis suggested more abundances of iron uptake genes were expressed to transport iron into the cytoplasm under an iron-limited condition in two VBBRs, and the metabolic pathway of PNP degradation went through 4-nitrocatechol and 1,2,4-benzenetriol. Our results provide a new insight for iron enhancing biofilm formation and PNP degradation.
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Affiliation(s)
- Lifeng Cao
- Department of Environmental Science and Engineering, School of Environmental and Geographical Science, Shanghai Normal University, Shanghai, 200234, PR China; School of Environment and State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing, 100084, China
| | - Ge Zhu
- Department of Environmental Science and Engineering, School of Environmental and Geographical Science, Shanghai Normal University, Shanghai, 200234, PR China
| | - Jinzhao Tao
- Department of Environmental Science and Engineering, School of Environmental and Geographical Science, Shanghai Normal University, Shanghai, 200234, PR China
| | - Yongming Zhang
- Department of Environmental Science and Engineering, School of Environmental and Geographical Science, Shanghai Normal University, Shanghai, 200234, PR China.
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Chen Z, Li D, Liu H, Wen Q. Effects of polyurethane foam carrier addition on anoxic/aerobic membrane bioreactor (A/O-MBR) for coal gasification wastewater (CGW) treatment: Performance and microbial community structure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:148037. [PMID: 34082207 DOI: 10.1016/j.scitotenv.2021.148037] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Coal gasification wastewater (CGW) is a typical toxic and refractory industrial wastewater with abundant phenols contained. Two identical anoxic/aerobic membrane bioreactors (with (R2) and without (R1) polyurethane (PU) foam) were carried out in parallel to investigate the role of PU foam addition in enhancing pollutants removal in CGW. Results showed that both systems exhibited effective removal of chemical oxygen demand (>93%) and total phenols (>97%) but poor ammonia nitrogen removal (<35%) constrained by ammonia oxidation process. GC-MS analysis revealed that aromatic and other refractory intermediates were dramatically reduced in R2. Moreover, the PU addition had negligible influence on the total soluble microbial products and extracellular polymeric substances contents but significantly alleviated membrane fouling with the operating time 33% prolonged. Microbial community revealed that Flavobacterium, Holophaga, and Geobacter were enriched on PU. Influent type might be a main driver for microbial community succession.
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Affiliation(s)
- Zhiqiang Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; School of Civil Engineering, Lanzhou University of Technology, Lanzhou 730070, China
| | - Da Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hongguo Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qinxue Wen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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Zhu S, Wu H, Wu C, Qiu G, Feng C, Wei C. Structure and function of microbial community involved in a novel full-scale prefix oxic coking wastewater treatment O/H/O system. WATER RESEARCH 2019; 164:114963. [PMID: 31421512 DOI: 10.1016/j.watres.2019.114963] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 06/10/2023]
Abstract
A novel full-scale prefix oxic coking wastewater (CWW) biological treatment O/H/O system had been operated steadily six years with the effluent quality meeting national discharge standard. Comparing to the traditional CWW biological treatment process, which usually have an anaerobic unit at the start of the process, here the O/H/O system has obvious advantages in COD removal, total nitrogen removal and reduced energy consumption. It is very necessary to illustrate the structure and function of the microbial community involved in different bioreactors of the O/H/O system. High-throughput MiSeq sequencing was used to examine the 16S rRNA genes in this system. Results revealed a contrasting microbial composition among the activated sludge samples of three sequential bioreactors: the β-Proteobacteria related sequences dominated in the O1 activated sludge with the relative abundance of 56.44% while 7.53% of the sequences were assigned to Thiobacillus; Rhodoplanes related sequences dominated in the bioreactor H and O2 activated sludge with relative abundance of 8.86% and 8.92%, respectively. The physico-chemical characteristics of CWW were analyzed by standard methods and the operational parameters were routinely monitored to examine their effects on the microbial communities. The bioinformatics software package of phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) was used to predict the microbial community functional profiling and found three dominant genera of Rhodoplanes, Lysobacter and Leucobacter enriched the xenobiotics biodegradation and metabolism pathway. The diverse and distinct microbial community involved in biological treatment processes of CWW treatment indicating that water characteristics and operational parameters determined the microbial community composition. These results significantly expanded our knowledge of the biodiversity and population dynamics of microorganisms and discerned the relationships between bacterial communities and environmental variables in the biological treatment processes. Moreover, in this study, we proposed a comprehensive biodegradation model of CWW treatment and defined as O/H/O system.
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Affiliation(s)
- Shuang Zhu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; Center for Bioresources & Drug Discovery and School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Haizhen Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, PR China
| | - Chaofei Wu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Chunhua Feng
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China.
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Banerjee A, Li J, Molenda MA, Brennessel WW, Chavez FA. A Biomimetic System for Studying Salicylate Dioxygenase. ACS SYMPOSIUM SERIES. AMERICAN CHEMICAL SOCIETY 2019; 1317:71-83. [PMID: 33967356 PMCID: PMC8101989 DOI: 10.1021/bk-2019-1317.ch004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We report the characterization of [Fe(T1Et4iPrIP)(sal)] (2) (T1Et4iPrIP = tris(1-ethyl-4-isopropyl-imidazolyl)phosphine; sal2- = salicylate dianion), which serves as a model for substrate-bound salicylate dioxygenase (SDO). Complex 2 crystallizes in the monoclinic space group P21/n with a = 10.7853(12) Å, b = 16.5060(19) Å, c = 21.217(2) Å, β = 94.489(2)°, and V = 3765.5(7) Å3. The structure consists of FeII bonded in distorted square pyramidal geometry (τ = 0.32) with two salicylate oxygens and two T1Et4iPrIP nitrogens serving as the base and the apical position occupied by the other ligand nitrogen. [Fe(T1Et4iPrIP)(OTf)2] (1), the precursor for 2, catalyzes the cleavage of 1,4-dihydroxy-2-naphthoate in the presence of O2. Complex 1 is also capable of cleaving the salicylate aromatic ring in the presence of H2O2. The progression of this reaction toward product formation involves an FeIII-phenoxide species.
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Affiliation(s)
- Atanu Banerjee
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, United States
| | - Jia Li
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, United States
| | - Monika A. Molenda
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, United States
| | - William W. Brennessel
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, United States
| | - Ferman A. Chavez
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, United States
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Nguyen LN, Nghiem LD, Oh S. Aerobic biotransformation of the antibiotic ciprofloxacin by Bradyrhizobium sp. isolated from activated sludge. CHEMOSPHERE 2018; 211:600-607. [PMID: 30096573 DOI: 10.1016/j.chemosphere.2018.08.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 07/19/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
Ciprofloxacin (CIP) is an antibiotic that is widely used to treat bacterial infections and is poorly biodegraded during wastewater treatment. In this study, a CIP-degrading bacterial strain (GLC_01) was successfully retrieved from activated sludge by enrichment and isolation. The obtained bacterial strain shares over 99% nucleotide identity of the 16S rRNA gene with Bradyrhizobium spp. Results show that Bradyrhizobium sp. GLC_01 degraded CIP via cometabolism with another carbon substrate following a first-order kinetics degradation reaction. CIP degradation by Bradyrhizobium sp. GLC_01 increased when the concentration of the primary carbon source increased. The biodegradability of the primary carbon source also affected CIP degradation. The use of glucose and sodium acetate (i.e. readily biodegradable), respectively, as a primary carbon source enhanced CIP biotransformation, compared to starch (i.e. relatively slowly biodegradable). CIP degradation decreased with the increase of the initial CIP concentration. Over 70% CIP biotransformation was achieved at 0.05 mg L-1 whereas CIP degradation decreased to 26% at 10 mg L-1. The phylogenetic identification and experimental verification of this CIP-degrading bacterium can lead to a bioengineering approach to manage antibiotics and possibly other persistent organic contaminants during wastewater treatment.
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Affiliation(s)
- Luong N Nguyen
- Center for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia.
| | - Long D Nghiem
- Center for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Seungdae Oh
- Department of Civil Engineering, Kyung Hee University, 1732 Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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Eppinger E, Stolz A. Expansion of the substrate range of the gentisate 1,2-dioxygenase from Corynebacterium glutamicum for the conversion of monohydroxylated benzoates. Protein Eng Des Sel 2016; 30:57-65. [DOI: 10.1093/protein/gzw061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/24/2016] [Accepted: 11/07/2016] [Indexed: 11/13/2022] Open
Abstract
AbstractThe gentisate 1,2-dioxygenases (GDOs) from Corynebacterium glutamicum and various other organisms oxidatively cleave the aromatic nucleus of gentisate (2,5-dihydroxybenzoate), but are not able to convert salicylate (2-hydroxybenzoate). In contrast, the α-proteobacterium Pseudaminobacter salicylatoxidans synthesises an enzyme (‘salicylate dioxygenase’, SDO) which cleaves gentisate, but also (substituted) salicylate(s). Sequence comparisons showed that the SDO belongs to a group of GDOs mainly originating from Gram-positive bacteria which also include the GDO from C. glutamicum ATCC 13032. The combination of sequence comparisons with previously performed structural and mutational analyses of the SDO allowed to identify an amino acid residue (Ala112) which might prevent the oxidation of (substituted) salicylate(s) by the GDO from C. glutamicum. Therefore, the relevant mutation (Ala→Gly) was introduced into the GDO from C. glutamicum. The GDO variant obtained gained the ability to oxidise salicylate and several other monohydroxylated substrates. In order to screen a broader range of enzyme variants a chromogenic assay was developed which allowed the detection of bacterial colonies converting salicylate. The applicability of this test system was proven by screening a set of GDO variants obtained by saturation mutagenesis at different positions. This demonstrated that also GDO variants carrying the mutations Ala112→Ser, Ala112→Ile and Ala112→Asp converted salicylate.
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Kalyoncu S, Heaner DP, Kurt Z, Bethel CM, Ukachukwu CU, Chakravarthy S, Spain JC, Lieberman RL. Enzymatic hydrolysis by transition-metal-dependent nucleophilic aromatic substitution. Nat Chem Biol 2016; 12:1031-1036. [PMID: 27694799 PMCID: PMC5110390 DOI: 10.1038/nchembio.2191] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/29/2016] [Indexed: 12/22/2022]
Abstract
Nitroaromatic compounds are typically toxic and resistant to degradation. Bradyrhizobium species strain JS329 metabolizes 5-nitroanthranilic acid (5NAA), which is a molecule secreted by Streptomyces scabies, the plant pathogen responsible for potato scab. The first biodegradation enzyme is 5NAA-aminohydrolase (5NAA-A), a metalloprotease family member that converts 5NAA to 5-nitrosalicylic acid. We characterized 5NAA-A biochemically and obtained snapshots of its mechanism. 5NAA-A, an octamer that can use several divalent transition metals for catalysis in vitro, employs a nucleophilic aromatic substitution mechanism. Unexpectedly, the metal in 5NAA-A is labile but is readily loaded in the presence of substrate. 5NAA-A is specific for 5NAA and cannot hydrolyze other tested derivatives, which are likewise poor inhibitors. The 5NAA-A structure and mechanism expand our understanding of the chemical ecology of an agriculturally important plant and pathogen, and will inform bioremediation and biocatalytic approaches to mitigate the environmental and ecological impact of nitroanilines and other challenging substrates.
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Affiliation(s)
- Sibel Kalyoncu
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - David P. Heaner
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - Zohre Kurt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA
| | - Casey M. Bethel
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | | | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Advanced Photon Source, Argonne National Labs, Lemont, IL
| | - Jim C. Spain
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, FL
| | - Raquel L. Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA
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Puranik S, Pal RR, More RP, Purohit HJ. Metagenomic approach to characterize soil microbial diversity of Phumdi at Loktak Lake. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 74:2075-2086. [PMID: 27842027 DOI: 10.2166/wst.2016.370] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Loktak, one of the largest freshwater lakes of India, is known for floating islands (Phumdi), being made up of a heterogeneous biomass of vegetation and soil. This ecological site represents an exclusive environmental habitat wherein the rhizospheric microbial community of Phumdi plays a key role in biogeochemical cycling of nutrients. A culture-independent whole genome shotgun sequencing based metagenomic approach was employed to unravel the composition of the microbial community and its corresponding functional potential at this environmental habitat. Proteobacteria (51%) was found to be the most dominant bacterial phylum followed by Acidobacteria (10%), Actinobacteria (9%) and Bacteroidetes (7%). Furthermore, Loktak metagenome data were compared with available metagenomes from four other aquatic habitats, varying from pristine to highly polluted eutrophic habitats. The comparative metagenomics approach aided by statistical analysis revealed that Candidatus Solibacter, Bradyrhizobium, Candidatus Koribacter, Pedosphaera, Methylobacterium, Anaeromyxobacter, Sorangium, Opitutus and Acidobacterium genera are selectively dominant at this habitat. Correspondingly, 12 different functional categories were found to be exclusively prevalent at Phumdi compared to other freshwater habitats. These differential features have been attributed to the unique habitat at Phumdi and correlated to the phenomenon of bioremediation at Loktak Lake.
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Affiliation(s)
- Sampada Puranik
- Environmental Genomics Division, National Environmental Engineering Research Institute, CSIR-NEERI, Nehru Marg, Nagpur 440020, India E-mail: ; ; Equal contributors
| | - Rajesh Ramavadh Pal
- Environmental Genomics Division, National Environmental Engineering Research Institute, CSIR-NEERI, Nehru Marg, Nagpur 440020, India E-mail: ; ; Equal contributors
| | - Ravi Prabhakar More
- Environmental Genomics Division, National Environmental Engineering Research Institute, CSIR-NEERI, Nehru Marg, Nagpur 440020, India E-mail: ;
| | - Hemant J Purohit
- Environmental Genomics Division, National Environmental Engineering Research Institute, CSIR-NEERI, Nehru Marg, Nagpur 440020, India E-mail: ;
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Implications of Limited Thermophilicity of Nitrite Reduction for Control of Sulfide Production in Oil Reservoirs. Appl Environ Microbiol 2016; 82:4190-4199. [PMID: 27208132 DOI: 10.1128/aem.00599-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 04/28/2016] [Indexed: 01/15/2023] Open
Abstract
UNLABELLED Nitrate reduction to nitrite in oil fields appears to be more thermophilic than the subsequent reduction of nitrite. Concentrated microbial consortia from oil fields reduced both nitrate and nitrite at 40 and 45°C but only nitrate at and above 50°C. The abundance of the nirS gene correlated with mesophilic nitrite reduction activity. Thauera and Pseudomonas were the dominant mesophilic nitrate-reducing bacteria (mNRB), whereas Petrobacter and Geobacillus were the dominant thermophilic NRB (tNRB) in these consortia. The mNRB Thauera sp. strain TK001, isolated in this study, reduced nitrate and nitrite at 40 and 45°C but not at 50°C, whereas the tNRB Petrobacter sp. strain TK002 and Geobacillus sp. strain TK003 reduced nitrate to nitrite but did not reduce nitrite further from 50 to 70°C. Testing of 12 deposited pure cultures of tNRB with 4 electron donors indicated reduction of nitrate in 40 of 48 and reduction of nitrite in only 9 of 48 incubations. Nitrate is injected into high-temperature oil fields to prevent sulfide formation (souring) by sulfate-reducing bacteria (SRB), which are strongly inhibited by nitrite. Injection of cold seawater to produce oil creates mesothermic zones. Our results suggest that preventing the temperature of these zones from dropping below 50°C will limit the reduction of nitrite, allowing more effective souring control. IMPORTANCE Nitrite can accumulate at temperatures of 50 to 70°C, because nitrate reduction extends to higher temperatures than the subsequent reduction of nitrite. This is important for understanding the fundamentals of thermophilicity and for the control of souring in oil fields catalyzed by SRB, which are strongly inhibited by nitrite.
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Arora PK. Bacterial degradation of monocyclic aromatic amines. Front Microbiol 2015; 6:820. [PMID: 26347719 PMCID: PMC4539516 DOI: 10.3389/fmicb.2015.00820] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/27/2015] [Indexed: 01/13/2023] Open
Abstract
Aromatic amines are an important group of industrial chemicals, which are widely used for manufacturing of dyes, pesticides, drugs, pigments, and other industrial products. These compounds have been considered highly toxic to human beings due to their carcinogenic nature. Three groups of aromatic amines have been recognized: monocyclic, polycyclic, and heterocyclic aromatic amines. Bacterial degradation of several monocyclic aromatic amines has been studied in a variety of bacteria, which utilizes monocyclic aromatic amines as their sole source of carbon and energy. Several degradation pathways have been proposed and the related enzymes and genes have also been characterized. Many reviews have been reviewed toxicity of monocyclic aromatic amines; however, there is lack of review on biodegradation of monocyclic aromatic amines. The aim of this review is to summarize bacterial degradation of monocyclic aromatic amines. This review will increase our current understanding of biochemical and molecular basis of bacterial degradation of monocyclic aromatic amines.
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Affiliation(s)
- Pankaj K. Arora
- School of Biotechnology, Yeungnam UniversityGyeongsan, South Korea
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Eppinger E, Ferraroni M, Bürger S, Steimer L, Peng G, Briganti F, Stolz A. Function of different amino acid residues in the reaction mechanism of gentisate 1,2-dioxygenases deduced from the analysis of mutants of the salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1425-37. [PMID: 26093111 DOI: 10.1016/j.bbapap.2015.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/28/2015] [Accepted: 06/15/2015] [Indexed: 11/24/2022]
Abstract
The genome of the α-proteobacterium Pseudaminobacter salicylatoxidans codes for a ferrous iron containing ring-fission dioxygenase which catalyzes the 1,2-cleavage of (substituted) salicylate(s), gentisate (2,5-dihydroxybenzoate), and 1-hydroxy-2-naphthoate. Sequence alignments suggested that the "salicylate 1,2-dioxygenase" (SDO) from this strain is homologous to gentisate 1,2-dioxygenases found in bacteria, archaea and fungi. In the present study the catalytic mechanism of the SDO and gentisate 1,2-dioxygenases in general was analyzed based on sequence alignments, mutational and previously performed crystallographic studies and mechanistic comparisons with "extradiol- dioxygenases" which cleave aromatic nuclei in the 2,3-position. Different highly conserved amino acid residues that were supposed to take part in binding and activation of the organic substrates were modified in the SDO by site-specific mutagenesis and the enzyme variants subsequently analyzed for the conversion of salicylate, gentisate and 1-hydroxy-2-naphthoate. The analysis of enzyme variants which carried exchanges in the positions Arg83, Trp104, Gly106, Gln108, Arg127, His162 and Asp174 demonstrated that Arg83 and Arg127 were indispensable for enzymatic activity. In contrast, residual activities were found for variants carrying mutations in the residues Trp104, Gly106, Gln108, His162, and Asp174 and some of these mutants still could oxidize gentisate, but lost the ability to convert salicylate. The results were used to suggest a general reaction mechanism for gentisate-1,2-dioxygenases and to assign to certain amino acid residues in the active site specific functions in the cleavage of (substituted) salicylate(s).
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Affiliation(s)
- Erik Eppinger
- Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany
| | - Marta Ferraroni
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentin, Italy
| | - Sibylle Bürger
- Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany
| | - Lenz Steimer
- Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany
| | - Grace Peng
- Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany
| | - Fabrizio Briganti
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentin, Italy
| | - Andreas Stolz
- Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany.
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Aerobic biodegradation of 2,4-Dinitroanisole by Nocardioides sp. strain JS1661. Appl Environ Microbiol 2014; 80:7725-31. [PMID: 25281383 DOI: 10.1128/aem.02752-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2,4-Dinitroanisole (DNAN) is an insensitive munition ingredient used in explosive formulations as a replacement for 2,4,6-trinitrotoluene (TNT). Little is known about the environmental behavior of DNAN. There are reports of microbial transformation to dead-end products, but no bacteria with complete biodegradation capability have been reported. Nocardioides sp. strain JS1661 was isolated from activated sludge based on its ability to grow on DNAN as the sole source of carbon and energy. Enzyme assays indicated that the first reaction involves hydrolytic release of methanol to form 2,4-dinitrophenol (2,4-DNP). Growth yield and enzyme assays indicated that 2,4-DNP underwent subsequent degradation by a previously established pathway involving formation of a hydride-Meisenheimer complex and release of nitrite. Identification of the genes encoding the key enzymes suggested recent evolution of the pathway by recruitment of a novel hydrolase to extend the well-characterized 2,4-DNP pathway.
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Khan F, Vyas B, Pal D, Cameotra SS. Aerobic degradation of N-methyl-4-nitroaniline (MNA) by Pseudomonas sp. strain FK357 isolated from soil. PLoS One 2013; 8:e75046. [PMID: 24116023 PMCID: PMC3792944 DOI: 10.1371/journal.pone.0075046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 08/08/2013] [Indexed: 11/18/2022] Open
Abstract
N-Methyl-4-nitroaniline (MNA) is used as an additive to lower the melting temperature of energetic materials in the synthesis of insensitive explosives. Although the biotransformation of MNA under anaerobic condition has been reported, its aerobic microbial degradation has not been documented yet. A soil microcosms study showed the efficient aerobic degradation of MNA by the inhabitant soil microorganisms. An aerobic bacterium, Pseudomonas sp. strain FK357, able to utilize MNA as the sole carbon, nitrogen, and energy source, was isolated from soil microcosms. HPLC and GC-MS analysis of the samples obtained from growth and resting cell studies showed the formation of 4-nitroaniline (4-NA), 4-aminophenol (4-AP), and 1, 2, 4-benzenetriol (BT) as major metabolic intermediates in the MNA degradation pathway. Enzymatic assay carried out on cell-free lysates of MNA grown cells confirmed N-demethylation reaction is the first step of MNA degradation with the formation of 4-NA and formaldehyde products. Flavin-dependent transformation of 4-NA to 4-AP in cell extracts demonstrated that the second step of MNA degradation is a monooxygenation. Furthermore, conversion of 4-AP to BT by MNA grown cells indicates the involvement of oxidative deamination (release of NH2 substituent) reaction in third step of MNA degradation. Subsequent degradation of BT occurs by the action of benzenetriol 1, 2-dioxygenase as reported for the degradation of 4-nitrophenol. This is the first report on aerobic degradation of MNA by a single bacterium along with elucidation of metabolic pathway.
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Affiliation(s)
- Fazlurrahman Khan
- Environmental Biotechnology and Microbial Biochemistry Laboratory, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh, India
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Khan F, Pal D, Vikram S, Cameotra SS. Metabolism of 2-chloro-4-nitroaniline via novel aerobic degradation pathway by Rhodococcus sp. strain MB-P1. PLoS One 2013; 8:e62178. [PMID: 23614030 PMCID: PMC3629101 DOI: 10.1371/journal.pone.0062178] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 03/18/2013] [Indexed: 11/21/2022] Open
Abstract
2-chloro-4-nitroaniline (2-C-4-NA) is used as an intermediate in the manufacture of dyes, pharmaceuticals, corrosion inhibitor and also used in the synthesis of niclosamide, a molluscicide. It is marked as a black-listed substance due to its poor biodegradability. We report biodegradation of 2-C-4-NA and its pathway characterization by Rhodococcus sp. strain MB-P1 under aerobic conditions. The strain MB-P1 utilizes 2-C-4-NA as the sole carbon, nitrogen, and energy source. In the growth medium, the degradation of 2-C-4-NA occurs with the release of nitrite ions, chloride ions, and ammonia. During the resting cell studies, the 2-C-4-NA-induced cells of strain MB-P1 transformed 2-C-4-NA stoichiometrically to 4-amino-3-chlorophenol (4-A-3-CP), which subsequently gets transformed to 6-chlorohydroxyquinol (6-CHQ) metabolite. Enzyme assays by cell-free lysates prepared from 2-C-4-NA-induced MB-P1 cells, demonstrated that the first enzyme in the 2-C-4-NA degradation pathway is a flavin-dependent monooxygenase that catalyzes the stoichiometric removal of nitro group and production of 4-A-3-CP. Oxygen uptake studies on 4-A-3-CP and related anilines by 2-C-4-NA-induced MB-P1 cells demonstrated the involvement of aniline dioxygenase in the second step of 2-C-4-NA degradation. This is the first report showing 2-C-4-NA degradation and elucidation of corresponding metabolic pathway by an aerobic bacterium.
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Affiliation(s)
- Fazlurrahman Khan
- Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Deepika Pal
- Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Surendra Vikram
- Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Swaranjit Singh Cameotra
- Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
- * E-mail:
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Ferraroni M, Matera I, Bürger S, Reichert S, Steimer L, Scozzafava A, Stolz A, Briganti F. The salicylate 1,2-dioxygenase as a model for a conventional gentisate 1,2-dioxygenase: crystal structures of the G106A mutant and its adducts with gentisate and salicylate. FEBS J 2013; 280:1643-52. [DOI: 10.1111/febs.12173] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/02/2013] [Accepted: 01/30/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Marta Ferraroni
- Dipartimento di Chimica ‘Ugo Schiff’; Università di Firenze; Sesto Fiorentino; Italy
| | - Irene Matera
- Dipartimento di Chimica ‘Ugo Schiff’; Università di Firenze; Sesto Fiorentino; Italy
| | - Sibylle Bürger
- Institut für Mikrobiologie; Universität Stuttgart; Stuttgart; Germany
| | - Sabrina Reichert
- Institut für Mikrobiologie; Universität Stuttgart; Stuttgart; Germany
| | - Lenz Steimer
- Institut für Mikrobiologie; Universität Stuttgart; Stuttgart; Germany
| | - Andrea Scozzafava
- Dipartimento di Chimica ‘Ugo Schiff’; Università di Firenze; Sesto Fiorentino; Italy
| | - Andreas Stolz
- Institut für Mikrobiologie; Universität Stuttgart; Stuttgart; Germany
| | - Fabrizio Briganti
- Dipartimento di Chimica ‘Ugo Schiff’; Università di Firenze; Sesto Fiorentino; Italy
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Isolation of a gene responsible for the oxidation of trans-anethole to para-anisaldehyde by Pseudomonas putida JYR-1 and its expression in Escherichia coli. Appl Environ Microbiol 2012; 78:5238-46. [PMID: 22610435 DOI: 10.1128/aem.00781-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A plasmid, pTA163, in Escherichia coli contained an approximately 34-kb gene fragment from Pseudomonas putida JYR-1 that included the genes responsible for the metabolism of trans-anethole to protocatechuic acid. Three Tn5-disrupted open reading frame 10 (ORF 10) mutants of plasmid pTA163 lost their abilities to catalyze trans-anethole. Heterologously expressed ORF 10 (1,047 nucleotides [nt]) under a T7 promoter in E. coli catalyzed oxidative cleavage of a propenyl group of trans-anethole to an aldehyde group, resulting in the production of para-anisaldehyde, and this gene was designated tao (trans-anethole oxygenase). The deduced amino acid sequence of TAO had the highest identity (34%) to a hypothetical protein of Agrobacterium vitis S4 and likely contained a flavin-binding site. Preferred incorporation of an oxygen molecule from water into p-anisaldehyde using (18)O-labeling experiments indicated stereo preference of TAO for hydrolysis of the epoxide group. Interestingly, unlike the narrow substrate range of isoeugenol monooxygenase from Pseudomonas putida IE27 and Pseudomonas nitroreducens Jin1, TAO from P. putida JYR-1 catalyzed isoeugenol, O-methyl isoeugenol, and isosafrole, all of which contain the 2-propenyl functional group on the aromatic ring structure. Addition of NAD(P)H to the ultrafiltered cell extracts of E. coli (pTA163) increased the activity of TAO. Due to the relaxed substrate range of TAO, it may be utilized for the production of various fragrance compounds from plant phenylpropanoids in the future.
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Ferraroni M, Matera I, Steimer L, Bürger S, Scozzafava A, Stolz A, Briganti F. Crystal structures of salicylate 1,2-dioxygenase-substrates adducts: A step towards the comprehension of the structural basis for substrate selection in class III ring cleaving dioxygenases. J Struct Biol 2012; 177:431-8. [DOI: 10.1016/j.jsb.2011.11.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 11/22/2011] [Accepted: 11/23/2011] [Indexed: 10/14/2022]
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Abstract
Ring-cleaving dioxygenases catalyze key reactions in the aerobic microbial degradation of aromatic compounds. Many pathways converge to catecholic intermediates, which are subject to ortho or meta cleavage by intradiol or extradiol dioxygenases, respectively. However, a number of degradation pathways proceed via noncatecholic hydroxy-substituted aromatic carboxylic acids like gentisate, salicylate, 1-hydroxy-2-naphthoate, or aminohydroxybenzoates. The ring-cleaving dioxygenases active toward these compounds belong to the cupin superfamily, which is characterized by a six-stranded β-barrel fold and conserved amino acid motifs that provide the 3His or 2- or 3His-1Glu ligand environment of a divalent metal ion. Most cupin-type ring cleavage dioxygenases use an Fe(II) center for catalysis, and the proposed mechanism is very similar to that of the canonical (type I) extradiol dioxygenases. The metal ion is presumed to act as an electron conduit for single electron transfer from the metal-bound substrate anion to O(2), resulting in activation of both substrates to radical species. The family of cupin-type dioxygenases also involves quercetinase (flavonol 2,4-dioxygenase), which opens up two C-C bonds of the heterocyclic ring of quercetin, a wide-spread plant flavonol. Remarkably, bacterial quercetinases are capable of using different divalent metal ions for catalysis, suggesting that the redox properties of the metal are relatively unimportant for the catalytic reaction. The major role of the active-site metal ion could be to correctly position the substrate and to stabilize transition states and intermediates rather than to mediate electron transfer. The tentative hypothesis that quercetinase catalysis involves direct electron transfer from metal-bound flavonolate to O(2) is supported by model chemistry.
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Molecular and biochemical characterization of the 5-nitroanthranilic acid degradation pathway in Bradyrhizobium sp. strain JS329. J Bacteriol 2011; 193:3057-63. [PMID: 21498645 DOI: 10.1128/jb.01188-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biodegradation pathways of synthetic nitroaromatic compounds and anilines are well documented, but little is known about those of nitroanilines. We previously reported that the initial step in 5-nitroanthranilic acid (5NAA) degradation by Bradyrhizobium sp. strain JS329 is a hydrolytic deamination to form 5-nitrosalicylic acid (5NSA), followed by ring fission catalyzed by 5NSA dioxygenase. The mechanism of release of the nitro group was unknown. In this study, we subcloned, sequenced, and expressed the genes encoding 5NAA deaminase (5NAA aminohydrolase, NaaA), 5NSA dioxygenase (NaaB) and lactonase (NaaC), the key genes responsible for 5NAA degradation. Sequence analysis and enzyme characterization revealed that NaaA is a hydrolytic metalloenzyme with a narrow substrate range. The nitro group is spontaneously eliminated as nitrite concomitant with the formation of a lactone from the ring fission product of 5NSA dioxygenation. The elimination of the nitro group during lactone formation is a previously unreported mechanism for denitration of nitro aliphatic compounds.
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Qu Y, Spain JC. Catabolic pathway for 2-nitroimidazole involves a novel nitrohydrolase that also confers drug resistance. Environ Microbiol 2011; 13:1010-7. [DOI: 10.1111/j.1462-2920.2010.02406.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Nitroaromatic compounds are relatively rare in nature and have been introduced into the environment mainly by human activities. This important class of industrial chemicals is widely used in the synthesis of many diverse products, including dyes, polymers, pesticides, and explosives. Unfortunately, their extensive use has led to environmental contamination of soil and groundwater. The nitro group, which provides chemical and functional diversity in these molecules, also contributes to the recalcitrance of these compounds to biodegradation. The electron-withdrawing nature of the nitro group, in concert with the stability of the benzene ring, makes nitroaromatic compounds resistant to oxidative degradation. Recalcitrance is further compounded by their acute toxicity, mutagenicity, and easy reduction into carcinogenic aromatic amines. Nitroaromatic compounds are hazardous to human health and are registered on the U.S. Environmental Protection Agency's list of priority pollutants for environmental remediation. Although the majority of these compounds are synthetic in nature, microorganisms in contaminated environments have rapidly adapted to their presence by evolving new biodegradation pathways that take advantage of them as sources of carbon, nitrogen, and energy. This review provides an overview of the synthesis of both man-made and biogenic nitroaromatic compounds, the bacteria that have been identified to grow on and completely mineralize nitroaromatic compounds, and the pathways that are present in these strains. The possible evolutionary origins of the newly evolved pathways are also discussed.
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Affiliation(s)
- Kou-San Ju
- Department of Microbiology, University of California, Davis, California 95616
| | - Rebecca E. Parales
- Department of Microbiology, University of California, Davis, California 95616
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