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Han Q, Xing Y, Yan L, Cao L, Li Z, Jiang J, Xu X, Chen C. Biodegradation of Cyromazine by Mycobacterium sp. M15: Performance, Degradation Pathways, and Key Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18840-18850. [PMID: 39140307 DOI: 10.1021/acs.jafc.4c04637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Cyromazine, a triazine insecticide, raises food safety concerns due to residues in vegetables like cowpeas. Microbial metabolism is key for pesticide elimination, but bacteria efficient in cyromazine degradation are limited, with uncharacterized enzymes. This study isolated a highly efficient cyromazine-degrading bacterium, Mycobacterium sp. M15, from a cowpea field. M15 utilized cyromazine as the sole carbon source for its growth and completely degraded 0.5 mM cyromazine within 24 h. The degradation pathway involved hydrolyzing cyromazine to N-cyclopropylammeline and further to N-cyclopropylammelide, with amino groups removed sequentially. The cyclopropylamine group in N-cyclopropionamide continued to hydrolyze to cyanuric acid. A protein, CriA, identified as an aminohydrolase in M15, degraded cyromazine to N-cyclopropylammeline. Using CriA reduced cyromazine residues on cowpea surfaces and completely degraded them in immersion solutions. These findings offer insights into cyromazine's microbial degradation mechanism and highlight the potential of cyromazine-degrading enzymes in enhancing food safety.
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Affiliation(s)
- Qi Han
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Youwen Xing
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lulu Yan
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lulu Cao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zehao Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiandong Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xihui Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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2
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Chen S, Ma L, Wang Y. Kinetic isotope effects of C and N indicate different transformation mechanisms between atzA- and trzN-harboring strains in dechlorination of atrazine. Biodegradation 2022; 33:207-221. [PMID: 35257297 DOI: 10.1007/s10532-022-09977-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/18/2022] [Indexed: 11/02/2022]
Abstract
Compound-specific stable isotope analysis provides an alternative method to insight into the biotransformation mechanisms of diffuse organic pollutants in the environment, e.g., the endocrine disruptor herbicide atrazine. Biotic hydrolysis process catalyzed by chlorohydrolase AtzA and TrzN plays an important role in the detoxification of atrazine, while the catalytic mechanism of AtzA is still speculative. To investigate the catalytic mechanism of AtzA and answer whether both enzymes catalyze hydrolytic dechlorination of atrazine by the same mechanism, in this study, apparent kinetic isotope effects (AKIE) for carbon and nitrogen were observed by three atzA-harboring bacterial isolates and their membrane-free extracts. The AKIEs obtained from atzA-harboring bacterial isolates (AKIEC = 1.021 ± 0.010, AKIEN = 0.992 ± 0.003) were statistically different from that of trzN-harboring strains (AKIEC = 1.040 ± 0.006, AKIEN = 0.983 ± 0.006), confirming the different activation mechanisms of atrazine preceding to nucleophilic aromatic substitution of Cl atom in actual enzymatic reaction catalyzed by AtzA and TrzN, despite the limitation of variable dual-element isotope plots. The lower degree of normal carbon and inverse nitrogen isotope fractionation observed from atzA-harboring strains, suggesting AtzA catalyzing hydrolytic dechlorination of atrazine by coordination of Cl and one aromatic N to the Fe2+ drawing electron density from carbon-chlorine bond that facilitating the nucleophilic attack, rather than in TrzN case that protonation of aromatic N increasing nucleophilic substitution of Cl atom. This study suggests considering the potential influences of phylogenetic diversity of bacterial isolates and evolution of enzymes on the applications of CSIA method in future study.
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Affiliation(s)
- Songsong Chen
- College of Architecture and Urban Planning, Tongji University, 1239, Siping Road, Shanghai, 200092, People's Republic of China
| | - Limin Ma
- College of Environmental Science and Engineering, Tongji University, 1239, Siping Road, Shanghai, 200092, People's Republic of China.
| | - Yuncai Wang
- College of Architecture and Urban Planning, Tongji University, 1239, Siping Road, Shanghai, 200092, People's Republic of China.
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3
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Copley SD. Evolution of new enzymes by gene duplication and divergence. FEBS J 2021; 287:1262-1283. [PMID: 32250558 DOI: 10.1111/febs.15299] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 12/22/2022]
Abstract
Thousands of new metabolic and regulatory enzymes have evolved by gene duplication and divergence since the dawn of life. New enzyme activities often originate from promiscuous secondary activities that have become important for fitness due to a change in the environment or a mutation. Mutations that make a promiscuous activity physiologically relevant can occur in the gene encoding the promiscuous enzyme itself, but can also occur elsewhere, resulting in increased expression of the enzyme or decreased competition between the native and novel substrates for the active site. If a newly useful activity is inefficient, gene duplication/amplification will set the stage for divergence of a new enzyme. Even a few mutations can increase the efficiency of a new activity by orders of magnitude. As efficiency increases, amplified gene arrays will shrink to provide two alleles, one encoding the original enzyme and one encoding the new enzyme. Ultimately, genomic rearrangements eliminate co-amplified genes and move newly evolved paralogs to a distant region of the genome.
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Affiliation(s)
- Shelley D Copley
- Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA
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Zhou N, Wang J, Wang W, Wu X. Purification, characterization, and catalytic mechanism of N-Isopropylammelide isopropylaminohydrolase (AtzC) involved in the degradation of s-triazine herbicides. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115803. [PMID: 33158617 DOI: 10.1016/j.envpol.2020.115803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
Deamination is ubiquitous in nature and has important biological significance. Leucobacter triazinivorans JW-1, recently isolated from sludge, can rapidly degrade s-triazine herbicides. The responsible enzymes, however, have not been purified and characterized. Herein, we purified an amidohydrolase, i.e., N-isopropylammelide isopropylaminohydrolase (AtzC) from JW-1 cells by ammonium sulfate precipitation and three chromatography steps. The purified AtzC catalyzed amidohydrolysis of N-isopropylammelide to cyanuric acid. The optimal catalytic conditions of the purified AtzC were 42 °C and pH 7.0, and the Km and Vmax of AtzC was 0.811 mM and 28.19 mmol/min·mg. AtzC could catalyze amidohydrolysis of an N-alkyl substituent from dihydroxy s-triazines to cyanuric acid. Molecular docking and structural alignments were used to infer AtzC catalytic mechanism. The structural architecture of AtzC resembled that of cytosine deaminase in class III amidohydrolase, with a single Zn2+ coordinated by His and Asp. Interestingly, the AtzC lacks an acidic residue putatively to activate water for hydrolysis as compared to the other amidohydrolases. His253 in AtzC probably functions as a single general acid-base catalyst. These findings further enhance our understanding how aminohydrolases catalyze the metabolism of s-triazine herbicides.
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Affiliation(s)
- Nan Zhou
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China
| | - Jie Wang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China
| | - Wenbo Wang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China
| | - Xiangwei Wu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China.
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Biochemical and Genetic Analysis of 4-Hydroxypyridine Catabolism in Arthrobacter sp. Strain IN13. Microorganisms 2020; 8:microorganisms8060888. [PMID: 32545463 PMCID: PMC7356986 DOI: 10.3390/microorganisms8060888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 11/16/2022] Open
Abstract
N-Heterocyclic compounds are widely spread in the biosphere, being constituents of alkaloids, cofactors, allelochemicals, and artificial substances. However, the fate of such compounds including a catabolism of hydroxylated pyridines is not yet fully understood. Arthrobacter sp. IN13 is capable of using 4-hydroxypyridine as a sole source of carbon and energy. Three substrate-inducible proteins were detected by comparing protein expression profiles, and peptide mass fingerprinting was performed using MS/MS. After partial sequencing of the genome, we were able to locate genes encoding 4-hydroxypyridine-inducible proteins and identify the kpi gene cluster consisting of 16 open reading frames. The recombinant expression of genes from this locus in Escherichia coli and Rhodococcus erytropolis SQ1 allowed an elucidation of the biochemical functions of the proteins. We report that in Arthrobacter sp. IN13, the initial hydroxylation of 4-hydroxypyridine is catalyzed by a flavin-dependent monooxygenase (KpiA). A product of the monooxygenase reaction is identified as 3,4-dihydroxypyridine, and a subsequent oxidative opening of the ring is performed by a hypothetical amidohydrolase (KpiC). The 3-(N-formyl)-formiminopyruvate formed in this reaction is further converted by KpiB hydrolase to 3-formylpyruvate. Thus, the degradation of 4-hydroxypyridine in Arthrobacter sp. IN13 was analyzed at genetic and biochemical levels, elucidating this catabolic pathway.
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Catlin DS, Yang X, Bennett B, Holz RC, Liu D. Structural basis for the hydrolytic dehalogenation of the fungicide chlorothalonil. J Biol Chem 2020; 295:8668-8677. [PMID: 32358058 DOI: 10.1074/jbc.ra120.013150] [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: 02/21/2020] [Revised: 04/29/2020] [Indexed: 11/06/2022] Open
Abstract
Cleavage of aromatic carbon-chlorine bonds is critical for the degradation of toxic industrial compounds. Here, we solved the X-ray crystal structure of chlorothalonil dehalogenase (Chd) from Pseudomonas sp. CTN-3, with 15 of its N-terminal residues truncated (ChdT), using single-wavelength anomalous dispersion refined to 1.96 Å resolution. Chd has low sequence identity (<15%) compared with all other proteins whose structures are currently available, and to the best of our knowledge, we present the first structure of a Zn(II)-dependent aromatic dehalogenase that does not require a coenzyme. ChdT forms a "head-to-tail" homodimer, formed between two α-helices from each monomer, with three Zn(II)-binding sites, two of which occupy the active sites, whereas the third anchors a structural site at the homodimer interface. The catalytic Zn(II) ions are solvent-accessible via a large hydrophobic (8.5 × 17.8 Å) opening to bulk solvent and two hydrophilic branched channels. Each active-site Zn(II) ion resides in a distorted trigonal bipyramid geometry with His117, His257, Asp116, Asn216, and a water/hydroxide as ligands. A conserved His residue, His114, is hydrogen-bonded to the Zn(II)-bound water/hydroxide and likely functions as the general acid-base. We examined substrate binding by docking chlorothalonil (2,4,5,6-tetrachloroisophtalonitrile, TPN) into the hydrophobic channel and observed that the most energetically favorable pose includes a TPN orientation that coordinates to the active-site Zn(II) ions via a CN and that maximizes a π-π interaction with Trp227 On the basis of these results, along with previously reported kinetics data, we propose a refined catalytic mechanism for Chd-mediated TPN dehalogenation.
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Affiliation(s)
- Daniel S Catlin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA
| | - Xinhang Yang
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA
| | - Brian Bennett
- Department of Physics, Marquette University, Milwaukee, Wisconsin, USA
| | - Richard C Holz
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA; Department of Chemistry, Colorado School of Mines, Golden, Colorado, USA.
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA.
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Lopes RDO, Pereira PM, Pereira ARB, Fernandes KV, Carvalho JF, França ADSD, Valente RH, da Silva M, Ferreira-Leitão VS. Atrazine, desethylatrazine (DEA) and desisopropylatrazine (DIA) degradation by Pleurotus ostreatus INCQS 40310. BIOCATAL BIOTRANSFOR 2020. [DOI: 10.1080/10242422.2020.1754805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Raquel de Oliveira Lopes
- Biocatalysis Laboratory, National Institute of Technology (INT), Ministry of Science, Technology, Innovation and Communication (MCTIC), Rio de Janeiro, Brazil
| | - Patrícia Maia Pereira
- Biocatalysis Laboratory, National Institute of Technology (INT), Ministry of Science, Technology, Innovation and Communication (MCTIC), Rio de Janeiro, Brazil
- Department of Biochemistry, Federal University of Rio de Janeiro, Institute of Chemistry, Rio de Janeiro, Brazil
| | - Aline Ramalho Brandão Pereira
- Biocatalysis Laboratory, National Institute of Technology (INT), Ministry of Science, Technology, Innovation and Communication (MCTIC), Rio de Janeiro, Brazil
- Department of Biochemistry, Federal University of Rio de Janeiro, Institute of Chemistry, Rio de Janeiro, Brazil
| | - Keysson Vieira Fernandes
- Biocatalysis Laboratory, National Institute of Technology (INT), Ministry of Science, Technology, Innovation and Communication (MCTIC), Rio de Janeiro, Brazil
| | - Julia Finamor Carvalho
- Biocatalysis Laboratory, National Institute of Technology (INT), Ministry of Science, Technology, Innovation and Communication (MCTIC), Rio de Janeiro, Brazil
- Department of Biochemistry, Federal University of Rio de Janeiro, Institute of Chemistry, Rio de Janeiro, Brazil
| | - Alexandre da Silva de França
- Biocatalysis Laboratory, National Institute of Technology (INT), Ministry of Science, Technology, Innovation and Communication (MCTIC), Rio de Janeiro, Brazil
| | - Richard Hemmi Valente
- Department of Biochemistry, Federal University of Rio de Janeiro, Institute of Chemistry, Rio de Janeiro, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Manuela da Silva
- Vice-Presidency of Research and Biological Collections, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - Viridiana S. Ferreira-Leitão
- Biocatalysis Laboratory, National Institute of Technology (INT), Ministry of Science, Technology, Innovation and Communication (MCTIC), Rio de Janeiro, Brazil
- Department of Biochemistry, Federal University of Rio de Janeiro, Institute of Chemistry, Rio de Janeiro, Brazil
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Esquirol L, Peat TS, Sugrue E, Balotra S, Rottet S, Warden AC, Wilding M, Hartley CJ, Jackson CJ, Newman J, Scott C. Bacterial catabolism of s-triazine herbicides: biochemistry, evolution and application. Adv Microb Physiol 2020; 76:129-186. [PMID: 32408946 DOI: 10.1016/bs.ampbs.2020.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The synthetic s-triazines are abundant, nitrogen-rich, heteroaromatic compounds used in a multitude of applications including, herbicides, plastics and polymers, and explosives. Their presence in the environment has led to the evolution of bacterial catabolic pathways in bacteria that allow use of these anthropogenic chemicals as a nitrogen source that supports growth. Herbicidal s-triazines have been used since the mid-twentieth century and are among the most heavily used herbicides in the world, despite being withdrawn from use in some areas due to concern about their safety and environmental impact. Bacterial catabolism of the herbicidal s-triazines has been studied extensively. Pseudomonas sp. strain ADP, which was isolated more than thirty years after the introduction of the s-triazine herbicides, has been the model system for most of these studies; however, several alternative catabolic pathways have also been identified. Over the last five years, considerable detail about the molecular mode of action of the s-triazine catabolic enzymes has been uncovered through acquisition of their atomic structures. These structural studies have also revealed insights into the evolutionary origins of this newly acquired metabolic capability. In addition, s-triazine-catabolizing bacteria and enzymes have been used in a range of applications, including bioremediation of herbicides and cyanuric acid, introducing metabolic resistance to plants, and as a novel selectable marker in fermentation organisms. In this review, we cover the discovery and characterization of bacterial strains, metabolic pathways and enzymes that catabolize the s-triazines. We also consider the evolution of these new enzymes and pathways and discuss the practical applications that have been considered for these bacteria and enzymes. One Sentence Summary: A detailed understanding of bacterial herbicide catabolic enzymes and pathways offer new evolutionary insights and novel applied tools.
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Affiliation(s)
- Lygie Esquirol
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia; Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Thomas S Peat
- CSIRO Biomedical Manufacturing, Parkville, VIC, Australia
| | - Elena Sugrue
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Sahil Balotra
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Sarah Rottet
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia; Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Andrew C Warden
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Matthew Wilding
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia; CSIRO Biomedical Manufacturing, Parkville, VIC, Australia; Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Carol J Hartley
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Janet Newman
- CSIRO Biomedical Manufacturing, Parkville, VIC, Australia
| | - Colin Scott
- Biocatalysis & Synthetic Biology Team, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia; Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
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Dennis ML, Esquirol L, Nebl T, Newman J, Scott C, Peat TS. The evolving story of AtzT, a periplasmic binding protein. Acta Crystallogr D Struct Biol 2019; 75:995-1002. [PMID: 31692473 PMCID: PMC6834077 DOI: 10.1107/s2059798319013883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 10/11/2019] [Indexed: 11/20/2022] Open
Abstract
Atrazine is an s-triazine-based herbicide that is used in many countries around the world in many millions of tons per year. A small number of organisms, such as Pseudomonas sp. strain ADP, have evolved to use this modified s-triazine as a food source, and the various genes required to metabolize atrazine can be found on a single plasmid. The atomic structures of seven of the eight proteins involved in the breakdown of atrazine by Pseudomonas sp. strain ADP have been determined by X-ray crystallography, but the structures of the proteins required by the cell to import atrazine for use as an energy source are still lacking. The structure of AtzT, a periplasmic binding protein that may be involved in the transport of a derivative of atrazine, 2-hydroxyatrazine, into the cell for mineralization, has now been determined. The structure was determined by SAD phasing using an ethylmercury phosphate derivative that diffracted X-rays to beyond 1.9 Å resolution. `Native' (guanine-bound) and 2-hydroxyatrazine-bound structures were also determined to high resolution (1.67 and 1.65 Å, respectively), showing that 2-hydroxyatrazine binds in a similar way to the purportedly native ligand. Structural similarities led to the belief that it may be possible to evolve AtzT from a purine-binding protein to a protein that can bind and detect atrazine in the environment.
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Affiliation(s)
- Matthew L. Dennis
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Lygie Esquirol
- CSIRO Synthetic Biology Future Science Platform, GPO Box 1700, Acton, Canberra, ACT 2601, Australia
| | - Tom Nebl
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Janet Newman
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Colin Scott
- CSIRO Synthetic Biology Future Science Platform, GPO Box 1700, Acton, Canberra, ACT 2601, Australia
| | - Thomas S. Peat
- Biomedical Manufacturing Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
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In silico design of potentially functional artificial metallo-haloalkane dehalogenase containing catalytic zinc. 3 Biotech 2018; 8:314. [PMID: 30023146 DOI: 10.1007/s13205-018-1333-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/02/2018] [Indexed: 01/05/2023] Open
Abstract
Artificial metalloenzymes are unique as they combine the good features of homogeneous and enzymatic catalysts, and they can potentially improve some difficult catalytic assays. This study reports a method that can be used to create an artificial metal-binding site prior to proving it to be functional in a wet lab. Haloalkane dehalogenase was grafted into a metal-binding site to form an artificial metallo-haloalkane dehalogenase and was studied for its potential functionalities in silico. Computational protocols regarding dynamic metal docking were studied using native metalloenzymes and functional artificial metalloenzymes. Using YASARA Structure, a simulation box covering template structure was created to be filled with water molecules followed by one mutated water molecule closest to the metal-binding site to metal ion. A simple energy minimization step was subsequently run using an AMBER force field to allow the metal ion to interact with the metal-binding residues. Long molecular dynamic simulation using YASARA Structure was performed to analyze the stability of the metal-binding site and the distance between metal-binding residues. Metal ions fluctuating around 2.0 Å across a 20 ns simulation indicated a stable metal-binding site. Metal-binding energies were predicted using FoldX, with a native metalloenzyme (carbonic anhydrase) scoring 18.0 kcal/mol and the best mutant model (C1a) scoring 16.4 kcal/mol. Analysis of the metal-binding site geometry was performed using CheckMyMetal, and all scores for the metalloenzymes and mutant models were in an acceptable range. Like native metalloenzymes, the metal-binding site of C1a was supported by residues in the second coordination shell to maintain a more coordinated metal-binding site. Short-chain multihalogenated alkanes (1,2-dibromoethane and 1,2,3-trichloropropane) were able to dock in the active site of C1a. The halides of the substrate were in contact with both the metal and halide-stabilizing residues, thus indicating a better stabilization of the substrate. The simple catalytic mechanism proposed is that the metal ion interacted with halogen and polarized the carbon-halogen bond, thus making the alpha carbon susceptible to attack by nucleophilic hydroxide. The interaction between halogen in the metal ion and halide-stabilizing residues may help to improve the stabilization of the substrate-enzyme complex and reduce the activation energy. This study reports a modified dynamic metal-docking protocol and validation tests to verify the metal-binding site. These approaches can be applied to design different kinds of artificial metalloenzymes or metal-binding sites.
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Ang TF, Maiangwa J, Salleh AB, Normi YM, Leow TC. Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications. Molecules 2018; 23:E1100. [PMID: 29735886 PMCID: PMC6100074 DOI: 10.3390/molecules23051100] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/07/2018] [Accepted: 04/09/2018] [Indexed: 11/16/2022] Open
Abstract
The variety of halogenated substances and their derivatives widely used as pesticides, herbicides and other industrial products is of great concern due to the hazardous nature of these compounds owing to their toxicity, and persistent environmental pollution. Therefore, from the viewpoint of environmental technology, the need for environmentally relevant enzymes involved in biodegradation of these pollutants has received a great boost. One result of this great deal of attention has been the identification of environmentally relevant bacteria that produce hydrolytic dehalogenases—key enzymes which are considered cost-effective and eco-friendly in the removal and detoxification of these pollutants. These group of enzymes catalyzing the cleavage of the carbon-halogen bond of organohalogen compounds have potential applications in the chemical industry and bioremediation. The dehalogenases make use of fundamentally different strategies with a common mechanism to cleave carbon-halogen bonds whereby, an active-site carboxylate group attacks the substrate C atom bound to the halogen atom to form an ester intermediate and a halide ion with subsequent hydrolysis of the intermediate. Structurally, these dehalogenases have been characterized and shown to use substitution mechanisms that proceed via a covalent aspartyl intermediate. More so, the widest dehalogenation spectrum of electron acceptors tested with bacterial strains which could dehalogenate recalcitrant organohalides has further proven the versatility of bacterial dehalogenators to be considered when determining the fate of halogenated organics at contaminated sites. In this review, the general features of most widely studied bacterial dehalogenases, their structural properties, basis of the degradation of organohalides and their derivatives and how they have been improved for various applications is discussed.
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Affiliation(s)
- Thiau-Fu Ang
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Jonathan Maiangwa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Yahaya M Normi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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Esquirol L, Peat TS, Wilding M, Liu JW, French NG, Hartley CJ, Onagi H, Nebl T, Easton CJ, Newman J, Scott C. An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme. J Biol Chem 2018. [PMID: 29523689 DOI: 10.1074/jbc.ra118.001996] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyanuric acid is a metabolic intermediate of s-triazines, such as atrazine (a common herbicide) and melamine (used in resins and plastics). Cyanuric acid is mineralized to ammonia and carbon dioxide by the soil bacterium Pseudomonas sp. strain ADP via three hydrolytic enzymes (AtzD, AtzE, and AtzF). Here, we report the purification and biochemical and structural characterization of AtzE. Contrary to previous reports, we found that AtzE is not a biuret amidohydrolase, but instead it catalyzes the hydrolytic deamination of 1-carboxybiuret. X-ray crystal structures of apo AtzE and AtzE bound with the suicide inhibitor phenyl phosphorodiamidate revealed that the AtzE enzyme complex consists of two independent molecules in the asymmetric unit. We also show that AtzE forms an α2β2 heterotetramer with a previously unidentified 68-amino acid-long protein (AtzG) encoded in the cyanuric acid mineralization operon from Pseudomonas sp. strain ADP. Moreover, we observed that AtzG is essential for the production of soluble, active AtzE and that this obligate interaction is a vestige of their shared evolutionary origin. We propose that AtzEG was likely recruited into the cyanuric acid-mineralizing pathway from an ancestral glutamine transamidosome that required protein-protein interactions to enforce the exclusion of solvent from the transamidation reaction.
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Affiliation(s)
- Lygie Esquirol
- From the Biocatalysis and Synthetic Biology Team and.,the Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, and
| | - Thomas S Peat
- CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria 3052, Australia
| | - Matthew Wilding
- the Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, and.,CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria 3052, Australia
| | - Jian-Wei Liu
- From the Biocatalysis and Synthetic Biology Team and
| | | | | | - Hideki Onagi
- the Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, and
| | - Thomas Nebl
- CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria 3052, Australia
| | - Christopher J Easton
- the Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, and
| | - Janet Newman
- CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria 3052, Australia
| | - Colin Scott
- From the Biocatalysis and Synthetic Biology Team and .,Synthetic Biology Future Science Platform, CSIRO Land and Water, Canberra, Australian Capital Territory 2601
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13
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Esquirol L, Peat TS, Wilding M, Lucent D, French NG, Hartley CJ, Newman J, Scott C. Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841. PLoS One 2018; 13:e0192736. [PMID: 29425231 PMCID: PMC5806882 DOI: 10.1371/journal.pone.0192736] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/29/2018] [Indexed: 11/24/2022] Open
Abstract
Biuret deamination is an essential step in cyanuric acid mineralization. In the well-studied atrazine degrading bacterium Pseudomonas sp. strain ADP, the amidase AtzE catalyzes this step. However, Rhizobium leguminosarum bv. viciae 3841 uses an unrelated cysteine hydrolase, BiuH, instead. Herein, structures of BiuH, BiuH with bound inhibitor and variants of BiuH are reported. The substrate is bound in the active site by a hydrogen bonding network that imparts high substrate specificity. The structure of the inactive Cys175Ser BiuH variant with substrate bound in the active site revealed that an active site cysteine (Cys175), aspartic acid (Asp36) and lysine (Lys142) form a catalytic triad, which is consistent with biochemical studies of BiuH variants. Finally, molecular dynamics simulations highlighted the presence of three channels from the active site to the enzyme surface: a persistent tunnel gated by residues Val218 and Gln215 forming a potential substrate channel and two smaller channels formed by Val28 and a mobile loop (including residues Phe41, Tyr47 and Met51) that may serve as channels for co-product (ammonia) or co-substrate (water).
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Affiliation(s)
- Lygie Esquirol
- CSIRO Biocatalysis and Synthetic Biology, Canberra, Australian Capital Territory, Australia
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Thomas S. Peat
- CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria, Australia
| | - Matthew Wilding
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
- CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria, Australia
| | - Del Lucent
- Department of Electrical Engineering and Physics, Wilkes University, Wilkes-Barre, Pennsylvania, United States of America
| | - Nigel G. French
- CSIRO Biocatalysis and Synthetic Biology, Canberra, Australian Capital Territory, Australia
| | - Carol J. Hartley
- CSIRO Biocatalysis and Synthetic Biology, Canberra, Australian Capital Territory, Australia
| | - Janet Newman
- CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria, Australia
| | - Colin Scott
- CSIRO Biocatalysis and Synthetic Biology, Canberra, Australian Capital Territory, Australia
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14
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Öztürk B, Ghequire M, Nguyen TPO, De Mot R, Wattiez R, Springael D. Expanded insecticide catabolic activity gained by a single nucleotide substitution in a bacterial carbamate hydrolase gene. Environ Microbiol 2016; 18:4878-4887. [PMID: 27312345 DOI: 10.1111/1462-2920.13409] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/05/2016] [Accepted: 06/06/2016] [Indexed: 01/29/2023]
Abstract
Carbofuran-mineralizing strain Novosphingobium sp. KN65.2 produces the CfdJ enzyme that converts the N-methylcarbamate insecticide to carbofuran phenol. Purified CfdJ shows a remarkably low KM towards carbofuran. Together with the carbaryl hydrolase CehA of Rhizobium sp. strain AC100, CfdJ represents a new protein family with several uncharacterized bacterial members outside the proteobacteria. Although both enzymes differ by only four amino acids, CehA does not recognize carbofuran as a substrate whereas CfdJ also hydrolyzes carbaryl. None of the CfdJ amino acids that differ from CehA were shown to be silent regarding carbofuran hydrolytic activity but one particular amino acid substitution, i.e., L152 to F152, proved crucial. CfdJ is more efficient in degrading methylcarbamate pesticides with an aromatic side chain whereas CehA is more efficient in degrading the oxime carbamate nematicide oxamyl. The presence of common flanking sequences suggest that the cfdJ gene is located on a remnant of the mobile genetic element Tnceh carrying cehA. Our results suggest that these enzymes can be acquired through horizontal gene transfer and can evolve to degrade new carbamate substrates by limited amino acid substitutions. We demonstrate that a carbaryl hydrolase can gain the additional capacity to degrade carbofuran by a single nucleotide transversion.
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Affiliation(s)
- Başak Öztürk
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Maarten Ghequire
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Thi Phi Oanh Nguyen
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium.,Department of Biology, College of Natural Sciences, Cantho University, Vietnam
| | - René De Mot
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, University of Mons, Mons, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
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15
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Guo Y, Zhao P, Zhang W, Li X, Chen X, Chen D. Catalytic improvement and structural analysis of atrazine chlorohydrolase by site-saturation mutagenesis. Biosci Biotechnol Biochem 2016; 80:1336-43. [DOI: 10.1080/09168451.2016.1156481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
To improve the catalytic activity of atrazine chlorohydrolase (AtzA), amino acid residues involved in substrate binding (Gln71) and catalytic efficiency (Val12, Ile393, and Leu395) were targeted to generate site-saturation mutagenesis libraries. Seventeen variants were obtained through Haematococcus pluvialis-based screening, and their specific activities were 1.2–5.2-fold higher than that of the wild type. For these variants, Gln71 tended to be substituted by hydrophobic amino acids, Ile393 and Leu395 by polar ones, especially arginine, and Val12 by alanine, respectively. Q71R and Q71M significantly decreased the Km by enlarging the substrate-entry channel and affecting N-ethyl binding. Mutations at sites 393 and 395 significantly increased the kcat/Km, probably by improving the stability of the dual β-sheet domain and the whole enzyme, owing to hydrogen bond formation. In addition, the contradictory relationship between the substrate affinity improvement by Gln71 mutation and the catalytic efficiency improvement by the dual β-sheet domain modification was discussed.
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Affiliation(s)
- Yuan Guo
- College of Life Sciences, Nankai University, Tianjin, China
| | - Panjie Zhao
- College of Life Sciences, Nankai University, Tianjin, China
| | - Wenhao Zhang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Xiaolong Li
- College of Life Sciences, Nankai University, Tianjin, China
| | - Xiwen Chen
- College of Life Sciences, Nankai University, Tianjin, China
| | - Defu Chen
- College of Life Sciences, Nankai University, Tianjin, China
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16
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X-Ray Structure and Mutagenesis Studies of the N-Isopropylammelide Isopropylaminohydrolase, AtzC. PLoS One 2015; 10:e0137700. [PMID: 26390431 PMCID: PMC4577212 DOI: 10.1371/journal.pone.0137700] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 08/19/2015] [Indexed: 12/01/2022] Open
Abstract
The N-isopropylammelide isopropylaminohydrolase from Pseudomonas sp. strain ADP, AtzC, provides the third hydrolytic step in the mineralization of s-triazine herbicides, such as atrazine. We obtained the X-ray crystal structure of AtzC at 1.84 Å with a weak inhibitor bound in the active site and then used a combination of in silico docking and site-directed mutagenesis to understand the interactions between AtzC and its substrate, isopropylammelide. The substitution of an active site histidine residue (His249) for an alanine abolished the enzyme’s catalytic activity. We propose a plausible catalytic mechanism, consistent with the biochemical and crystallographic data obtained that is similar to that found in carbonic anhydrase and other members of subtype III of the amidohydrolase family
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