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Łomża P, Krucoń T, Tabernacka A. Potential of Microbial Communities to Perform Dehalogenation Processes in Natural and Anthropogenically Modified Environments-A Metagenomic Study. Microorganisms 2023; 11:1702. [PMID: 37512875 PMCID: PMC10385969 DOI: 10.3390/microorganisms11071702] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/15/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Halogenated organic compounds (HOCs) pose a serious problem for the environment. Many are highly toxic and accumulate both in soil and in organisms. Their biological transformation takes place by dehalogenation, in which the halogen substituents are detached from the carbon in the organic compound by enzymes produced by microorganisms. This increases the compounds' water solubility and bioavailability, reduces toxicity, and allows the resulting compound to become more susceptible to biodegradation. The microbial halogen cycle in soil is an important part of global dehalogenation processes. The aim of the study was to examine the potential of microbial communities inhabiting natural and anthropogenically modified environments to carry out the dehalogenation process. The potential of microorganisms was assessed by analyzing the metagenomes from a natural environment (forest soils) and from environments subjected to anthropopression (agricultural soil and sludge from wastewater treatment plants). Thirteen genes encoding enzymes with dehalogenase activity were identified in the metagenomes of both environments, among which, 2-haloacid dehalogenase and catechol 2,3-dioxygenase were the most abundant genes. Comparative analysis, based on comparing taxonomy, identified genes, total halogens content and content of DDT derivatives, demonstrated the ability of microorganisms to transform HOCs in both environments, indicating the presence of these compounds in the environment for a long period of time and the adaptive need to develop mechanisms for their detoxification. Metagenome analyses and comparative analyses indicate the genetic potential of microorganisms of both environments to carry out dehalogenation processes, including dehalogenation of anthropogenic HOCs.
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Affiliation(s)
- Pola Łomża
- Department of Biology, Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, 20 Nowowiejska Street, 00-653 Warsaw, Poland
| | - Tomasz Krucoń
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, University of Warsaw, 1 Miecznikowa Street, 02-089 Warsaw, Poland
| | - Agnieszka Tabernacka
- Department of Biology, Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, 20 Nowowiejska Street, 00-653 Warsaw, Poland
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2
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Whole-genome sequencing, genome mining, metabolic reconstruction and evolution of pentachlorophenol and other xenobiotic degradation pathways in Bacillus tropicus strain AOA-CPS1. Funct Integr Genomics 2021; 21:171-193. [PMID: 33547987 DOI: 10.1007/s10142-021-00768-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 09/30/2020] [Accepted: 01/19/2021] [Indexed: 12/11/2022]
Abstract
A pentachlorophenol degrading bacterium was isolated from effluent of a wastewater treatment plant in Durban, South Africa, and identified as Bacillus tropicus strain AOA-CPS1 (BtAOA). The isolate degraded 29% of pentachlorophenol (PCP) within 9 days at an initial PCP concentration of 100 mg L-1 and 62% of PCP when the initial concentration was set at 350 mg L-1. The whole-genome of BtAOA was sequenced using Pacific Biosciences RS II sequencer with the Single Molecule, Real-Time (SMRT) Link (version 7.0.1.66975) and analysed using the HGAP4-de-novo assembly application. The contigs were annotated at NCBI, RASTtk and PROKKA prokaryotic genome annotation pipelines. The BtAOA genome is comprised of a 5,246,860-bp chromosome and a 58,449-bp plasmid with a GC content of 35.4%. The metabolic reconstruction for BtAOA showed that the organism has been naturally exposed to various chlorophenolic compounds including PCP and other xenobiotics. The chromosome encodes genes for core processes, stress response and PCP catabolic genes. Analogues of PCP catabolic gene (cpsBDCAE, and p450) sequences were identified from the NCBI annotation data, PCR-amplified from the whole genome of BtAOA, cloned into pET15b expression vector, overexpressed in E. coli BL21 (DE3) expression host, purified and characterized. Sequence mining and comparative analysis of the metabolic reconstruction of the BtAOA genome with closely related strains suggests that the operon encoding the first two enzymes in the PCP degradation pathway were acquired from a pre-existing pterin-carbinolamine dehydratase subsystem. The other two enzymes were recruited via horizontal gene transfer (HGT) from the pool of hypothetical proteins with no previous specific function, while the last enzyme was recruited from pre-existing enzymes from the TCA or serine-glyoxalase cycle via HGT events. This study provides a comprehensive understanding of the role of BtAOA in PCP degradation and its potential exploitation for bioremediation of other xenobiotic compounds.
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3
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Tang K, Rosborg P, Rasmussen ES, Hambly A, Madsen M, Jensen NM, Hansen AA, Sund C, Andersen HG, Torresi E, Kragelund C, Andersen HR. Impact of intermittent feeding on polishing of micropollutants by moving bed biofilm reactors (MBBR). JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123536. [PMID: 32823027 DOI: 10.1016/j.jhazmat.2020.123536] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/12/2020] [Accepted: 07/21/2020] [Indexed: 05/25/2023]
Abstract
Moving bed biofilm reactors (MBBRs) were placed at two wastewater treatment plants, where they were constantly fed with effluent and intermittently fed with primary wastewater. Each reactor was subjected to different feast/famine periods and flow rates of primary wastewater, thus the different organic and nutrient loads (chemical oxygen demand(COD), ammonium(NH4-N)) resulted in different feast-famine conditions applied to the biomass. In batch experiments, this study investigated the effects of various feast-famine conditions on the biodegradation of micropollutants by MBBRs applied as an effluent polishing step. Rate constants of micropollutant removals were found to be positively correlated to the load of the total COD and NH4-N, indicating that higher organic loads were favourable for the growth of micropollutant degraders in these MBBRs. Rate constant of atenolol was five times higher when the biomass was fed with the highest COD and NH4-N load than it was fed with the lowest COD and NH4-N load. For diclofenac, mycophenolic acid and iohexol, their maximum rate constants were obtained with feeding of COD and NH4-N of approximately 570 mgCOD/d and 40∼60 mgNH4-N/d respectively. This also supports the concept that co-metabolism (rather competition inhibition or catabolic repression) plays an important role in micropollutants biodegradation in wastewater.
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Affiliation(s)
- Kai Tang
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej 113, 2800 Kgs. Lyngby, Denmark.
| | - Peter Rosborg
- Department of Chemistry and Biotechnology, Danish Technological Institute, Kongsvang Allé 29, DK-8000 Århus C, Denmark
| | - Emma S Rasmussen
- Department of Bioscoence-Microbiology, Århus University, Ny Munkegade 116, 8000 Aarhus C, Denmark
| | - Adam Hambly
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej 113, 2800 Kgs. Lyngby, Denmark
| | | | | | - Aviaja A Hansen
- Veolia Water Technologies, Haslegårdsvænger 18, 8210 Århus V, Denmark
| | - Christina Sund
- Veolia Water Technologies, Haslegårdsvænger 18, 8210 Århus V, Denmark
| | - Heidi G Andersen
- Veolia Water Technologies, Haslegårdsvænger 18, 8210 Århus V, Denmark
| | - Elena Torresi
- AnoxKaldnes Technology, Klosterängsvägen 11A, 226 47 Lund, Sweden
| | - Caroline Kragelund
- Department of Chemistry and Biotechnology, Danish Technological Institute, Kongsvang Allé 29, DK-8000 Århus C, Denmark
| | - Henrik R Andersen
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej 113, 2800 Kgs. Lyngby, Denmark
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4
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Mustonen V, Muruganandam G, Loris R, Kursula P, Ruskamo S. Crystal and solution structure of NDRG1, a membrane-binding protein linked to myelination and tumour suppression. FEBS J 2021; 288:3507-3529. [PMID: 33305529 DOI: 10.1111/febs.15660] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/27/2020] [Accepted: 12/07/2020] [Indexed: 01/13/2023]
Abstract
N-myc downstream-regulated gene 1 (NDRG1) is a tumour suppressor involved in vesicular trafficking and stress response. NDRG1 participates in peripheral nerve myelination, and mutations in the NDRG1 gene lead to Charcot-Marie-Tooth neuropathy. The 43-kDa NDRG1 is considered as an inactive member of the α/β hydrolase superfamily. In addition to a central α/β hydrolase fold domain, NDRG1 consists of a short N terminus and a C-terminal region with three 10-residue repeats. We determined the crystal structure of the α/β hydrolase domain of human NDRG1 and characterised the structure and dynamics of full-length NDRG1. The structure of the α/β hydrolase domain resembles the canonical α/β hydrolase fold with a central β sheet surrounded by α helices. Small-angle X-ray scattering and CD spectroscopy indicated a variable conformation for the N- and C-terminal regions. NDRG1 binds to various types of lipid vesicles, and the conformation of the C-terminal region is modulated upon lipid interaction. Intriguingly, NDRG1 interacts with metal ions, such as nickel, but is prone to aggregation in their presence. Our results uncover the structural and dynamic features of NDRG1, as well as elucidate its interactions with metals and lipids, and encourage studies to identify a putative hydrolase activity of NDRG1. DATABASES: The coordinates and structure factors for the crystal structure of human NDRG1 were deposited to PDB (PDB ID: 6ZMM).
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Affiliation(s)
- Venla Mustonen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Gopinath Muruganandam
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Belgium
| | - Remy Loris
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium.,Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Belgium
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland.,Department of Biomedicine, University of Bergen, Norway
| | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
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Cloning, overexpression, purification, characterization and structural modelling of a metabolically active Fe 2+ dependent 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (CpsA) from Bacillus cereus strain AOA-CPS_1. Int J Biol Macromol 2020; 161:247-257. [PMID: 32512093 DOI: 10.1016/j.ijbiomac.2020.05.268] [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: 01/05/2020] [Revised: 05/24/2020] [Accepted: 05/30/2020] [Indexed: 11/23/2022]
Abstract
2,6-Dichloro-p-hydroquinone (DiCHQ) aromatic-ring cleavage by DiCHQ 1,2-dioxygenase (CpsA) is very crucial for complete transformation of pentachlorophenol (PCP) to 2-chloromaleylacetate in Bacillus cereus AOA-CPS_1 (BcAOA). The 978 bp gene (cpsA) was detected and amplified in the genome of BcAOA; cloned, overexpressed and purified to homogeneity. CpsA showed a single ≅36.9 kDa protein band on SDS-PAGE and exhibited optimum activity at 30 °C and pH 9.0. CpsA was stable between 20 °C and 40 °C, and also retained about 90% of its activity at 60 °C for 120 min. The enzyme retained about 90% activity between pH 9.0 and 11.5 and 60% activity at pH 13.0. CpsA was found to be Fe2+ dependent as about 90% increased activity was observed in the presence of FeSO4. CpsA showed apparent vmax, Km, kcat and kcat/Km of 27.77 ± 0.9 μMs-1, 0.990 ± 0.03 mM, 4.20 ± 0.04 s-1 and 4.24 ± 0.03 s-1 mM-1, respectively at pH 9.0. Analysis of the reaction products via GC-MS confirmed 2-chloromaleylacetate as the ring-cleavage product. CpsA 3D structure revealed a conserved 2-His-1-carboxylate facial triad motif (His 9, His 244 and Thr 11), with Fe3+ at the centre. Findings from this study provide new insights into the involvement of this enzyme in PCP degradation and suggests alternate possible mechanism of ring-cleavage by dioxygenases.
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6
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Sharma V, Kumar R, Sharma VK, Yadav AK, Tiirola M, Sharma PK. Expression, purification, characterization and in silico analysis of newly isolated hydrocarbon degrading bleomycin resistance dioxygenase. Mol Biol Rep 2019; 47:533-544. [PMID: 31724125 DOI: 10.1007/s11033-019-05159-x] [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: 07/09/2019] [Accepted: 10/23/2019] [Indexed: 10/25/2022]
Abstract
In the present investigation, we report cloning, expression, purification and characterization of a novel Bleomycin Resistance Dioxygenase (BRPD). His-tagged fusion protein was purified to homogeneity using Ni-NTA affinity chromatography, yielding 1.2 mg of BRPD with specific activity of 6.25 U mg-1 from 600 ml of E. coli culture. Purified enzyme was a dimer with molecular weight ~ 26 kDa in SDS-PAGE and ~ 73 kDa in native PAGE analysis. The protein catalyzed breakdown of hydrocarbon substrates, including catechol and hydroquinone, in the presence of metal ions, as characterized via spectrophotometric analysis of the enzymatic reactions. Bleomycin binding was proven using the EMSA gel retardation assay, and the putative bleomycin binding site was further determined by in silico analysis. Molecular dynamic simulations revealed that BRPD attains octahedral configuration in the presence of Fe2+ ion, forming six co-ordinate complexes to degrade hydroquinone-like molecules. In contrary, in the presence of Zn2+ ion BRPD adopts tetrahedral configuration, which enables degradation of catechol-like molecules.
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Affiliation(s)
- Vinay Sharma
- Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Pb, India
| | - Rajender Kumar
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
| | | | | | - Marja Tiirola
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, 40014, Jyvaskyla, Finland
| | - Pushpender Kumar Sharma
- Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Pb, India.
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7
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Wang Y, Shin I, Fu Y, Colabroy KL, Liu A. Crystal Structures of L-DOPA Dioxygenase from Streptomyces sclerotialus. Biochemistry 2019; 58:5339-5350. [PMID: 31180203 DOI: 10.1021/acs.biochem.9b00396] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Extradiol dioxygenases are essential biocatalysts for breaking down catechols. The vicinal oxygen chelate (VOC) superfamily contains a large number of extradiol dioxygenases, most of which are found as part of catabolic pathways degrading a variety of natural and human-made aromatic rings. The l-3,4-dihydroxyphenylalanine (L-DOPA) extradiol dioxygenases compose a multitude of pathways that produce various antibacterial or antitumor natural products. The structural features of these dioxygenases are anticipated to be distinct from those of other VOC extradiol dioxygenases. Herein, we identified a new L-DOPA dioxygenase from the thermophilic bacterium Streptomyces sclerotialus (SsDDO) through a sequence and genome context analysis. The activity of SsDDO was kinetically characterized with L-DOPA using an ultraviolet-visible spectrophotometer and an oxygen electrode. The optimal temperature of the assay was 55 °C, at which the Km and kcat of SsDDO were 110 ± 10 μM and 2.0 ± 0.1 s-1, respectively. We determined the de novo crystal structures of SsDDO in the ligand-free form and as a substrate-bound complex, refined to 1.99 and 2.31 Å resolution, respectively. These structures reveal that SsDDO possesses a form IV arrangement of βαβββ modules, the first characterization of this assembly from among the VOC/type I extradiol dioxygenase protein family. Electron paramagnetic resonance spectra of Fe-NO adducts for the resting and substrate-bound enzyme were obtained. This work contributes to our understanding of a growing class of topologically distinct VOC dioxygenases, and the obtained structural features will improve our understanding of the extradiol cleavage reaction within the VOC superfamily.
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Affiliation(s)
- Yifan Wang
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Inchul Shin
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
| | - Yizhi Fu
- Department of Chemistry , Muhlenberg College , Allentown , Pennsylvania 18104 , United States
| | - Keri L Colabroy
- Department of Chemistry , Muhlenberg College , Allentown , Pennsylvania 18104 , United States
| | - Aimin Liu
- Department of Chemistry , University of Texas at San Antonio , San Antonio , Texas 78249 , United States
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8
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Burrows JE, Paulson MQ, Altman ER, Vukovic I, Machonkin TE. The role of halogen substituents and substrate pK a in defining the substrate specificity of 2,6-dichlorohydroquinone 1,2-dioxygenase (PcpA). J Biol Inorg Chem 2019; 24:575-589. [PMID: 31089822 DOI: 10.1007/s00775-019-01663-4] [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: 03/29/2019] [Accepted: 05/07/2019] [Indexed: 12/01/2022]
Abstract
2,6-Dichlorohydroquinone 1,2-dioxygenase (PcpA) is a non-heme Fe(II) enzyme that is specific for ortho-dihalohydroquinones. Here we deconvolute the role of halogen polarizability vs. substrate pKa in defining this specificity, and show how substrate binding compares to the structurally homologous catechol extradiol dioxygenases. The substrates 2,6-dichloro- and 2,6-dibromohydroquinone (polarizable halogens, pKa1 = 7.3), 2,6-difluorohydroquinone (nonpolarizable halogens, pKa1 = 7.5), and 2-chloro-6-methylhydroquinone (polarizable halogen, pKa1 = 9.0) were examined through spectrophotometric titrations and steady-state kinetics. The results show that binding of the substrates to the enzyme decreased [Formula: see text] by about 0.5, except for 2,6-difluorohydroquinone, which showed no change. Additionally, the Kd values of 2,6-dichloro- and 2,6-dibromohydroquinone are about equal to their respective [Formula: see text]. For comparison, with catechol 2,3-dioxygenase (XylE), the substrates 4-methyl- and 3-bromocatechol are bound to the enzyme exclusively in the monoanion form over a wide pH range, indicating a [Formula: see text] of at least - 2.9 and - 1.2, respectively. The steady-state kinetic studies showed that 2,6-difluorohydroquinone is a poor substrate, with [Formula: see text] approximately 40-fold lower and [Formula: see text] 20-fold higher than 2,6-dichlorohydroquinone, despite its similar pKa1. Likewise, the pH dependence of [Formula: see text] for 2-chloro-6-methylhydroquinone is nearly identical to that of 2,6-dichlorohydroquinone, despite its very different pKa1. These results show that (1) it is clearly the halogen polarizability and not the lower substrate pKa that determines the substrate specificity of PcpA, and (2) that PcpA, unlike the catechol extradiol dioxygenases, lacks an active site base that assists with substrate deprotonation, highlighting a key functional difference in what are otherwise similar active sites that defines their different reactivity.
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Affiliation(s)
- Julia E Burrows
- Department of Chemistry, Whitman College, 345 Boyer Ave, Walla Walla, WA, 99362, USA
| | - Monica Q Paulson
- Department of Chemistry, Whitman College, 345 Boyer Ave, Walla Walla, WA, 99362, USA
| | - Emma R Altman
- Department of Chemistry, Whitman College, 345 Boyer Ave, Walla Walla, WA, 99362, USA
| | - Ivana Vukovic
- Department of Chemistry, Whitman College, 345 Boyer Ave, Walla Walla, WA, 99362, USA
| | - Timothy E Machonkin
- Department of Chemistry, Whitman College, 345 Boyer Ave, Walla Walla, WA, 99362, USA.
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9
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Cheng M, Yan X, He J, Qiu J, Chen Q. Comparative genome analysis reveals the evolution of chloroacetanilide herbicide mineralization in Sphingomonas wittichii DC-6. Arch Microbiol 2019; 201:907-918. [PMID: 30997539 DOI: 10.1007/s00203-019-01660-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/13/2022]
Abstract
The environmental fate of the extensively used chloroacetanilide herbicides (CH) has been a cause of increasing concern in the past decade because of their carcinogenic properties. Although microbes play important roles in CH degradation, Sphingomonas wittichii DC-6 was the first reported CH-mineralizing bacterium. In this study, the complete genome of strain DC-6 was sequenced and comparative genomic analysis was performed using strain DC-6 and other three partial CH-degrading bacteria, Sphingobium quisquiliarum DC-2, Sphingobium baderi DE-13, and Sphingobium sp. MEA3-1. 16S rDNA phylogenetic analysis indicated that strain DC-2, MEA3-1, and DE-13 are closely related and DC-6 has relatively distant genetic relationship with the other three strains. The identified CH degradation genes responsible for the upstream and downstream pathway, including cndA, cmeH, meaXY, and meaAB, were all located in conserved DNA fragments (or genetic islands) in the vicinity of mobile element proteins. Protein BLAST in the NCBI database showed that cndA and cmeH were present in the genomes of other sequenced strains isolated from various habitats; however, the gene compositions in these host strains were completely different from those of other sphingomonads, and codon usage of genes for upstream pathway were also different from that of downstream pathway. These results showed that the upstream and downstream pathways of CH degradation in strain DC-6 have evolved by horizontal gene transfer and gene combination. In addition, the genes of the ring-cleavage pathway were not conserved and may have evolved directly from bacterial degradation of hydroxyquinol. The present study provides insights into the evolutionary strategy and microbial catabolic pathway of CH mineralization.
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Affiliation(s)
- Minggen Cheng
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xin Yan
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jian He
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jiguo Qiu
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Qing Chen
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China. .,College of Life Sciences, Zaozhuang University, Zaozhuang, 277160, Shandong, China.
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10
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Jung JH, Joe MH, Kim DH, Park H, Choi JI, Lim S. Complete genome sequence of Planococcus sp. PAMC21323 isolated from Antarctica and its metabolic potential to detoxify pollutants. Stand Genomic Sci 2018; 13:31. [PMID: 30455841 PMCID: PMC6225704 DOI: 10.1186/s40793-018-0334-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 10/25/2018] [Indexed: 11/10/2022] Open
Abstract
The Planococcus sp. PAMC21323 is a yellow pigment-producing bacterium isolated from King George Island in Antarctica; it has a broad growth temperature range of 5-40 °C. Herein, we describe the complete genome sequence information of the genus Planococcus with its annotated sequence, genetic features for bioremediation, and oxidative stress capacity. The Planococcus sp. PAMC21323 possesses chromosomal DNA (3,196,500-bp) with plasmid DNA (3364-bp). The complete 3,199,864-bp of the genome consists of 3171 genes including 60 transfer RNAs and 24 ribosomal RNAs. Strain PAMC21323 encodes various genes associated with detoxification of heavy metal ions and aromatic hydrocarbons. Moreover, it is equipped with diverse stress response systems, which can be used to sense the internal and oxidative stresses caused by detoxification. This is the first report highlighting the genetic potential of Planococcus sp. PAMC21323 in bioremediation, suggesting application of this psychrotrophic strain in bioremediation in harsh environments.
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Affiliation(s)
- Jong-Hyun Jung
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212 Republic of Korea
- Department of Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, Daejeon, 34113 Republic of Korea
| | - Min-Ho Joe
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212 Republic of Korea
| | - Dong-Ho Kim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212 Republic of Korea
| | - Hyun Park
- Korea Polar Research Institute, Incheon, 21990 Republic of Korea
| | - Jong-il Choi
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju, 61186 Republic of Korea
| | - Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212 Republic of Korea
- Department of Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, Daejeon, 34113 Republic of Korea
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11
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Zhao H, Xu Y, Lin S, Spain JC, Zhou NY. The molecular basis for the intramolecular migration (NIH shift) of the carboxyl group duringpara-hydroxybenzoate catabolism. Mol Microbiol 2018; 110:411-424. [PMID: 30070064 DOI: 10.1111/mmi.14094] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Huan Zhao
- State Key Laboratory of Microbial Metabolism; and School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Ying Xu
- State Key Laboratory of Microbial Metabolism; and School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism; and School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Jim C. Spain
- Center for Environmental Diagnostics & Bioremediation; University of West Florida; 11000 University Parkway Pensacola FL 32514-5751 USA
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism; and School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
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12
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Ferraroni M, Da Vela S, Kolvenbach BA, Corvini PFX, Scozzafava A. The crystal structures of native hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 and of substrate and inhibitor complexes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:520-530. [PMID: 28232026 DOI: 10.1016/j.bbapap.2017.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/24/2017] [Accepted: 02/17/2017] [Indexed: 10/20/2022]
Abstract
The crystal structure of hydroquinone 1,2-dioxygenase, a Fe(II) ring cleaving dioxygenase from Sphingomonas sp. strain TTNP3, which oxidizes a wide range of hydroquinones to the corresponding 4-hydroxymuconic semialdehydes, has been solved by Molecular Replacement, using the coordinates of PnpCD from Pseudomonas sp. strain WBC-3. The enzyme is a heterotetramer, constituted of two subunits α and two β of 19 and 38kDa, respectively. Both the two subunits fold as a cupin, but that of the small α subunit lacks a competent metal binding pocket. Two tetramers are present in the asymmetric unit. Each of the four β subunits in the asymmetric unit binds one Fe(II) ion. The iron ion in each β subunit is coordinated to three protein residues, His258, Glu264, and His305 and a water molecule. The crystal structures of the complexes with the substrate methylhydroquinone, obtained under anaerobic conditions, and with the inhibitors 4-hydroxybenzoate and 4-nitrophenol were also solved. The structures of the native enzyme and of the complexes present significant differences in the active site region compared to PnpCD, the other hydroquinone 1,2-dioxygenase of known structure, and in particular they show a different coordination at the metal center.
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Affiliation(s)
- Marta Ferraroni
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Via della Lastruccia 3, I-50019, Sesto Fiorentino, FI, Italy.
| | - Stefano Da Vela
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Via della Lastruccia 3, I-50019, Sesto Fiorentino, FI, Italy.
| | - Boris A Kolvenbach
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, 4132 Muttenz, Switzerland.
| | - Philippe F X Corvini
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, 4132 Muttenz, Switzerland.
| | - Andrea Scozzafava
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Via della Lastruccia 3, I-50019, Sesto Fiorentino, FI, Italy.
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13
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Fernandez-Fontaina E, Gomes IB, Aga DS, Omil F, Lema JM, Carballa M. Biotransformation of pharmaceuticals under nitrification, nitratation and heterotrophic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 541:1439-1447. [PMID: 26479917 DOI: 10.1016/j.scitotenv.2015.10.010] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/02/2015] [Accepted: 10/03/2015] [Indexed: 06/05/2023]
Abstract
The effect of nitrification, nitratation and heterotrophic conditions on the biotransformation of several pharmaceuticals in a highly enriched nitrifying activated sludge was evaluated in this study by selective activation of ammonia oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB) and heterotrophic bacteria. Nitrifiers displayed a noticeable capacity to process ibuprofen due to hydroxylation by ammonia monooxygenase (AMO) to produce 2-hydroxy-ibuprofen. Naproxen was also biotransformed under nitrifying conditions. On the other hand, heterotrophic bacteria present in the nitrifying activated sludge (NAS) biotransformed sulfamethoxazole. In contrast, both nitrifying and heterotrophic activities were ineffective against diclofenac, diazepam, carbamazepine and trimethoprim. Similar biotransformation rates of erythromycin, roxithromycin and fluoxetine were observed under all conditions tested. Overall, results from this study give more evidence on the role of the different microbial communities present in activated sludge reactors on the biological removal of pharmaceuticals.
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Affiliation(s)
- E Fernandez-Fontaina
- Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - I B Gomes
- Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - D S Aga
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, United States
| | - F Omil
- Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - J M Lema
- Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - M Carballa
- Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
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14
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Schofield JA, Brennessel WW, Urnezius E, Rokhsana D, Boshart MD, Juers DH, Holland PL, Machonkin TE. Metal-Halogen Secondary Bonding in a 2,5-Dichlorohydroquinonate Cobalt(II) Complex: Insight into Substrate Coordination in the Chlorohydroquinone Dioxygenase PcpA. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500845] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Liu S, Su T, Zhang C, Zhang WM, Zhu D, Su J, Wei T, Wang K, Huang Y, Guo L, Xu S, Zhou NY, Gu L. Crystal structure of PnpCD, a two-subunit hydroquinone 1,2-dioxygenase, reveals a novel structural class of Fe2+-dependent dioxygenases. J Biol Chem 2015; 290:24547-60. [PMID: 26304122 DOI: 10.1074/jbc.m115.673558] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Indexed: 11/06/2022] Open
Abstract
Aerobic microorganisms have evolved a variety of pathways to degrade aromatic and heterocyclic compounds. However, only several classes of oxygenolytic fission reaction have been identified for the critical ring cleavage dioxygenases. Among them, the most well studied dioxygenases proceed via catecholic intermediates, followed by noncatecholic hydroxy-substituted aromatic carboxylic acids. Therefore, the recently reported hydroquinone 1,2-dioxygenases add to the diversity of ring cleavage reactions. Two-subunit hydroquinone 1,2-dioxygenase PnpCD, the key enzyme in the hydroquinone pathway of para-nitrophenol degradation, catalyzes the ring cleavage of hydroquinone to γ-hydroxymuconic semialdehyde. Here, we report three PnpCD structures, named apo-PnpCD, PnpCD-Fe(3+), and PnpCD-Cd(2+)-HBN (substrate analog hydroxyenzonitrile), respectively. Structural analysis showed that both the PnpC and the C-terminal domains of PnpD comprise a conserved cupin fold, whereas PnpC cannot form a competent metal binding pocket as can PnpD cupin. Four residues of PnpD (His-256, Asn-258, Glu-262, and His-303) were observed to coordinate the iron ion. The Asn-258 coordination is particularly interesting because this coordinating residue has never been observed in the homologous cupin structures of PnpCD. Asn-258 is proposed to play a pivotal role in binding the iron prior to the enzymatic reaction, but it might lose coordination to the iron when the reaction begins. PnpD also consists of an intriguing N-terminal domain that might have functions other than nucleic acid binding in its structural homologs. In summary, PnpCD has no apparent evolutionary relationship with other iron-dependent dioxygenases and therefore defines a new structural class. The study of PnpCD might add to the understanding of the ring cleavage of dioxygenases.
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Affiliation(s)
- Shiheng Liu
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Tiantian Su
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Cong Zhang
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Wen-Mao Zhang
- the Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071
| | - Deyu Zhu
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Jing Su
- the College of Food Science and Engineering, Qilu University of Technology, Jinan, Shandong 250353, and
| | - Tiandi Wei
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Kang Wang
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Yan Huang
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Liming Guo
- the Rizhao Center for Diseases Prevention and Control, Rizhao Health Bureau, Rizhao, Shandong 276826, China
| | - Sujuan Xu
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100
| | - Ning-Yi Zhou
- the Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, the State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240,
| | - Lichuan Gu
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100,
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16
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Eppinger E, Ferraroni M, Bürger S, Steimer L, Peng G, Briganti F, Stolz A. Function of different amino acid residues in the reaction mechanism of gentisate 1,2-dioxygenases deduced from the analysis of mutants of the salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1425-37. [PMID: 26093111 DOI: 10.1016/j.bbapap.2015.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/28/2015] [Accepted: 06/15/2015] [Indexed: 11/24/2022]
Abstract
The genome of the α-proteobacterium Pseudaminobacter salicylatoxidans codes for a ferrous iron containing ring-fission dioxygenase which catalyzes the 1,2-cleavage of (substituted) salicylate(s), gentisate (2,5-dihydroxybenzoate), and 1-hydroxy-2-naphthoate. Sequence alignments suggested that the "salicylate 1,2-dioxygenase" (SDO) from this strain is homologous to gentisate 1,2-dioxygenases found in bacteria, archaea and fungi. In the present study the catalytic mechanism of the SDO and gentisate 1,2-dioxygenases in general was analyzed based on sequence alignments, mutational and previously performed crystallographic studies and mechanistic comparisons with "extradiol- dioxygenases" which cleave aromatic nuclei in the 2,3-position. Different highly conserved amino acid residues that were supposed to take part in binding and activation of the organic substrates were modified in the SDO by site-specific mutagenesis and the enzyme variants subsequently analyzed for the conversion of salicylate, gentisate and 1-hydroxy-2-naphthoate. The analysis of enzyme variants which carried exchanges in the positions Arg83, Trp104, Gly106, Gln108, Arg127, His162 and Asp174 demonstrated that Arg83 and Arg127 were indispensable for enzymatic activity. In contrast, residual activities were found for variants carrying mutations in the residues Trp104, Gly106, Gln108, His162, and Asp174 and some of these mutants still could oxidize gentisate, but lost the ability to convert salicylate. The results were used to suggest a general reaction mechanism for gentisate-1,2-dioxygenases and to assign to certain amino acid residues in the active site specific functions in the cleavage of (substituted) salicylate(s).
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Affiliation(s)
- Erik Eppinger
- Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany
| | - Marta Ferraroni
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentin, Italy
| | - Sibylle Bürger
- Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany
| | - Lenz Steimer
- Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany
| | - Grace Peng
- Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany
| | - Fabrizio Briganti
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentin, Italy
| | - Andreas Stolz
- Institut für Mikrobiologie, Universität Stuttgart, Stuttgart, Germany.
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17
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Sattler SA, Wang X, Lewis KM, DeHan PJ, Park CM, Xin Y, Liu H, Xian M, Xun L, Kang C. Characterizations of Two Bacterial Persulfide Dioxygenases of the Metallo-β-lactamase Superfamily. J Biol Chem 2015; 290:18914-23. [PMID: 26082492 DOI: 10.1074/jbc.m115.652537] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Indexed: 12/21/2022] Open
Abstract
Persulfide dioxygenases (PDOs), also known as sulfur dioxygenases (SDOs), oxidize glutathione persulfide (GSSH) to sulfite and GSH. PDOs belong to the metallo-β-lactamase superfamily and play critical roles in animals, plants, and microorganisms, including sulfide detoxification. The structures of two PDOs from human and Arabidopsis thaliana have been reported; however, little is known about the substrate binding and catalytic mechanism. The crystal structures of two bacterial PDOs from Pseudomonas putida and Myxococcus xanthus were determined at 1.5- and 2.5-Å resolution, respectively. The structures of both PDOs were homodimers, and their metal centers and β-lactamase folds were superimposable with those of related enzymes, especially the glyoxalases II. The PDOs share similar Fe(II) coordination and a secondary coordination sphere-based hydrogen bond network that is absent in glyoxalases II, in which the corresponding residues are involved instead in coordinating a second metal ion. The crystal structure of the complex between the Pseudomonas PDO and GSH also reveals the similarity of substrate binding between it and glyoxalases II. Further analysis implicates an identical mode of substrate binding by known PDOs. Thus, the data not only reveal the differences in metal binding and coordination between the dioxygenases and the hydrolytic enzymes in the metallo-β-lactamase superfamily, but also provide detailed information on substrate binding by PDOs.
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Affiliation(s)
- Steven A Sattler
- From the School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660
| | - Xia Wang
- From the School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China, and
| | - Kevin M Lewis
- the Department of Chemistry, Washington State University, Pullman, Washington 99164-4630
| | - Preston J DeHan
- From the School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660
| | - Chung-Min Park
- the Department of Chemistry, Washington State University, Pullman, Washington 99164-4630
| | - Yufeng Xin
- the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China, and
| | - Honglei Liu
- the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China, and
| | - Ming Xian
- the Department of Chemistry, Washington State University, Pullman, Washington 99164-4630
| | - Luying Xun
- From the School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China, and
| | - ChulHee Kang
- From the School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, the Department of Chemistry, Washington State University, Pullman, Washington 99164-4630
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18
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Hayes RP, Moural TW, Lewis KM, Onofrei D, Xun L, Kang C. Structures of the inducer-binding domain of pentachlorophenol-degrading gene regulator PcpR from Sphingobium chlorophenolicum. Int J Mol Sci 2014; 15:20736-52. [PMID: 25397598 PMCID: PMC4264193 DOI: 10.3390/ijms151120736] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/29/2014] [Accepted: 10/30/2014] [Indexed: 11/16/2022] Open
Abstract
PcpR is a LysR-type transcription factor from Sphingobium chlorophenolicum L-1 that is responsible for the activation of several genes involved in polychlorophenol degradation. PcpR responds to several polychlorophenols in vivo. Here, we report the crystal structures of the inducer-binding domain of PcpR in the apo-form and binary complexes with pentachlorophenol (PCP) and 2,4,6-trichlorophenol (2,4,6-TCP). Both X-ray crystal structures and isothermal titration calorimetry data indicated the association of two PCP molecules per PcpR, but only one 2,4,6-TCP molecule. The hydrophobic nature and hydrogen bonds of one binding cavity allowed the tight association of both PCP (Kd = 110 nM) and 2,4,6-TCP (Kd = 22.8 nM). However, the other cavity was unique to PCP with much weaker affinity (Kd = 70 μM) and thus its significance was not clear. Neither phenol nor benzoic acid displayed any significant affinity to PcpR, indicating a role of chlorine substitution in ligand specificity. When PcpR is compared with TcpR, a LysR-type regulator controlling the expression of 2,4,6-trichlorophenol degradation in Cupriavidus necator JMP134, most of the residues constituting the two inducer-binding cavities of PcpR are different, except for their general hydrophobic nature. The finding concurs that PcpR uses various polychlorophenols as long as it includes 2,4,6-trichlorophenol, as inducers; whereas TcpR is only responsive to 2,4,6-trichlorophenol.
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Affiliation(s)
- Robert P Hayes
- Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA.
| | - Timothy W Moural
- Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA.
| | - Kevin M Lewis
- Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA.
| | - David Onofrei
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA.
| | - Luying Xun
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA.
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, WA 99164-4630, USA.
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19
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Machonkin TE, Boshart MD, Schofield JA, Rodriguez MM, Grubel K, Rokhsana D, Brennessel WW, Holland PL. Structural and spectroscopic characterization of iron(II), cobalt(II), and nickel(II) ortho-dihalophenolate complexes: insights into metal-halogen secondary bonding. Inorg Chem 2014; 53:9837-48. [PMID: 25167329 DOI: 10.1021/ic501424e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metal complexes incorporating the tris(3,5-diphenylpyrazolyl)borate ligand (Tp(Ph2)) and ortho-dihalophenolates were synthesized and characterized in order to explore metal-halogen secondary bonding in biorelevant model complexes. The complexes Tp(Ph2)ML were synthesized and structurally characterized, where M was Fe(II), Co(II), or Ni(II) and L was either 2,6-dichloro- or 2,6-dibromophenolate. All six complexes exhibited metal-halogen secondary bonds in the solid state, with distances ranging from 2.56 Å for the Tp(Ph2)Ni(2,6-dichlorophenolate) complex to 2.88 Å for the Tp(Ph2)Fe(2,6-dibromophenolate) complex. Variable temperature NMR spectra of the Tp(Ph2)Co(2,6-dichlorophenolate) and Tp(Ph2)Ni(2,6-dichlorophenolate) complexes showed that rotation of the phenolate, which requires loss of the secondary bond, has an activation barrier of ~30 and ~37 kJ/mol, respectively. Density functional theory calculations support the presence of a barrier for disruption of the metal-halogen interaction during rotation of the phenolate. On the other hand, calculations using the spectroscopically calibrated angular overlap method suggest essentially no contribution of the halogen to the ligand-field splitting. Overall, these results provide the first quantitative measure of the strength of a metal-halogen secondary bond and demonstrate that it is a weak noncovalent interaction comparable in strength to a hydrogen bond. These results provide insight into the origin of the specificity of the enzyme 2,6-dichlorohydroquinone 1,2-dioxygenase (PcpA), which is specific for ortho-dihalohydroquinone substrates and phenol inhibitors.
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Affiliation(s)
- Timothy E Machonkin
- Department of Chemistry, Whitman College , Walla Walla, Washington 99362, United States
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20
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Fielding AJ, Lipscomb JD, Que L. A two-electron-shell game: intermediates of the extradiol-cleaving catechol dioxygenases. J Biol Inorg Chem 2014; 19:491-504. [PMID: 24615282 DOI: 10.1007/s00775-014-1122-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 02/13/2014] [Indexed: 11/29/2022]
Abstract
Extradiol-cleaving catechol dioxygenases function by binding both the organic substrate and O2 at a divalent metal center in the active site. They have proven to be a particularly versatile group of enzymes with which to study the O2 activation process. Here, recent studies of homoprotocatechuate 2,3-dioxygenase are summarized, showing how nature can utilize the enzyme structure and the properties of the metal and the substrate to select among many possible chemical paths to achieve both specificity and efficiency. Possible intermediates in the mechanism have been trapped by swapping active-site metals, introducing active-site amino acid substituted variants, and using substrates with different electron-donating capacities. Although each of these intermediates could form part of a viable reaction pathway, kinetic measurements significantly limit the likely candidates. Structural, kinetic, spectroscopic, and computational analyses of the various intermediates shed light on how catalytic efficiency can be achieved.
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Affiliation(s)
- Andrew J Fielding
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
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Hydroquinone: environmental pollution, toxicity, and microbial answers. BIOMED RESEARCH INTERNATIONAL 2013; 2013:542168. [PMID: 23936816 PMCID: PMC3727088 DOI: 10.1155/2013/542168] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 06/20/2013] [Indexed: 12/12/2022]
Abstract
Hydroquinone is a major benzene metabolite, which is a well-known haematotoxic and carcinogenic agent associated with malignancy in occupational environments. Human exposure to hydroquinone can occur by dietary, occupational, and environmental sources. In the environment, hydroquinone showed increased toxicity for aquatic organisms, being less harmful for bacteria and fungi. Recent pieces of evidence showed that hydroquinone is able to enhance carcinogenic risk by generating DNA damage and also to compromise the general immune responses which may contribute to the impaired triggering of the host immune reaction. Hydroquinone bioremediation from natural and contaminated sources can be achieved by the use of a diverse group of microorganisms, ranging from bacteria to fungi, which harbor very complex enzymatic systems able to metabolize hydroquinone either under aerobic or anaerobic conditions. Due to the recent research development on hydroquinone, this review underscores not only the mechanisms of hydroquinone biotransformation and the role of microorganisms and their enzymes in this process, but also its toxicity.
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