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Liu Y, Yamamoto T, Kohaya N, Yamamoto K, Okano K, Sumiyoshi T, Hasegawa Y, Lau PCK, Iwaki H. Cloning of two gene clusters involved in the catabolism of 2,4-dinitrophenol by Paraburkholderia sp. strain KU-46 and characterization of the initial DnpAB enzymes and a two-component monooxygenases DnpC1C2. J Biosci Bioeng 2023; 136:223-231. [PMID: 37344279 DOI: 10.1016/j.jbiosc.2023.05.013] [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: 03/14/2023] [Revised: 05/23/2023] [Accepted: 05/31/2023] [Indexed: 06/23/2023]
Abstract
Little is currently known about the metabolism of the industrial pollutant 2,4-dinitrophenol (DNP), particularly among gram-negative bacteria. In this study, we identified two non-contiguous genetic loci spanning 22 kb of Paraburkholderia (formerly Burkholderia) sp. strain KU-46. Additionally, we characterized four key initial genes (dnpA, dnpB, and dnpC1C2) responsible for DNP degradation, providing molecular and biochemical evidence for the degradation of DNP via the formation of 4-nitrophenol (NP), a pathway that is unique among DNP utilizing bacteria. Reverse transcription polymerase chain reaction (PCR) analysis indicated that dnpA, which encodes the initial hydride transferase, and dnpB which encodes a nitrite-eliminating enzyme, were induced by DNP and organized in an operon. Moreover, we purified DnpA and DnpB from recombinant Escherichia coli to demonstrate their effect on the transformation of DNP to NP through the formation of a hydride-Meisenheimer complex of DNP, designated as H--DNP. The function of DnpB appears new since all homologs of the DnpB sequences in the protein database are annotated as putative nitrate ABC transporter substrate-binding proteins. The gene cluster responsible for the degradation of DNP after NP formation was designated dnpC1C2DXFER, and DnpC1 and DnpC2 were functionally characterized as the FAD reductase and oxygenase components of the two-component DNP monooxygenase, respectively. By elucidating the hqdA1A2BCD gene cluster, we are now able to delineate the final degradation pathway of hydroquinone to β-ketoadipate before it enters the tricarboxylic acid cycle.
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Affiliation(s)
- Yaxuan Liu
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Taisei Yamamoto
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Nozomi Kohaya
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Kota Yamamoto
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Kenji Okano
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Takaaki Sumiyoshi
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Yoshie Hasegawa
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Peter C K Lau
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montréal, Quebec H3A 2B4, Canada
| | - Hiroaki Iwaki
- Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan.
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2
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Kumari S, Das S. Bacterial enzymatic degradation of recalcitrant organic pollutants: catabolic pathways and genetic regulations. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:79676-79705. [PMID: 37330441 DOI: 10.1007/s11356-023-28130-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/01/2023] [Indexed: 06/19/2023]
Abstract
Contamination of soil and natural water bodies driven by increased organic pollutants remains a universal concern. Naturally, organic pollutants contain carcinogenic and toxic properties threatening all known life forms. The conventional physical and chemical methods employed to remove these organic pollutants ironically produce toxic and non-ecofriendly end-products. Whereas microbial-based degradation of organic pollutants provides an edge, they are usually cost-effective and take an eco-friendly approach towards remediation. Bacterial species, including Pseudomonas, Comamonas, Burkholderia, and Xanthomonas, have the unique genetic makeup to metabolically degrade toxic pollutants, conferring their survival in toxic environments. Several catabolic genes, such as alkB, xylE, catA, and nahAc, that encode enzymes and allow bacteria to degrade organic pollutants have been identified, characterized, and even engineered for better efficacy. Aerobic and anaerobic processes are followed by bacteria to metabolize aliphatic saturated and unsaturated hydrocarbons such as alkanes, cycloalkanes, aldehydes, and ethers. Bacteria use a variety of degrading pathways, including catechol, protocatechuate, gentisate, benzoate, and biphenyl, to remove aromatic organic contaminants such as polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pesticides from the environment. A better understanding of the principle, mechanisms, and genetics would be beneficial for improving the metabolic efficacy of bacteria to such ends. With a focus on comprehending the mechanisms involved in various catabolic pathways and the genetics of the biotransformation of these xenobiotic compounds, the present review offers insight into the various sources and types of known organic pollutants and their toxic effects on health and the environment.
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Affiliation(s)
- Swetambari Kumari
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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3
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Zhang ST, Li T, Deng SK, Spain JC, Zhou NY. A cytochrome P450 system initiates 4-nitroanisole degradation in Rhodococcus sp. strain JS3073. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131886. [PMID: 37348368 DOI: 10.1016/j.jhazmat.2023.131886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/24/2023]
Abstract
Nitroanisoles are used widely as synthetic intermediates and explosives. Although bacteria have been reported to degrade 4-nitroanisole (4NA) under aerobic conditions, the key enzymes and the catalytic mechanism have remained elusive. Rhodococcus sp. strain JS3073 was isolated for its ability to grow on 4NA as the sole carbon and energy source. In this study, whole cell biotransformation experiments indicated that 4NA degradation is initiated by O-demethylation to form 4-nitrophenol (PNP), which undergoes subsequent degradation by a previously established pathway involving formation of 1,2,4-benzenetriol and release of nitrite. Based on comparative transcriptomics and heterologous expression, a novel three-component cytochrome P450 system encoded by pnaABC initiates the O-demethylation of 4NA to yield formaldehyde and PNP. The pnaABC genes encode a phthalate dioxygenase type reductase (PnaA), a cytochrome P450 monooxygenase (PnaB), and an EthD family protein (PnaC) with putative function similar to ferredoxins. This unusual P450 system also has a broad substrate specificity for nitroanisole derivatives. Sequence analysis of PnaAB revealed high identity with multiple self-sufficient P450s of the CYP116B subfamily. The findings revealed the molecular basis of the catabolic pathway for 4NA initiated by an unusual O-demethylase PnaABC and extends the understanding of the diversity among P450s and their electron transport chains.
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Affiliation(s)
- Shu-Ting Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shi-Kai Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jim C Spain
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, 11000 University Parkway, Pensacola, FL 32514-5751, USA
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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4
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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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5
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Pimviriyakul P, Chaiyen P. Formation and stabilization of C4a-hydroperoxy-FAD by the Arg/Asn pair in HadA monooxygenase. FEBS J 2023; 290:176-195. [PMID: 35942637 DOI: 10.1111/febs.16591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/25/2022] [Accepted: 08/08/2022] [Indexed: 01/14/2023]
Abstract
HadA monooxygenase catalyses the detoxification of halogenated phenols and nitrophenols via dehalogenation and denitration respectively. C4a-hydroperoxy-FAD is a key reactive intermediate wherein its formation, protonation and stabilization reflect enzyme efficiency. Herein, transient kinetics, site-directed mutagenesis and pH-dependent behaviours of HadA reaction were employed to identify key features stabilizing C4a-adducts in HadA. The formation of C4a-hydroperoxy-FAD is pH independent, whereas its decay and protonation of distal oxygen are associated with pKa values of 8.5 and 8.4 respectively. These values are correlated with product formation within a pH range of 7.6-9.1, indicating the importance of adduct stabilization to enzymatic efficiency. We identified Arg101 as a key residue for reduced FAD (FADH- ) binding and C4a-hydroperoxy-FAD formation due to the loss of these abilities as well as enzyme activity in HadAR101A and HadAR101Q . Mutations of the neighbouring Asn447 do not affect the rate of C4a-hydroperoxy-FAD formation; however, they impair FADH- binding. The disruption of Arg101/Asn447 hydrogen bond networking in HadAN447A increases the pKa value of C4a-hydroperoxy-FAD decay to 9.5; however, this pKa was not altered in HadAN447D (pKa of 8.5). Thus, Arg101/Asn447 pair should provide important interactions for FADH- binding and maintain the pKa associated with H2 O2 elimination from C4a-hydroperoxy-FAD in HadA. In the presence of substrate, the formation of C4a-hydroxy-FAD at the hydroxylation step is pH insensitive, and it dehydrates to form the oxidized FAD with pKa of 7.9. This structural feature might help elucidate how the reactive intermediate was stabilized in other flavin-dependent monooxygenases.
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Affiliation(s)
- Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
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Hu C, Yang C, Wang X, Wang X, Zhen S, Zhan L, Huang C, Li Y. Rapid and facile synthesis of Au nanoparticle-decorated porous MOFs for the efficient reduction of 4‑nitrophenol. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.121801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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7
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Yu Y, Liu T, Liu L, Chen Y, Tang J, Peng W, Tan H. Application of the mushroom volatile 1-octen-3-ol to suppress a morel disease caused by Paecilomyces penicillatus. Appl Microbiol Biotechnol 2022; 106:4787-4799. [PMID: 35759038 DOI: 10.1007/s00253-022-12038-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/13/2022] [Accepted: 06/16/2022] [Indexed: 11/02/2022]
Abstract
Morels (Morchella spp.) are of great economic and scientific value. Paecilomyces penicillatus can cause white mold disease (WMD) widely emerging on morel ascocarps and is also a potential factor causing morel fructification failure. 1-octen-3-ol is a mushroom volatile compound with broad-spectrum antimicrobial activities. This study aimed to control the morel disease caused by P. penicillatus through suppressing P. penicillatus in the soil cultivated with Morchella sextelata using 1-octen-3-ol. Safe concentration of 1-octen-3-ol was estimated by comparing its inhibitory effect against P. penicillatus and M. sextelata, respectively, with mycelium-growth experiments on agar plates. The results showed that M. sextelata possesses a higher tolerance to 1-octen-3-ol than P. penicillatus with a 1-octen-3-ol concentration between 0 and 200 µL/L. Based on that, a sandy soil was supplemented with low (50 µL/L) or high concentration (200 µL/L) of 1-octen-3-ol. The effects of 1-octen-3-ol on soil microbial communities, WMD incidence, and morel yield were investigated. Compared to the non-supplemented control group, the incidence of WMD and the proportion of Paecilomyces in the soils of low- and high-concentration treatment groups were significantly decreased, corresponding to a significant increase in morel ascocarp yield. It suggests that 1-octen-3-ol effectively suppressed P. penicillatus in the soil, thereby reducing the severity of WMD and improving the morel yield. The diversity of soil bacterial communities was also altered by 1-octen-3-ol supplement. The proportion of Rhodococcus spp. in the soil was positively correlated with the 1-octen-3-ol concentration and ascocarp yield, suggesting its potential role in improving morel yield. KEY POINTS: • A novel method for morel disease suppression was proposed. • Paecilomyces in soil affects white mold disease and fructification yield of morel. • 1-Octen-3-ol suppresses Paecilomyces and alters bacterial community in soil.
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Affiliation(s)
- Yang Yu
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Ministry of Agriculture and Rural Affairs, National Observing and Experimental Station of Agricultural Microbiology in Chengdu, Chengdu, China
| | - Tianhai Liu
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Ministry of Agriculture and Rural Affairs, National Observing and Experimental Station of Agricultural Microbiology in Chengdu, Chengdu, China
| | - Lixu Liu
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Ministry of Agriculture and Rural Affairs, National Observing and Experimental Station of Agricultural Microbiology in Chengdu, Chengdu, China
| | - Ying Chen
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Ministry of Agriculture and Rural Affairs, National Observing and Experimental Station of Agricultural Microbiology in Chengdu, Chengdu, China
| | - Jie Tang
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Ministry of Agriculture and Rural Affairs, National Observing and Experimental Station of Agricultural Microbiology in Chengdu, Chengdu, China
| | - Weihong Peng
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Ministry of Agriculture and Rural Affairs, National Observing and Experimental Station of Agricultural Microbiology in Chengdu, Chengdu, China
| | - Hao Tan
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, China. .,Ministry of Agriculture and Rural Affairs, National Observing and Experimental Station of Agricultural Microbiology in Chengdu, Chengdu, China. .,Drylands Salinization Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.
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Pimviriyakul P, Pholert P, Somjitt S, Choowongkomon K. Role of conserved arginine in
HadA
monooxygenase for
4‐nitrophenol
and
4‐chlorophenol
detoxification. Proteins 2022; 90:1291-1302. [DOI: 10.1002/prot.26312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/18/2022]
Affiliation(s)
- Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science Kasetsart University Chatuchak Bangkok Thailand
| | - Patipan Pholert
- Department of Biochemistry, Faculty of Science Kasetsart University Chatuchak Bangkok Thailand
| | - Supamas Somjitt
- Department of Biochemistry, Faculty of Science Kasetsart University Chatuchak Bangkok Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science Kasetsart University Chatuchak Bangkok Thailand
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Characterization of the 2,6-Dimethylphenol Monooxygenase MpdAB and Evaluation of Its Potential in Vitamin E Precursor Synthesis. Appl Environ Microbiol 2022; 88:e0011022. [PMID: 35380460 DOI: 10.1128/aem.00110-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2,6-Dimethylphenol (2,6-DMP) is a widely used chemical intermediate whose residue has been frequently detected in the environment, posing a threat to some aquatic organisms. Microbial degradation is an effective method to eliminate 2,6-DMP in nature. However, the genetic and biochemical mechanisms of 2,6-DMP metabolism remain unknown. Mycobacterium neoaurum B5-4 is a 2,6-DMP-degrading bacterium isolated in our previous study. Here, a 2,6-DMP degradation-deficient mutant of strain B5-4 was screened. Comparative genomic, transcriptomic, gene disruption, and genetic complementation data indicated that mpdA and mpdB are responsible for the initial step of 2,6-DMP degradation in M. neoaurum B5-4. MpdAB was predicted to be a two-component flavin-dependent monooxygenase system, which shows 32% and 36% identities with HsaAB from Mycobacterium tuberculosis CDC1551. The transcription of mpdA and mpdB was substantially increased upon exposure to 2,6-DMP. Nuclear magnetic resonance analysis showed that purified 6×His-MpdA and 6×His-MpdB hydroxylated 2,6-DMP and 2,3,6-trimethylphenol (2,3,6-TMP) at the para-position using NADH and flavin adenine dinucleotide (FAD) as cofactors. The apparent Km values of MpdAB for 2,6-DMP and 2,3,6-TMP were 0.12 ± 0.01 and 0.17 ± 0.01 mM, respectively, and the corresponding kcat/Km values were 4.02 and 2.84 s-1 mM-1, respectively. Since para-hydroxylated 2,3,6-TMP is a major precursor for vitamin E synthesis, the potential of MpdAB in vitamin E synthesis was preliminarily evaluated using whole-cell catalysis. Low expression levels of MpdA and 2,3,6-TMP cytotoxicity limited the efficiency of whole-cell catalysis. Together, this study reveals the genetic and biochemical basis for the initial step of 2,6-DMP biodegradation and provides candidate enzymes for vitamin E synthesis. IMPORTANCE Although the microbial degradation of the six isomers of dimethylphenol has been extensively studied, the genetic and biochemical mechanisms of 2,6-DMP degradation remain unclear. This study identified the genes responsible for the initial step in the 2,6-DMP catabolic pathway in M. neoaurum B5-4. Moreover, MpdAB also catalyzed the transformation of 2,3,6-TMP to 2,3,5-trimethylhydroquinone (2,3,5-TMHQ), a crucial step in vitamin E synthesis. Overall, this study provides candidate enzymes for both the bioremediation of 2,6-DMP contamination and the development of a green method to synthesize vitamin E.
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Min J, Fang S, Peng J, Lv X, Xu L, Li Y, Hu X. Microbial detoxification of 2,4,6-tribromophenol via a novel process with consecutive oxidative and hydrolytic debromination: Biochemical, genetic and evolutionary characterization. ENVIRONMENTAL RESEARCH 2022; 205:112494. [PMID: 34890595 DOI: 10.1016/j.envres.2021.112494] [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: 08/23/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 06/13/2023]
Abstract
As a typical brominated flame retardants (BFRs), 2,4,6-tribromophenol (TBP) has serious hazard to the environmental health and its environmental fate has attracted considerable attention. Dehalogenation reaction plays key role in microbial TBP degradation and detoxification. So far, several halophenols-degrading enzymes have been reported to transform their substrate by oxidative dehalogenation; however, the molecular and biochemistry characterization of microbial hydrolytic dehalogenation is limited. In this study, Cupriavidus sp. CNP-8 with high TBP degradation activity was found to degrade TBP via an obviously differnet pathway as compared to other reported TBP-degraders. The transcription of hnp genes were significantly upregulated with TBP stimulation, indicating their involvment in TBP degradation. Enzymatic assays with 18O-labeling experiments showed that HnpAB, a two-component FAD-dependent monooxygenase, transformed TBP via consecutive oxidative and hydrolytic debromination reactions with the formation of 6-bromo-1,2,4-benzenetriol (BBT) as the ring-cleavage substrate. The function of the BBT ring-cleavage enzyme (HnpC) was also characterized both in vitro and in vivo. This finding provides new molecular mechanism of microbial detoxification of TBP and novel information of the environmental fate of this BFRs. Furthermore, to investigate the frequency of this novel dehalogenation mechanism in microbes, we also analyzed the distribution as well as the genetic structure of the hnpABC cluster by comparative genomics. Although hnpA homolog is distributed in several bacterial genera including Cupriavidus, Paraburkholderia, Variovorax and Streptomyces, the complete hnpABC cluster is only retrieved from Cupriavidus and strictly conservative in the genomes. This indicated that Cupriavidus have unique evolutionary pattern in acquiring the hnpABC to degrade TBP and its analogs, enhancing our understanding of the microbial adaptive evolution in halophenols-contaminated environment.
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Affiliation(s)
- Jun Min
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Suyun Fang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Jian Peng
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Xin Lv
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Lingxue Xu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Yan Li
- College of Life Science of Yantai University, Yantai, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
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11
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Single-Component and Two-Component para-Nitrophenol Monooxygenases: Structural Basis for Their Catalytic Difference. Appl Environ Microbiol 2021; 87:e0117121. [PMID: 34469195 DOI: 10.1128/aem.01171-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
para-Nitrophenol (PNP) is a hydrolytic product of organophosphate insecticides, such as parathion and methylparathion, in soil. Aerobic microbial degradation of PNP has been classically shown to proceed via the "hydroquinone (HQ) pathway" in Gram-negative degraders, whereas it proceeds via the "benzenetriol (BT) pathway" in Gram-positive ones. The "HQ pathway" is initiated by a single-component PNP 4-monooxygenase and the "BT pathway" by a two-component PNP 2-monooxygenase. Their regioselectivity intrigued us enough to investigate their catalytic difference through structural study. PnpA1 is the oxygenase component of the two-component PNP 2-monooxygenase from Gram-positive Rhodococcus imtechensis strain RKJ300. It also catalyzes the hydroxylation of 4-nitrocatechol (4NC) and 2-chloro-4-nitrophenol (2C4NP). However, the mechanisms are unknown. Here, PnpA1 was structurally determined to be a member of the group D flavin-dependent monooxygenases with an acyl coenzyme A (acyl-CoA) dehydrogenase fold. The crystal structure and site-directed mutagenesis underlined the direct involvement of Arg100 and His293 in catalysis. The bulky side chain of Val292 was proposed to push the substrate toward flavin adenine dinucleotide (FAD), hence positioning the substrate properly. An N450A variant was found with improved activity for 4NC and 2C4NP-probably because of the reduced steric hindrance. PnpA1 shows an obvious difference in substrate selectivity with its close homologues TcpA and TftD, which may be caused by the unique Thr296 and a different conformation in the loop from positions 449 to 454 (loop 449-454). Above all, our study allows structural comparison between the two types of PNP monooxygenases. An explanation that accounts for their regioselectivity was proposed: the different PNP binding manners determine their choice of ortho- or para-hydroxylation on PNP. IMPORTANCE Single-component PNP monoxygenases hydroxylate PNP at the 4 position, while two-component ones do so at the 2 position. However, their catalytic and structural differences remain elusive. The structure of single-component PNP 4-monooxygenase has previously been determined. In this study, to illustrate their catalytic difference, we resolved the crystal structure of PnpA1, a typical two-component PNP 2-monooxygenase. The roles of several key amino acid residues in substrate binding and catalysis were revealed, and a variant with improved activities toward 4NC and 2C4NP was obtained. Moreover, through comparison of the two types of PNP monooxygenases, a hypothesis was proposed to account for their catalytic difference, which gives us a better understanding of these two similar reactions at the molecular level. In addition, these results will also be of further aid in rational design of enzymes in bioremediation and biosynthesis.
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Ke Z, Lan M, Yang T, Jia W, Gou Z, Chen K, Jiang J. A two-component monooxygenase for continuous denitration and dechlorination of chlorinated 4-nitrophenol in Ensifer sp. strain 22-1. ENVIRONMENTAL RESEARCH 2021; 198:111216. [PMID: 33971135 DOI: 10.1016/j.envres.2021.111216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
The environmental fates of chlorinated 4-nitrophenols, 2,6-dichloro-4-nitrophenol (2,6-DCNP) and 2-chloro-4-nitrophenol (2C4NP), mediated via microbial catabolism have attracted great attention due to their high toxicity and persistence in the environment. In this study, a strain of Ensifer sp. 22-1 that was capable of degrading both 2,6-DCNP and 2C4NP was isolated from a halogenated aromatic-contaminated soil sample. A gene cluster cnpBADCERM was predicted to be involved in the catabolism of 2,6-DCNP and 2C4NP based on genome sequence analysis. A two-component monooxygenase CnpAB, composed of an oxygenase component (CnpA) and a reductase component (CnpB), was confirmed to catalyze the continuous denitration and dechlorination of 2,6-DCNP and 2C4NP to 6-chlorohydroxyquinol (6-CHQ) and hydroxyquinol (HQ), respectively. Knockout of cnpA resulted in the complete loss of the capacity for strain 22-1 to degrade 2,6-DCNP and 2C4NP. Homologous modeling and docking showed that Val155~Ala159, Phe206~Pro209 and Phe446~Arg461 of CnpA participated in the formation of the FAD-binding pocket, and Arg101, Val155 and Asn447 formed hydrogen bonds with 2,6-DCNP/2C4NP in the substrate-binding pocket. This work characterized a new two-component monooxygenase for 2,6-DCNP and 2C4NP, and enriched our understanding of the degradation mechanism of chlorinated nitrophenols (CNPs) by microorganisms.
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Affiliation(s)
- Zhuang Ke
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Minjian Lan
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Tunan Yang
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Weibin Jia
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhenjiu Gou
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Kai Chen
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China; Jiangsu Key Lab for Solid Organic Waste Utilization, 210095, Nanjing, China.
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Huang H, Liu Z, Qiu Y, Wang X, Wang H, Xiao H, Lu Z. Efficient electrotransformation of Rhodococcus ruber YYL with abundant extracellular polymeric substances via a cell wall-weakening strategy. FEMS Microbiol Lett 2021; 368:6273628. [PMID: 33974050 DOI: 10.1093/femsle/fnab049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 05/08/2021] [Indexed: 11/14/2022] Open
Abstract
Rhodococcus spp. have broad potential applications related to the degradation of organic contaminants and the transformation or synthesis of useful compounds. However, some Gram-positive bacteria are difficult to manipulate genetically due to low transformation efficiency. In this study, we investigated the effects of chemicals including glycine, isonicotinic acid hydrazide (INH), Tween 80 and penicillin G, as well as cell growth status, competent cell concentration, electroporation field strength, electroporation time and heat shock time, on the electrotransformation efficiency of the tetrahydrofuran-degrading bacterium Rhodococcus ruber YYL with low transformation efficiency. The highest electrotransformation efficiency was 1.60 × 106 CFU/µg DNA after parameter optimization. GmhD (D-glycero-D-manno-heptose 1-phosphate guanosyltransferase) gene, which is important in the biosynthesis of lipopolysaccharide, was deleted via the optimized electrotransformation method. Compared with wild-type strain, YYL ΔgmhD showed extremely high electrotransformation efficiency because the surface of it had no mushroom-like extracellular polymeric substances (EPS). In addition, the results showed that cell wall-weakening reagents might cause some translucent substances like EPS, to detach from the cells, increasing the electrotransformation efficiency of strain YYL. We propose that these results could provide a new strategy for unique bacteria that are rich in EPS, for which genetic manipulation systems are difficult to establish.
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Affiliation(s)
- Hui Huang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zubi Liu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yiyang Qiu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xuejun Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Haixia Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hailong Xiao
- Hangzhou Institute for Food and Drug Control, Hangzhou, Zhejiang 310018, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Genome and transcriptome sequencing of a newly isolated 2,4-dinitrophenol-degrading strain Rhodococcus imtechensis XM24D. Genes Genomics 2021; 43:829-835. [PMID: 33932219 DOI: 10.1007/s13258-021-01101-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 04/09/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND 2,4-Dinitrophenol (2,4-DNP) is an important organic environmental pollutant that is highly toxic to all forms of living organisms. A gram-positive strain (designated XM24D) was isolated from 2,4-DNP-contaminated soil by an enrichment technique. OBJECTIVE The study was designed to analyze the ability of XM24D to degrade 2,4-DNP and its analogs and to reveal the degradation pathways of these aromatic compounds. METHODS The degradation ability of XM24D was tested by a growth experiment. 2,4-DNP and its analog degradation pathways were predicted by genome and comparative transcriptome sequencing. RESULTS Growth profiles showed that XM24D was able to utilize 2,4-DNP as the sole source of carbon, nitrogen and energy. Analogs of 2,4-DNP, including 4-nitrophenol (PNP) and 2-chloro-4-nitrophenol (2C4NP), can also be degraded by XM24D. Genome analysis showed that the XM24D genome contains two chromosomes with a combined size of 9.08 Mb and an average GC content of 67.07 %. Average nucleotide identity analysis indicated that Rhodococcus imtechensis RKJ300 is the most closely related strain to XM24D. Comparative transcriptome analysis revealed that the 2,4-DNP/PNP/2C4NP degradation pathway in XM24D is highly similar in sequence and organization to the 2,4-DNP degradation pathway in Rhodococcus opacus HL PM-1, the PNP degradation pathway in Rhodococcus opacus SAO101 and the 2C4NP degradation pathway in Rhodococcus imtechensis RKJ300. These results suggested that 2,4-DNP/PNP/2C4NP was degraded via the 2,4-dinitrocyclohexanone/4-nitrocatechol/hydroxyquinol pathway in XM24D. CONCLUSIONS Genomic and transcriptomic information on XM24D provides a valuable reference for further investigating the evolutionary characteristics of nitrophenol degradation pathways in microorganisms.
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Li N, Peng Q, Yao L, He Q, Qiu J, Cao H, He J, Niu Q, Lu Y, Hui F. Roles of the Gentisate 1,2-Dioxygenases DsmD and GtdA in the Catabolism of the Herbicide Dicamba in Rhizorhabdus dicambivorans Ndbn-20. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9287-9298. [PMID: 32786824 DOI: 10.1021/acs.jafc.0c01523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
3-Chlorogentisate is a key intermediate in the catabolism of the herbicide dicamba in R. dicambivorans Ndbn-20. In this study, we identified two gentisate 1,2-dioxygenases (GDOs), DsmD and GtdA, from Ndbn-20. The amino acid sequence similarity between DsmD and GtdA is 51%. Both of them are dimers and showed activities to gentisate and 3-chlorogentisate but not 3,6-dichlorogentisate (3,6-DCGA) or 6-chlorogentisate in vitro. The kcat/Km of DsmD for 3-chlorogentisate was 28.7 times higher than that of GtdA, whereas the kcat/Km of DsmD for gentisate was only one-fourth of that of GtdA. Transcription of dsmD was dramatically induced by 3-chlorogentisate but not gentisate, whereas gtdA was not induced. Disruption of dsmD resulted in a significant decline in the degradation rates of 3-chlorogentisate and dicamba but had no effect on the degradation of gentisate, whereas the result of disruption of gtdA was converse; the disruption of both dsmD and gtdA led to the inability to degrade 3-chlorogentisate and gentisate. This study revealed that 3-chlorogentisate but not gentisate or 3,6-DCGA is the ring-cleavage substrate in the dicamba degradation pathway in R. dicambivorans Ndbn-20; DsmD is specifically responsible for cleavage of 3-chlorogentisate, whereas GtdA is a general GDO involved in the catabolism of various natural aromatic compounds.
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Affiliation(s)
- Na Li
- School of Life Science and Technology, Nanyang Normal University, Nanyang, Henan 473061, China
| | - Qian Peng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Li Yao
- School of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224002, China
| | - Qin He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Qiuhong Niu
- School of Life Science and Technology, Nanyang Normal University, Nanyang, Henan 473061, China
| | - Yunfeng Lu
- School of Life Science and Technology, Nanyang Normal University, Nanyang, Henan 473061, China
- State Key Laboratory of Motor Vehicle Biofuel Technology, Nanyang, Henan 473000, China
| | - Fengli Hui
- School of Life Science and Technology, Nanyang Normal University, Nanyang, Henan 473061, China
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Min J, Xu L, Fang S, Chen W, Hu X. Microbial degradation kinetics and molecular mechanism of 2,6-dichloro-4-nitrophenol by a Cupriavidus strain. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113703. [PMID: 31818627 DOI: 10.1016/j.envpol.2019.113703] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/03/2019] [Accepted: 11/29/2019] [Indexed: 06/10/2023]
Abstract
2,6-Dichloro-4-nitrophenol (2,6-DCNP) is an emerging chlorinated nitroaromatic pollutant, and its fate in the environment is an important question. However, microorganisms with the ability to utilize 2,6-DCNP have not been reported. In this study, Cupriavidus sp. CNP-8 having been previously reported to degrade various halogenated nitrophenols, was verified to be also capable of degrading 2,6-DCNP. Biodegradation kinetics assay showed that it degraded 2,6-DCNP with the specific growth rate of 0.124 h-1, half saturation constant of 0.038 mM and inhibition constant of 0.42 mM. Real-time quantitative PCR analyses indicated that the hnp gene cluster was involved in the catabolism of 2,6-DCNP. The hnpA and hnpB gene products were purified to homogeneity by Ni-NTA chromatography. Enzymatic assays showed that HnpAB, a FAD-dependent two-component monooxygenase, converted 2,6-DCNP to 6-chlorohydroxyquinol with a Km of 3.9 ± 1.4 μM and a kcat/Km of 0.12 ± 0.04 μΜ-1 min-1. As the oxygenase component encoding gene, hnpA is necessary for CNP-8 to grow on 2,6-DCNP by gene knockout and complementation. The phylogenetic analysis showed that the hnp cluster originated from the cluster involved in the catabolism of chlorophenols rather than nitrophenols. To our knowledge, CNP-8 is the first bacterium with the ability to utilize 2,6-DCNP, and this study fills a gap in the microbial degradation mechanism of this pollutant at the molecular, biochemical and genetic levels. Moreover, strain CNP-8 could degrade three chlorinated nitrophenols rapidly from the synthetic wastewater, indicating its potential in the bioremediation of chlorinated nitrophenols polluted environments.
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Affiliation(s)
- Jun Min
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Lingxue Xu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China; College of Life Science of Yantai University, Yantai, China
| | - Suyun Fang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Weiwei Chen
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
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A Bph-Like Nitroarene Dioxygenase Catalyzes the Conversion of 3-Nitrotoluene to 3-Methylcatechol by Rhodococcus sp. Strain ZWL3NT. Appl Environ Microbiol 2020; 86:AEM.02517-19. [PMID: 31811044 DOI: 10.1128/aem.02517-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 11/27/2019] [Indexed: 11/20/2022] Open
Abstract
All nitroarene dioxygenases reported so far originated from Nag-like naphthalene dioxygenase of Gram-negative strains, belonging to group III of aromatic ring-hydroxylating oxygenases (RHOs). Gram-positive Rhodococcus sp. strain ZWL3NT utilizes 3-nitrotoluene (3NT) as the sole source of carbon, nitrogen, and energy for growth. It was also reported that 3NT degradation was constitutive and the intermediate was 3-methylcatechol. In this study, a gene cluster (bndA1A2A3A4) encoding a multicomponent dioxygenase, belonging to group IV of RHOs, was identified. Recombinant Rhodococcus imtechensis RKJ300 carrying bndA1A2A3A4 exhibited 3NT dioxygenase activity, converting 3NT into 3-methylcatechol exclusively, with nitrite release. The identity of the product 3-methylcatechol was confirmed using liquid chromatography-mass spectrometry. A time course of biotransformation showed that the 3NT consumption was almost equal to the 3-methylcatechol accumulation, indicating a stoichiometry conversion of 3NT to 3-methylcatechol. Unlike reported Nag-like dioxygenases transforming 3NT into 4-methylcatechol or both 4-methylcatechol and 3-methylcatechol, this Bph-like dioxygenase (dioxygenases homologous to the biphenyl dioxygenase from Rhodococcus sp. strain RHA1) converts 3NT to 3-methylcatechol without forming 4-methylcatechol. Furthermore, whole-cell biotransformation of strain RKJ300 with bndA1A2A3A4 and strain ZWL3NT exhibited the extended and same substrate specificity against a number of nitrobenzene or substituted nitrobenzenes, suggesting that BndA1A2A3A4 is likely the native form of 3NT dioxygenase in strain ZWL3NT.IMPORTANCE Nitroarenes are synthetic molecules widely used in the chemical industry. Microbial degradation of nitroarenes has attracted extensive attention, not only because this class of xenobiotic compounds is recalcitrant in the environment but also because the microbiologists working in this field are curious about the evolutionary origin and process of the nitroarene dioxygenases catalyzing the initial reaction in the catabolism. In contrast to previously reported nitroarene dioxygenases from Gram-negative strains, which originated from a Nag-like naphthalene dioxygenase, the 3-nitrotoluene (3NT) dioxygenase in this study is from a Gram-positive strain and is an example of a Bph-like nitroarene dioxygenase. The preference of hydroxylation of this enzyme at the 2,3 positions of the benzene ring to produce 3-methylcatechol exclusively from 3NT is also a unique property among the studied nitroarene dioxygenases. These findings will enrich our understanding of the diversity and origin of nitroarene dioxygenase in microorganisms.
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Cheng X, Dong S, Chen D, Rui Q, Guo J, Jiang J. Potential of esterase DmtH in transforming plastic additive dimethyl terephthalate to less toxic mono-methyl terephthalate. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 187:109848. [PMID: 31670182 DOI: 10.1016/j.ecoenv.2019.109848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/16/2019] [Accepted: 10/19/2019] [Indexed: 06/10/2023]
Abstract
Dimethyl terephthalate (DMT) is a primary ingredient widely used in the manufacture of polyesters and industrial plastics; its environmental fate is of concern due to its global use. Microorganisms play key roles in the dissipation of DMT from the environment; however, the enzymes responsible for the initial transformation of DMT and the possible altered toxicity due to this biotransformation have not been extensively studied. To reduce DMT toxicity, we identified the esterase gene dmtH involved in the initial transformation of DMT from the AOPP herbicide-transforming strain Sphingobium sp. C3. DmtH shows 24-41% identity with α/β-hydrolases and belongs to subfamily V of bacterial esterases. The purified recombinant DmtH was capable of transforming DMT to mono-methyl terephthalate (MMT) and potentially transforming other p-phthalic acid esters, including diallyl terephthalate (DAT) and diethyl terephthalate (DET). Using C. elegans as an assay model, we observed the severe toxicity of DMT in inducing reactive oxygen species (ROS) production, decreasing locomotion behavior, reducing lifespan, altering molecular basis for oxidative stress, and inducing mitochondrial stress. In contrast, exposure to MMT did not cause obvious toxicity, induce oxidative stress, and activate mitochondrial stress in nematodes. Our study highlights the usefulness of Sphingobium sp. C3 and its esterase DmtH in transforming p-phthalic acid esters and reducing the toxicity of DMT to organisms.
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Affiliation(s)
- Xiaokun Cheng
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuangshuang Dong
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Medical School, Southeast University, Nanjing, 210009, China
| | - Dian Chen
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qi Rui
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingjing Guo
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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Tiwari J, Tarale P, Sivanesan S, Bafana A. Environmental persistence, hazard, and mitigation challenges of nitroaromatic compounds. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:28650-28667. [PMID: 31388957 DOI: 10.1007/s11356-019-06043-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/22/2019] [Indexed: 05/15/2023]
Abstract
Nitroaromatic compounds (NACs) are extensively used in different industries and are synthesized in large quantity due to their heavy demand worldwide. The broad use of NACs poses a serious pollution threat. The treatment processes used for the removal of NACs are not effective and sustainable, leading to their release into the environment. The nitro group attached to benzene ring makes the compounds recalcitrant due to which they persist in the environment. Being hazardous to human as well as other living organisms, NACs are listed in the USEPA's priority pollutant group. This review provides updated information on the sources of NACs, prevalence in different environmental matrices, and recent developments in methods of their detection, with emphasis on current trends as well as future prospects. The harmful effects of NACs due to exposure through different routes are also highlighted. Further, the technologies reported for the treatment of NACs, including physico-chemical and biological methods, and the challenges faced for their effective implementation are discussed. Thus, the review discusses relevant issues in detail making suitable recommendations, which can be helpful in guiding further research in this subject.
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Affiliation(s)
- Jyoti Tiwari
- AcSIR (Academy of Scientific and Innovative Research), CSIR-NEERI (National Environmental Engineering Research Institute) Campus, Nagpur, 440020, India
- Director's Research Cell, CSIR-NEERI (National Environmental Engineering Research Institute), Nagpur, 440020, Maharashtra, India
| | - Prashant Tarale
- Health and Toxicity Cell, CSIR-NEERI (National Environmental Engineering Research Institute), Nagpur, 440020, India
- Blood Research Institute, Versiti Wisconsin, 8727 Watertown Plank Road, Milwaukee, WI, 53213, USA
| | - Saravanadevi Sivanesan
- AcSIR (Academy of Scientific and Innovative Research), CSIR-NEERI (National Environmental Engineering Research Institute) Campus, Nagpur, 440020, India
- Health and Toxicity Cell, CSIR-NEERI (National Environmental Engineering Research Institute), Nagpur, 440020, India
| | - Amit Bafana
- AcSIR (Academy of Scientific and Innovative Research), CSIR-NEERI (National Environmental Engineering Research Institute) Campus, Nagpur, 440020, India.
- Director's Research Cell, CSIR-NEERI (National Environmental Engineering Research Institute), Nagpur, 440020, Maharashtra, India.
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The Properties of 5-Methyltetrahydrofolate Dehydrogenase (MetF1) and Its Role in the Tetrahydrofolate-Dependent Dicamba Demethylation System in Rhizorhabdus dicambivorans Ndbn-20. J Bacteriol 2019; 201:JB.00096-19. [PMID: 31209079 DOI: 10.1128/jb.00096-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/13/2019] [Indexed: 11/20/2022] Open
Abstract
The herbicide dicamba is initially degraded via the tetrahydrofolate (THF)-dependent demethylation system in Rhizorhabdus dicambivorans Ndbn-20. Two THF-dependent dicamba methyltransferase gene clusters, scaffold 50 and scaffold 66, were found in the genome of strain Ndbn-20. Each cluster contains a dicamba methyltransferase gene and three THF metabolism-related genes, namely, metF (coding for 5,10-CH2-THF reductase), folD (coding for 5,10-CH2-THF dehydrogenase-5,10-methenyl-THF cyclohydrolase), and purU (coding for 10-formyl-THF deformylase). In this study, reverse transcription-PCR (RT-PCR) results showed that only genes in scaffold 66, not those in scaffold 50, were transcribed in dicamba-cultured cells. The metF gene of scaffold 66 (metF1) was expressed in Escherichia coli BL21(DE3), and the product was purified as a His6-tagged protein. Purified MetF1 was found to be a monomer and exhibited 5-CH3-THF dehydrogenase activity in vitro The k cat and Km for 5-CH3-THF were 0.23 s-1 and 16.48 μM, respectively. However, 5,10-CH2-THF reductase activity was not detected for MetF1 under the conditions tested. Gene disruption results showed that metF1 is essential for dicamba degradation, whereas folD1 is dispensable.IMPORTANCE There are several THF-dependent methyltransferase genes and THF-metabolic genes in the genome of R. dicambivorans Ndbn-20; however, which genes are involved in dicamba demethylation and the mechanism underlying THF regeneration remain unknown. This study revealed that scaffold 66 is responsible for dicamba demethylation and that MetF1 physiologically catalyzes the dehydrogenation of 5-CH3-THF to 5,10-CH2-THF in the THF-dependent dicamba demethylation system in R. dicambivorans Ndbn-20. Furthermore, the results showed that MetF1 differs from previously characterized MetF in phylogenesis, biochemical properties, and catalytic activity; e.g., MetF1 in vitro did not show 5,10-CH2-THF reductase activity, which is the physiological function of Escherichia coli MetF. This study provides new insights into the mechanism of the THF-dependent methyltransferase system.
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Molecular and biochemical characterization of 2-chloro-4-nitrophenol degradation via the 1,2,4-benzenetriol pathway in a Gram-negative bacterium. Appl Microbiol Biotechnol 2019; 103:7741-7750. [DOI: 10.1007/s00253-019-09994-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/17/2019] [Accepted: 06/17/2019] [Indexed: 10/26/2022]
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Min J, Chen W, Hu X. Biodegradation of 2,6-dibromo-4-nitrophenol by Cupriavidus sp. strain CNP-8: Kinetics, pathway, genetic and biochemical characterization. JOURNAL OF HAZARDOUS MATERIALS 2019; 361:10-18. [PMID: 30176407 DOI: 10.1016/j.jhazmat.2018.08.063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/18/2018] [Accepted: 08/20/2018] [Indexed: 06/08/2023]
Abstract
Compound 2,6-dibromo-4-nitrophenol (2,6-DBNP) with high cytotoxicity and genotoxicity has been recently identified as an emerging brominated disinfection by-product during chloramination and chlorination of water, and its environmental fate is of great concern. To date, the biodegradation process of 2,6-DBNP is unknown. Herein, Cupriavidus sp. strain CNP-8 was reported to be able to utilize 2,6-DBNP as a sole source of carbon, nitrogen and energy. It degraded 2,6-DBNP in concentrations up to 0.7 mM, and the degradation of 2,6-DBNP conformed to Haldane inhibition model with μmax of 0.096 h-1, Ks of 0.05 mM and Ki of 0.31 mM. Comparative transcriptome and real-time quantitative PCR analyses suggested that the hnp gene cluster was likely responsible for 2,6-DBNP catabolism. Three Hnp proteins were purified and functionally verified. HnpA, a FADH2-dependent monooxygenase, was found to catalyze the sequential denitration and debromination of 2,6-DBNP to 6-bromohydroxyquinol (6-BHQ) in the presence of the flavin reductase HnpB. Gene knockout and complementation revealed that hnpA is essential for strain CNP-8 to utiluze 2,6-DBNP. HnpC, a 6-BHQ 1,2-dioxygenase was proposed to catalyze the ring-cleavage of 6-BHQ during 2,6-DBNP catabolism. These results fill a gap in the understanding of the microbial degradation process and mechanism of 2,6-DBNP.
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Affiliation(s)
- Jun Min
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Weiwei Chen
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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Zhang H, Yu T, Li J, Wang YR, Wang GL, Li F, Liu Y, Xiong MH, Ma YQ. Two dcm Gene Clusters Essential for the Degradation of Diclofop-methyl in a Microbial Consortium of Rhodococcus sp. JT-3 and Brevundimonas sp. JT-9. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12217-12226. [PMID: 30375865 DOI: 10.1021/acs.jafc.8b05382] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The metabolism of widely used aryloxyphenoxypropionate herbicides has been extensively studied in microbes. However, the information on the degradation of diclofop-methyl (DCM) is limited, with no genetic and biochemical investigation reported. The consortium L1 of Rhodococcus sp. JT-3 and Brevundimonas sp. JT-9 was able to degrade DCM through a synergistic metabolism. To elaborate the molecular mechanism of DCM degradation, the metabolic pathway for DCM was first investigated. DCM was initially transformed by strain JT-3 to diclofop acid and then by strain JT-9 to 2-(4-hydroxyphenoxy) propionic acid as well as 2,4-dichlorophenol. Subsequently, the two dcm gene clusters, dcmAE and dcmB1B2CD, involved in further degradation of 2,4-dichlorophenol, were successfully cloned from strain JT-3, and the functions of each gene product were identified. DcmA, a glutathione-dependent dehalogenase, was responsible for catalyzing the reductive dehalogenation of 2,4-dichlorophenol to 4-chlorophenol, which was then converted by the two-component monooxygenase DcmB1B2 to 4-chlorocatechol as the ring cleavage substrate of the dioxygenase DcmC. In this study, the overall DCM degradation pathway of the consortium L1 was proposed and, particularly, the lower part on the DCP degradation was characterized at the genetic and biochemical levels.
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Affiliation(s)
- Hui Zhang
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Ting Yu
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Jie Li
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Yi-Ran Wang
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Guang-Li Wang
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Feng Li
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Yuan Liu
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Ming-Hua Xiong
- College of Life Sciences , Huaibei Normal University , Huaibei 235000 , China
| | - Ying-Qun Ma
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute , Nanyang Technological University , 1 Cleantech Loop , Singapore 637141 , Singapore
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Zhang H, Yu T, Wang Y, Li J, Wang G, Ma Y, Liu Y. 4-Chlorophenol Oxidation Depends on the Activation of an AraC-Type Transcriptional Regulator, CphR, in Rhodococcus sp. Strain YH-5B. Front Microbiol 2018; 9:2481. [PMID: 30405555 PMCID: PMC6205950 DOI: 10.3389/fmicb.2018.02481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/28/2018] [Indexed: 11/13/2022] Open
Abstract
4-Chlorophenol (4-CP) oxidation plays an essential role in the detoxification of 4-CP. However, oxidative regulation of 4-CP at the genetic and biochemical levels has not yet been studied. To explore the regulation mechanism of 4-CP oxidation, a novel gene cluster, cphRA2A1, involved in biodegradation of 4-CP was identified and cloned from Rhodococcus sp. strain YH-5B by genome walking. The sequence analysis showed that the cphRA2A1 gene cluster encoded an AraC-type transcriptional regulator and a two-component monooxygenase enzyme, while quantitative real-time PCR analysis further revealed that cphR was constitutively expressed and positively regulated the transcription of cphA2A1 genes in response to 4-CP or phenol, as evidenced by gene knockout and complementation experiments. Through the transcriptional fusion of the mutated cphA2A1 promoter with the lacZ gene, it was found that the CphR regulator binding sites had two 15-bp imperfect direct repeats (TGCA-N6-GGNTA) at -35 to -69 upstream of the cphA2A1 transcriptional start site. Notably, the sub-motifs at the -46 to -49 positions played a critical role in the appropriate interaction with the CphR dimer. In addition, it was confirmed that the monooxygenase subunits CphA1 and CphA2, which were purified by His-tag affinity chromatography, were able to catalyze the conversion of 4-CP to 4-chlorocatechol, suggesting that strain YH-5B could degrade 4-CP via the 4-chlorocatechol pathway. This study enhances our understanding of the genetic and biochemical diversity in the transcriptional regulation of 4-CP oxidation in Gram-positive bacteria.
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Affiliation(s)
- Hui Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Ting Yu
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Yiran Wang
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Jie Li
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Guangli Wang
- College of Life Sciences, Huaibei Normal University, Huaibei, China
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore, Singapore
| | - Yingqun Ma
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore, Singapore
| | - Yu Liu
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
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Chen Q, Huang Y, Duan Y, Li Z, Cui Z, Liu W. Crystal structure of p-nitrophenol 4-monooxygenase PnpA from Pseudomonas putida DLL-E4: The key enzyme involved in p-nitrophenol degradation. Biochem Biophys Res Commun 2018; 504:715-720. [PMID: 30217456 DOI: 10.1016/j.bbrc.2018.09.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/07/2018] [Indexed: 02/07/2023]
Abstract
p-Nitrophenol 4-monooxygenase PnpA, the key enzyme in the hydroquinone pathway of p-nitrophenol (PNP) degradation, catalyzes the monooxygenase reaction of PNP to p-benzoquinone in the presence of FAD and NADH. Here, we determined the first crystal structure of PnpA from Pseudomonas putida DLL-E4 in its apo and FAD-complex forms to a resolution of 2.04 Å and 2.48 Å, respectively. The PnpA structure shares a common fold with hydroxybenzoate hydroxylases, despite a low amino sequence identity of 14-18%, confirming it to be a member of the Class A flavoprotein monooxygenases. However, substrate docking studies of PnpA indicated that the residues stabilizing the substrate in an orientation suitable for catalysis are not observed in other homologous hydroxybenzoate hydroxylases, suggesting PnpA employs a unique catalytic mechanism. This work expands our understanding on the reaction mode for this enzyme class.
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Affiliation(s)
- Qiongzhen Chen
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yajuan Duan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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Roles of Two Glutathione-Dependent 3,6-Dichlorogentisate Dehalogenases in Rhizorhabdus dicambivorans Ndbn-20 in the Catabolism of the Herbicide Dicamba. Appl Environ Microbiol 2018; 84:AEM.00623-18. [PMID: 29934333 DOI: 10.1128/aem.00623-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/18/2018] [Indexed: 11/20/2022] Open
Abstract
The herbicide dicamba is initially demethylated to 3,6-dichlorosalicylate (3,6-DCSA) in Rhizorhabdus dicambivorans Ndbn-20 and is subsequently 5-hydroxylated to 3,6-dichlorogentisate (3,6-DCGA). In the present study, two glutathione-dependent 3,6-DCGA dehalogenases, DsmH1 and DsmH2, were identified in strain Ndbn-20. DsmH2 shared a low identity (only 31%) with the tetrachlorohydroquinone (TCHQ) dehalogenase PcpC from Sphingobium chlorophenolicum ATCC 39723, while DsmH1 shared a high identity (79%) with PcpC. In the phylogenetic tree of related glutathione S-transferases (GSTs), DsmH1 and DsmH2, together with PcpC and the 2,5-dichlorohydroquinone dehalogenase LinD, formed a separate clade. DsmH1 and DsmH2 were synthesized in Escherichia coli BL21 and purified as His-tagged enzymes. Both enzymes required glutathione (GSH) as a cofactor and could 6-dechlorinate 3,6-DCGA to 3-chlorogentisate in vitro DsmH2 had a significantly higher catalytic efficiency toward 3,6-DCGA than DsmH1. Transcription and disruption analysis revealed that DsmH2 but not DsmH1 was responsible for the 6-dechlorination of 3,6-DCGA in strain Ndbn-20 in vivo Furthermore, we propose a novel eta class of GSTs to accommodate the four bacterial dehalogenases PcpC, LinD, DsmH1, and DsmH2.IMPORTANCE Dicamba is an important herbicide, and its use and leakage into the environment have dramatically increased since the large-scale planting of genetically modified (GM) dicamba-resistant crops in 2015. However, the complete catabolic pathway of dicamba has remained unknown, which limits ecotoxicological studies of this herbicide. Our previous study revealed that 3,6-DCGA was an intermediate of dicamba degradation in strain Ndbn-20. In this study, we identified two glutathione-dependent 3,6-DCGA dehalogenases, DsmH1 and DsmH2, and demonstrated that DsmH2 is physiologically responsible for the 6-dechlorination of 3,6-DCGA in strain Ndbn-20. GSTs play an important role in the detoxification and degradation of a variety of endogenous and exogenous toxic compounds. On the basis of their sequence identities, phylogenetic status, and functions, the four bacterial GSH-dependent dehalogenases (PcpC, LinD, DsmH1, and DsmH2) were reclassified as a new eta class of GSTs. This study helps us to elucidate the microbial catabolism of dicamba and enhances our understanding of the diversity and functions of GSTs.
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Ito K, Takagi K, Matsushima Y, Iwasaki A, Tanaka N, Kanesaki Y, Martin-Laurent Martin-Laurent FF, Igimi S. Identification of the novel hcbB operon catalyzing the dechlorination of pentachlorophenol in the Gram-positive bacterium Nocardioides sp. strain PD653. JOURNAL OF PESTICIDE SCIENCE 2018; 43:124-131. [PMID: 30363388 PMCID: PMC6173144 DOI: 10.1584/jpestics.d17-089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
While pcp genes are well known in Gram-negative bacteria to code for the enzymes responsible for pentachlorophenol (C6HCl5O; PCP) degradation, little is known about PCP-degrading genes in Gram-positive bacteria. Here we describe a novel gene operon possibly responsible for catalyzing the degradation of PCP in the Gram-positive bacterium Nocardioides sp. strain PD653, which is capable of mineralizing hexachlorobenzene (C6Cl6; HCB) via PCP. Transcriptome analysis based on RNA-Seq revealed overexpressed genes in strain PD653 following exposure to HCB. Based on in silico annotation, three open reading frames (ORFs) were selected as biodegrading enzyme candidates. Recombinant E. coli cells expressing candidate genes degraded approximately 9.4 µmol L-1 PCP in 2 hr. Therefore, we designated these genes as hcbB1, hcbB2, and hcbB3. Interestingly, PCP-degrading activity was recorded when hcbB3 was coexpressed with hcbB1 or hcbB2, and the function of HcbB3 was expected to be similar to chlorophenol 4-monooxygenase (TftD).
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Affiliation(s)
- Koji Ito
- Department of Agricultural Chemistry, Tokyo University of Agriculture
- Hazardous Chemicals Division, Institute for Agro-Environmental Sciences, NARO
| | - Kazuhiro Takagi
- Department of Agricultural Chemistry, Tokyo University of Agriculture
- Hazardous Chemicals Division, Institute for Agro-Environmental Sciences, NARO
- To whom correspondence should be addressed. E-mail:
| | | | - Akio Iwasaki
- Juntendo Medical Technology Innovation Center, Juntendo University
| | - Naoto Tanaka
- Department of Molecular Microbiology, Tokyo University of Agriculture
| | - Yu Kanesaki
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture
| | | | - Shizunobu Igimi
- Department of Agricultural Chemistry, Tokyo University of Agriculture
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Min J, Wang J, Chen W, Hu X. Biodegradation of 2-chloro-4-nitrophenol via a hydroxyquinol pathway by a Gram-negative bacterium, Cupriavidus sp. strain CNP-8. AMB Express 2018; 8:43. [PMID: 29560541 PMCID: PMC5861257 DOI: 10.1186/s13568-018-0574-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/12/2018] [Indexed: 11/21/2022] Open
Abstract
Cupriavidus sp. strain CNP-8 isolated from a pesticide-contaminated soil was able to utilize 2-chloro-4-nitrophenol (2C4NP) as a sole source of carbon, nitrogen and energy, together with the release of nitrite and chloride ions. It could degrade 2C4NP at temperatures from 20 to 40 °C and at pH values from 5 to 10, and degrade 2C4NP as high as 1.6 mM. Kinetics assay showed that biodegradation of 2C4NP followed Haldane substrate inhibition model, with the maximum specific growth rate (μmax) of 0.148/h, half saturation constant (Ks) of 0.022 mM and substrate inhibition constant (Ki) of 0.72 mM. Strain CNP-8 was proposed to degrade 2C4NP with hydroxyquinol (1,2,4-benzenetriol, BT) as the ring-cleavage substrate. The 2C4NP catabolic pathway in strain CNP-8 is significant from those reported in other Gram-negative 2C4NP utilizers. Enzymatic assay indicated that the monooxygenase initiating 2C4NP catabolism had different substrates specificity compared with previously reported 2C4NP monooxygenations. Capillary assays showed that strain CNP-8 exhibited metabolism-dependent chemotactic response toward 2C4NP at the optimum concentration of 0.5 mM with a maximum chemotaxis index of 37.5. Furthermore, microcosm studies demonstrated that strain CNP-8, especially the pre-induced cells, could remove 2C4NP rapidly from the 2C4NP-contaminated soil. Considering its adaptability to pH and temperature fluctuations and great degradation efficiency against 2C4NP, strain CNP-8 could be a promising candidate for the bioremediation of 2C4NP-contaminated sites.
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Comparative Transcriptome Analysis Reveals the Mechanism Underlying 3,5-Dibromo-4-Hydroxybenzoate Catabolism via a New Oxidative Decarboxylation Pathway. Appl Environ Microbiol 2018; 84:AEM.02467-17. [PMID: 29305508 DOI: 10.1128/aem.02467-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 12/13/2017] [Indexed: 02/07/2023] Open
Abstract
The compound 3,5-dibromo-4-hydroxybenzoate (DBHB) is both anthropogenically released into and naturally produced in the environment, and its environmental fate is of great concern. Aerobic and anaerobic reductive dehalogenations are the only two reported pathways for DBHB catabolism. In this study, a new oxidative decarboxylation pathway for DBHB catabolism was identified in a DBHB-utilizing strain, Pigmentiphaga sp. strain H8. The genetic determinants underlying this pathway were elucidated based on comparative transcriptome analysis and subsequent experimental validation. A gene cluster comprising orf420 to orf426, with transcripts that were about 33- to 4,400-fold upregulated in DBHB-induced cells compared with those in uninduced cells, was suspected to be involved in DBHB catabolism. The gene odcA (orf420), which is essential for the initial catabolism of DBHB, encodes a novel NAD(P)H-dependent flavin monooxygenase that mediates the oxidative decarboxylation of DBHB to 2,6-dibromohydroquinone (2,6-DBHQ). The substrate specificity of the purified OdcA indicated that the 4-hydroxyl group and its ortho-halogen(s) are important for hydroxylation of the C-1 site carboxyl group by OdcA. 2,6-DBHQ is then ring cleaved by the dioxygenase OdcB (Orf425) to 2-bromomaleylacetate, which is finally transformed to β-ketoadipate by the maleylacetate reductase OdcC (Orf426). These results provide a better understanding of the molecular mechanism underlying the catabolic diversity of halogenated para-hydroxybenzoates.IMPORTANCE Halogenated hydroxybenzoates (HBs), which are widely used synthetic precursors for chemical products and common metabolic intermediates from halogenated aromatics, exert considerable adverse effects on human health and ecological security. Microbial catabolism plays key roles in the dissipation of halogenated HBs in the environment. In this study, the discovery of a new catabolic pathway for 3,5-dibromo-4-hydroxybenzoate (DBHB) and clarification of the genetic determinants underlying the pathway broaden our knowledge of the catabolic diversity of halogenated HBs in microorganisms. Furthermore, the NAD(P)H-dependent flavin monooxygenase OdcA identified in Pigmentiphaga sp. strain H8 represents a novel 1-monooxygenase for halogenated para-HBs found in prokaryotes and enhances our knowledge of the decarboxylative hydroxylation of (halogenated) para-HBs.
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Arora PK, Srivastava A, Garg SK, Singh VP. Recent advances in degradation of chloronitrophenols. BIORESOURCE TECHNOLOGY 2018; 250:902-909. [PMID: 29229201 DOI: 10.1016/j.biortech.2017.12.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/03/2017] [Accepted: 12/04/2017] [Indexed: 06/07/2023]
Abstract
Chloronitrophenols (CNPs) constitute a group of environmental pollutants that are widely distributed in our surrounding environment due to human based activities. This group of chemicals is highly toxic to living beings due to its mutagenic and carcinogenic nature. Examples include 2-chloro-4-nitrophenol, 4-chloro-2-nitrophenol, 2-chloro-5-nitrophenol, 4-chloro-3-nitrophenol and 2,6-dichloro-4-nitrophenol. Several methods including advanced oxidation processes, adsorption and bacterial degradation have been used for degradation of CNPs. Among, bacterial degradation is an eco-friendly and effective way to degrade CNPs. Several bacterial metabolic pathways have been proposed for degradation of CNPs and their genes and enzymes have been identified in bacteria. These bacteria were able to degrade CNPs in broth culture and soil. Therefore, CNPs-degrading bacteria are suitable candidates for bioremediation of CNPs-contaminated sites. Few CNP-degrading bacteria exhibited chemotaxis towards CNPs to enhance their biodegradation. The present review summarizes recent progress in degradation of CNPs.
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Affiliation(s)
- Pankaj Kumar Arora
- Department of Plant Science, MJP Rohilkhand University, Bareilly 243006, India; Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, India.
| | - Alok Srivastava
- Department of Plant Science, MJP Rohilkhand University, Bareilly 243006, India
| | - Sanjay Kumar Garg
- Department of Plant Science, MJP Rohilkhand University, Bareilly 243006, India
| | - Vijai Pal Singh
- Department of Plant Science, MJP Rohilkhand University, Bareilly 243006, India
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Strahsburger E, de Lacey AML, Marotti I, DiGioia D, Biavati B, Dinelli G. In vivo assay to identify bacteria with β-glucosidase activity. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.08.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Min J, Chen W, Wang J, Hu X. Genetic and Biochemical Characterization of 2-Chloro-5-Nitrophenol Degradation in a Newly Isolated Bacterium, Cupriavidus sp. Strain CNP-8. Front Microbiol 2017; 8:1778. [PMID: 28959252 PMCID: PMC5604080 DOI: 10.3389/fmicb.2017.01778] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/31/2017] [Indexed: 11/13/2022] Open
Abstract
Compound 2-chloro-5-nitrophenol (2C5NP) is a typical chlorinated nitroaromatic pollutant. To date, the bacteria with the ability to degrade 2C5NP are rare, and the molecular mechanism of 2C5NP degradation remains unknown. In this study, Cupriavidus sp. strain CNP-8 utilizing 2-chloro-5-nitrophenol (2C5NP) and meta-nitrophenol (MNP) via partial reductive pathways was isolated from pesticide-contaminated soil. Biodegradation kinetic analysis indicated that 2C5NP degradation by this strain was concentration dependent, with a maximum specific degradation rate of 21.2 ± 2.3 μM h−1. Transcriptional analysis showed that the mnp genes are up-regulated in both 2C5NP- and MNP-induced strain CNP-8. Two Mnp proteins were purified to homogeneity by Ni-NTA affinity chromatography. In addition to catalyzing the reduction of MNP, MnpA, a NADPH-dependent nitroreductase, also catalyzes the partial reduction of 2C5NP to 2-chloro-5-hydroxylaminophenol via 2-chloro-5-nitrosophenol, which was firstly identified as an intermediate of 2C5NP catabolism. MnpC, an aminohydroquinone dioxygenase, is likely responsible for the ring-cleavage reaction of 2C5NP degradation. Gene knockout and complementation indicated that mnpA is necessary for both 2C5NP and MNP catabolism. To our knowledge, strain CNP-8 is the second 2C5NP-utilizing bacterium, and this is the first report of the molecular mechanism of microbial 2C5NP degradation.
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Affiliation(s)
- Jun Min
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantai, China
| | - Weiwei Chen
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantai, China
| | - Jinpei Wang
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantai, China
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Min J, Wang B, Hu X. Effect of inoculation of Burkholderia sp. strain SJ98 on bacterial community dynamics and para-nitrophenol, 3-methyl-4-nitrophenol, and 2-chloro-4-nitrophenol degradation in soil. Sci Rep 2017; 7:5983. [PMID: 28729667 PMCID: PMC5519733 DOI: 10.1038/s41598-017-06436-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/13/2017] [Indexed: 02/06/2023] Open
Abstract
para-Nitrophenol (PNP), 3-methyl-4-nitrophenol (3M4NP), and 2-chloro-4-nitrophenol (2C4NP) are highly toxic compounds that have caused serious environmental issues. We inoculated an artificially contaminated soil with Burkholderia sp. strain SJ98, which has the ability to degrade PNP, 3M4NP, and 2C4NP, and quantified bioremediation. There was accelerated degradation of all nitrophenols in inoculated treatments compared to the un-inoculated treatments. The indigenous bacteria were able to degrade PNP, but not 3M4NP or 2C4NP. Real-time PCR targeting the catabolic gene pnpA showed that levels of strain SJ98 remained stable over the incubation period. High-throughput sequencing revealed that both contamination and bioaugmentation influenced the bacterial community structure. Bioaugmentation seemed to protect Kineosporia, Nitrososphaera, and Schlesneria from nitrophenol inhibition, as well as led to a sharp increase in the abundance of Nonomuraea, Kribbella, and Saccharopolyspora. There was a significant increase in the relative abundances of Thermasporomyces, Actinomadura, and Streptomyces in both contaminated and bioaugmented treatments; this indicated that these bacteria are likely directly related to nitrophenol degradation. To our knowledge, this is the first report of the simultaneous removal of PNP, 3M4NP, and 2C4NP using bioaugmentation. This study provides valuable insights into the bioremediation of soils contaminated with nitrophenols.
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Affiliation(s)
- Jun Min
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China
| | - Bin Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, China.
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Min J, Lu Y, Hu X, Zhou NY. Biochemical Characterization of 3-Methyl-4-nitrophenol Degradation in Burkholderia sp. Strain SJ98. Front Microbiol 2016; 7:791. [PMID: 27252697 PMCID: PMC4879640 DOI: 10.3389/fmicb.2016.00791] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/09/2016] [Indexed: 11/24/2022] Open
Abstract
Several strains have been reported to grow on 3-methyl-4-nitrophenol (3M4NP), the primary breakdown product of the excessively used insecticide fenitrothion. However, the microbial degradation of 3M4NP at molecular and biochemical levels remains unknown. Here, methyl-1,4-benzoquinone (MBQ) and methylhydroquinone (MHQ), rather than catechol proposed previously, were identified as the intermediates before ring cleavage during 3M4NP degradation by Burkholderia sp. strain SJ98. Real-time quantitative PCR analysis indicated that the pnpABA1CDEF cluster involved in para-nitrophenol (PNP) and 2-chloro-4-nitrophenol (2C4NP) catabolism was also likely responsible for 3M4NP degradation in this strain. Purified PNP 4-monooxygenase (PnpA) is able to catalyze the monooxygenation of 3M4NP to MBQ and exhibited an apparent Km value of 20.3 ± 2.54 μM for 3M4NP, and pnpA is absolutely necessary for the catabolism of 3M4NP by gene knock-out and complementation. PnpB, a 1,4-benzoquinone reductase catalyzes the reduction of MBQ to MHQ, and also found to enhance PnpA activity in vitro in the conversion of 3M4NP to MBQ. By sequential catalysis assays, PnpCD, PnpE, and PnpF were likely involved in the lower pathway of 3M4NP catabolism. Although NpcCD, NpcE, and NpcF are able to catalyze the sequential conversion of MHQ in vitro, these enzymes are unlikely involved in 3M4NP catabolism because their coding genes were not upregulated by 3M4NP induction in vivo. These results revealed that the enzymes involved in PNP and 2C4NP catabolism were also responsible for 3M4NP degradation in strain SJ98. This fills a gap in our understanding of the microbial degradation of 3M4NP at molecular and biochemical levels and also provides another example to illustrate the adaptive flexibility in microbial catabolism for structurally similar compounds.
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Affiliation(s)
- Jun Min
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
| | - Yang Lu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
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