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Diviesti K, Russell-Parks GA, Trewyn BG, Holz RC. Atrazine Degradation Using Immobilized Triazine Hydrolase from Arthrobacter aurescens TC1 in Mesoporous Silica Nanomaterials. ACS ENVIRONMENTAL AU 2023; 3:361-369. [PMID: 38028742 PMCID: PMC10655591 DOI: 10.1021/acsenvironau.3c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023]
Abstract
Triazine hydrolase fromArthrobacter aurescens TC1 (TrzN) was successfully immobilized on mesoporous silica nanomaterials (MSNs) for the first time. For both nonfunctionalized MSNs and MSNs functionalized with Zn(II), three pore sizes were evaluated for their ability to immobilize wild-type TrzN: Mobile composition of matter no. 41 (small, 3 nm pores), mesoporous silica nanoparticle material with 10 nm pore diameter (MSN-10) (medium, 6-12 nm pores), and pore-expanded MSN-10 (large, 15-30 nm pores). Of these six TrzN:MSN biomaterials, it was shown that TrzN:MSN-10 was the most active (3.8 ± 0.4 × 10-5 U/mg) toward the hydrolysis of a 50 μM atrazine solution at 25 °C. The TrzN:MSN-10 biomaterial was then coated in chitosan (TrzN:MSN-10:Chit) as chitosan has been shown to increase stability in extreme conditions such as low/high pH, heat shock, and the presence of organic solvents. TrzN:MSN-10:Chit was shown to be a superior TrzN biomaterial to TrzN:MSN-10 as it exhibited higher activity under all storage conditions, in the presence of 20% MeOH, at low and high pH values, and at elevated temperatures up to 80 °C. Finally, the TrzN:MSN-10:Chit biomaterial was shown to be fully active in river water, which establishes it as a functional biomaterial under actual field conditions. A combination of these data indicate that the TrzN:MSN-10:Chit biomaterial exhibited the best overall catalytic profile making it a promising biocatalyst for the bioremediation of atrazine.
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Affiliation(s)
- Karla Diviesti
- Quantitative
Biosciences and Engineering Program, Colorado
School of Mines, 1012
14th Street, Golden, Colorado 80401, United States
| | - Glory A. Russell-Parks
- Department
of Chemistry, Colorado School of Mines, 1012 14th Street, Golden, Colorado 80401, United States
| | - Brian G. Trewyn
- Department
of Chemistry, Colorado School of Mines, 1012 14th Street, Golden, Colorado 80401, United States
- National
Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, Colorado 80401, United States
- Materials
Science Program, Colorado School of Mines, 1012 14th Street, Golden, Colorado 80401, United States
| | - Richard C. Holz
- Department
of Chemistry, Colorado School of Mines, 1012 14th Street, Golden, Colorado 80401, United States
- Quantitative
Biosciences and Engineering Program, Colorado
School of Mines, 1012
14th Street, Golden, Colorado 80401, United States
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Tang J, Yao J, Pan D, Huang J, Wang J, Li QX, Dong F, Wu X. Characterization and catalytic mechanism of a direct demethylsulfide hydrolase for catabolism of the methylthiol-s-triazine prometryn. JOURNAL OF HAZARDOUS MATERIALS 2023; 446:130708. [PMID: 36608577 DOI: 10.1016/j.jhazmat.2022.130708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/12/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Demethylthio is one of the most important ways for microorganisms to metabolize triazine herbicides. Previous studies have found that the initial reaction of prometryn catabolism in Leucobacter triazinivorans JW-1 was the hydroxylation of its methylthio group, however, the corresponding functional enzyme was not yet clear. In this study, the gene proA was responsible for the initial step of prometryn catabolism from the strain JW-1 was cloned and expressed, and the purified amidohydrolases ProA have the ability to transform prometryn to 2-hydroxypropazine and methanethiol. The optimized reaction temperature and pH of ProA were 45 °C and 7.0, respectively, and the kinetic constants Km and Vmax of ProA for the catalysis of prometryn were 32.6 μM and 0.09 μmol/min/mg, respectively. Molecular docking analyses revealed that different catalysis efficiency of ProA and TrzN (Nocardioides sp. C190) for prometryn and atrazine was due to non-covalent changes in amino acid residues. Our findings provide new insights into the understanding of s-triazine catabolism at the molecular level.
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Affiliation(s)
- Jun Tang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China
| | - Jinjin Yao
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China
| | - Dandan Pan
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China
| | - Junwei Huang
- 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
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, HI 96822, USA
| | - Fengshou Dong
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, 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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Catalytic Biomaterials for Atrazine Degradation. Catalysts 2023. [DOI: 10.3390/catal13010140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
In this paper, triazine hydrolase from Arthrobacter aurescens TC1 (TrzN) was successfully immobilized in alginate beads (TrzN:alginate), alginate beads coated in chitosan (TrzN:chitosan), and tetramethylorthosilicate (TMOS) gels using the sol–gel method (TrzN:sol–gel) for the first time. TrzN:alginate and TrzN:chitosan hydrolyzed 50 µM of atrazine in 6 h with negligible protein loss with an ~80% conversion rate. However, the TrzN:sol–gel biomaterial converted >95% of a 50 µM atrazine solution in an hour with negligible protein loss. The treatment of each of these biomaterials with trypsin confirmed that the catalytic activity was due to the encapsulated enzyme and not surface-bound TrzN. All three of the biomaterials showed potential for long-term storage and reuse, with the only limitation arising from the loss of protein in the storage buffer for the TrzN:alginate and TrzN:chitosan biomaterials, not the denaturation of the encapsulated TrzN. TrzN:sol–gel stood out, with ~100% activity being retained after 10 consecutive reactions. Additionally, the materials stayed active in methanol concentrations <10%, suggesting the ability to increase the solubility of atrazine with organic solvents. The structural integrity of the TrzN:alginate and TrzN:chitosan materials became limiting in extreme pH conditions, while TrzN:sol–gel outperformed WT TrzN. Overall, the TrzN:sol–gel biomaterial proved to be the best atrazine dichlorination biocatalyst. As sol–gels can be cast into any desired shape, including pellets, which can be used in columns, the TrzN:sol–gel biomaterial provides a new avenue for the design of bioremediation methodologies for the removal of atrazine from the environment.
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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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Bygd MD, Aukema KG, Richman JE, Wackett LP. Microwell Fluoride Screen for Chemical, Enzymatic, and Cellular Reactions Reveals Latent Microbial Defluorination Capacity for -CF 3 Groups. Appl Environ Microbiol 2022; 88:e0028822. [PMID: 35435713 PMCID: PMC9088286 DOI: 10.1128/aem.00288-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/29/2022] [Indexed: 12/11/2022] Open
Abstract
The capacity to defluorinate polyfluorinated organic compounds is a rare phenotype in microbes but is increasingly considered important for maintaining the environment. New discoveries will be greatly facilitated by the ability to screen many natural and engineered microbes in a combinatorial manner against large numbers of fluorinated compounds simultaneously. Here, we describe a low-volume, high-throughput screening method to determine defluorination capacity of microbes and their enzymes. The method is based on selective binding of fluoride to a lanthanum chelate complex that gives a purple-colored product. It was miniaturized to determine biodefluorination in 96-well microtiter plates by visual inspection or robotic handling and spectrophotometry. Chemicals commonly used in microbiological studies were examined to define usable buffers and reagents. Base-catalyzed, purified enzyme and whole-cell defluorination reactions were demonstrated with fluoroatrazine and showed correspondence between the microtiter assay and a fluoride electrode. For discovering new defluorination reactions and mechanisms, a chemical library of 63 fluorinated compounds was screened in vivo with Pseudomonas putida F1 in microtiter well plates. These data were also calibrated against a fluoride electrode. Our new method revealed 21 new compounds undergoing defluorination. A compound with four fluorine substituents, 4-fluorobenzotrifluoride, was shown to undergo defluorination to the greatest extent. The mechanism of its defluorination was studied to reveal a latent microbial propensity to defluorinate trifluoromethylphenyl groups, a moiety that is commonly incorporated into numerous pharmaceutical and agricultural chemicals. IMPORTANCE Thousands of organofluorine chemicals are known, and a number are considered to be persistent and toxic environmental pollutants. Environmental bioremediation methods are avidly being sought, but few bacteria biodegrade fluorinated chemicals. To find new organofluoride biodegradation, a rapid screening method was developed. The method is versatile, monitoring chemical, enzymatic, and whole-cell biodegradation. Biodegradation of organofluorine compounds invariably releases fluoride anions, which was sensitively detected. Our method uncovered 21 new microbial defluorination reactions. A general mechanism was delineated for the biodegradation of trifluoromethylphenyl groups that are increasingly being used in drugs and pesticides.
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Affiliation(s)
- Madison D. Bygd
- Microbial Engineering, University of Minnesota, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kelly G. Aukema
- Biotechnology Institute, University of Minnesota, Minneapolis, Minnesota, USA
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jack E. Richman
- Biotechnology Institute, University of Minnesota, Minneapolis, Minnesota, USA
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Lawrence P. Wackett
- Microbial Engineering, University of Minnesota, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota, Minneapolis, Minnesota, USA
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
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Parvulescu VI, Epron F, Garcia H, Granger P. Recent Progress and Prospects in Catalytic Water Treatment. Chem Rev 2021; 122:2981-3121. [PMID: 34874709 DOI: 10.1021/acs.chemrev.1c00527] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Presently, conventional technologies in water treatment are not efficient enough to completely mineralize refractory water contaminants. In this context, the implementation of catalytic processes could be an alternative. Despite the advantages provided in terms of kinetics of transformation, selectivity, and energy saving, numerous attempts have not yet led to implementation at an industrial scale. This review examines investigations at different scales for which controversies and limitations must be solved to bridge the gap between fundamentals and practical developments. Particular attention has been paid to the development of solar-driven catalytic technologies and some other emerging processes, such as microwave assisted catalysis, plasma-catalytic processes, or biocatalytic remediation, taking into account their specific advantages and the drawbacks. Challenges for which a better understanding related to the complexity of the systems and the coexistence of various solid-liquid-gas interfaces have been identified.
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Affiliation(s)
- Vasile I Parvulescu
- Department of Organic Chemistry, Biochemistry and Catalysis, University of Bucharest, B-dul Regina Elisabeta 4-12, Bucharest 030016, Romania
| | - Florence Epron
- Université de Poitiers, CNRS UMR 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), 4 rue Michel Brunet, TSA 51106, 86073 Poitiers Cedex 9, France
| | - Hermenegildo Garcia
- Instituto Universitario de Tecnología Química, Universitat Politecnica de Valencia-Consejo Superior de Investigaciones Científicas, Universitat Politencia de Valencia, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Pascal Granger
- CNRS, Centrale Lille, Univ. Artois, UMR 8181 - UCCS - Unité de Catalyse et Chimie du Solide, Univ. Lille, F-59000 Lille, France
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7
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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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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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Jiang Z, Chen J, Li J, Cao B, Chen Y, Liu D, Wang X, Zhang Y. Exogenous Zn 2+ enhance the biodegradation of atrazine by regulating the chlorohydrolase gene trzN transcription and membrane permeability of the degrader Arthrobacter sp. DNS10. CHEMOSPHERE 2020; 238:124594. [PMID: 31445334 DOI: 10.1016/j.chemosphere.2019.124594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/22/2019] [Accepted: 08/14/2019] [Indexed: 06/10/2023]
Abstract
Enhancing the biodegradation efficiency of atrazine, a kind of commonly applied herbicide, has been attracted much more concern. Here, Zn2+ which has long been considered essential in adjusting cell physiological status was selected to investigate its role on the biodegradation of atrazine by Arthrobacter sp. DNS10 as well as the transmembrane transport of atrazine during the biodegradation period. The results of gas chromatography showed that the atrazine removal percentages (initial concentration was 100 mg L-1) in 0.05 mM Zn2+ and 1.0 mM Zn2+ treatments were 94.42% and 86.02% respectively at 48 h, while there was also 66.43% of atrazine left in the treatment without exogenous Zn2+ existence. The expression of atrazine chlorohydrolase gene trzN in the strain DNS10 cultured with 0.05 mM and 1.0 mM Zn2+ was 7.30- and 4.67- times respectively compared with that of the non-zinc treatment. In addition, the flow cytometry test suggests that 0.05 mM of Zn2+ could better adjust the membrane permeability of strain DNS10, meanwhile, the amount of atrazine accumulation in the strain DNS10 co-cultured with this level Zn2+ was 2.21 times of that of the strain without Zn2+. This study may facilitate a better understanding of the mechanisms that exogenous Zn2+ enhances the biodegradation of atrazine by Arthrobacter sp. DNS10.
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Affiliation(s)
- Zhao Jiang
- School of Resources & Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Jianing Chen
- School of Resources & Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Jiaojiao Li
- School of Resources & Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Bo Cao
- School of Resources & Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Yukun Chen
- School of Resources & Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Di Liu
- School of Resources & Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Xinxin Wang
- School of Resources & Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Ying Zhang
- School of Resources & Environment, Northeast Agricultural University, Harbin, 150030, China.
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10
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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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11
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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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Ogawa T, Hattori S, Kamezaki K, Kato H, Yoshida N, Katayama Y. Isotopic Fractionation of Sulfur in Carbonyl Sulfide by Carbonyl Sulfide Hydrolase of Thiobacillus thioparus THI115. Microbes Environ 2017; 32:367-375. [PMID: 29199215 PMCID: PMC5745022 DOI: 10.1264/jsme2.me17130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/24/2017] [Indexed: 11/25/2022] Open
Abstract
Carbonyl sulfide (COS) is one of the major sources of stratospheric sulfate aerosols, which affect the global radiation balance and ozone depletion. COS-degrading microorganisms are ubiquitous in soil and important for the global flux of COS. We examined the sulfur isotopic fractionation during the enzymatic degradation of COS by carbonyl sulfide hydrolase (COSase) from Thiobacillus thioparus THI115. The isotopic fractionation constant (34ɛ value) was -2.2±0.2‰. Under experimental conditions performed at parts per million by volume level of COS, the 34ɛ value for intact cells of T. thioparus THI115 was -3.6±0.7‰, suggesting that, based on Rees' model, the 34ɛ value mainly depended on COS transport into the cytoplasm. The 34ɛ value for intact cells of T. thioparus THI115 was similar to those for Mycobacterium spp. and Williamsia sp., which are known to involve the conserved region of nucleotide sequences encoding the clade D of β-class carbonic anhydrase (β-CA) including COSase. On the other hand, the 34ɛ value was distinct from those for bacteria in the genus Cupriavidus. These results provide an insight into biological COS degradation, which is indispensable for estimating the COS global budget based on the isotope because of the significant contribution of COS degradation by microorganisms harboring β-CA family enzymes.
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Affiliation(s)
- Takahiro Ogawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology3–5–8 Saiwai-cho, Fuchu, Tokyo 183–8509Japan
| | - Shohei Hattori
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226–8502Japan
| | - Kazuki Kamezaki
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226–8502Japan
| | - Hiromi Kato
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-Ku, Sendai, Miyagi 980–8577Japan
| | - Naohiro Yoshida
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226–8502Japan
- Earth-Life Science Institute, Tokyo Institute of Technology2–12–1–IE–1 Ookayama, Meguro-ku, Tokyo 152–8550Japan
| | - Yoko Katayama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology3–5–8 Saiwai-cho, Fuchu, Tokyo 183–8509Japan
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Sugrue E, Scott C, Jackson CJ. Constrained evolution of a bispecific enzyme: lessons for biocatalyst design. Org Biomol Chem 2017; 15:937-946. [DOI: 10.1039/c6ob02355j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Analysis of the natural evolution of bispecificity in triazine hydrolase highlights the importance of epistasis in protein engineering and evolution.
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Affiliation(s)
- E. Sugrue
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - C. Scott
- Commonwealth Scientific and Industrial Research Organisation
- Canberra
- Australia
| | - C. J. Jackson
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
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Sugrue E, Carr PD, Scott C, Jackson CJ. Active Site Desolvation and Thermostability Trade-Offs in the Evolution of Catalytically Diverse Triazine Hydrolases. Biochemistry 2016; 55:6304-6313. [DOI: 10.1021/acs.biochem.6b00731] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elena Sugrue
- Research
School of Chemistry, Australian National University, Canberra, Australia
| | - Paul D. Carr
- Research
School of Chemistry, Australian National University, Canberra, Australia
| | | | - Colin J. Jackson
- Research
School of Chemistry, Australian National University, Canberra, Australia
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15
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Sugrue E, Hartley CJ, Scott C, Jackson CJ. The Evolution of New Catalytic Mechanisms for Xenobiotic Hydrolysis in Bacterial Metalloenzymes. Aust J Chem 2016. [DOI: 10.1071/ch16426] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An increasing number of bacterial metalloenzymes have been shown to catalyse the breakdown of xenobiotics in the environment, while others exhibit a variety of promiscuous xenobiotic-degrading activities. Several different evolutionary processes have allowed these enzymes to gain or enhance xenobiotic-degrading activity. In this review, we have surveyed the range of xenobiotic-degrading metalloenzymes, and discuss the molecular and catalytic basis for the development of new activities. We also highlight how our increased understanding of the natural evolution of xenobiotic-degrading metalloenzymes can be been applied to laboratory enzyme design.
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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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Schürner HKV, Seffernick JL, Grzybkowska A, Dybala-Defratyka A, Wackett LP, Elsner M. Characteristic isotope fractionation patterns in s-triazine degradation have their origin in multiple protonation options in the s-triazine hydrolase TrzN. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:3490-8. [PMID: 25688667 DOI: 10.1021/es5055385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
s-Triazine herbicides (atrazine, ametryn) are groundwater contaminants which may undergo microbial hydrolysis. Previously, inverse nitrogen isotope effects in atrazine degradation by Arthrobacter aurescens TC1 (i) delivered highly characteristic (13C/12C, 15N/14N) fractionation trends for pathway identification and (ii) suggested that the s-triazine ring nitrogen was protonated in the enzyme s-triazine hydrolase (TrzN) where (iii) TrzN crystal structure and mutagenesis indicated H+-transfer from the residue E241. This study tested the general validity of these conclusions for atrazine and ametryn with purified TrzN and a TrzN-E241Q site-directed mutant. TrzN-E241Q lacked activity with ametryn; otherwise, degradation consistently showed normal carbon isotope effects (εcarbon=-5.0‰±0.2‰ (atrazine/TrzN), εcarbon=-4.2‰±0.5‰ (atrazine/TrzN-E241Q), εcarbon=-2.4‰±0.3‰ (ametryn/TrzN)) and inverse nitrogen isotope effects (εnitrogen=2.5‰±0.1‰ (atrazine/TrzN), εnitrogen=2.1‰±0.3‰ (atrazine/TrzN-E241Q), εnitrogen=3.6‰±0.4‰ (ametryn/TrzN)). Surprisingly, TrzN-E241Q therefore still activated substrates through protonation implicating another proton donor besides E241. Sulfur isotope effects were larger in enzymatic (εsulfur=-14.7‰±1.0‰, ametryn/TrzN) than in acidic ametryn hydrolysis (εsulfur=-0.2‰±0.0‰, pH 1.75), indicating rate-determining C-S bond cleavage in TrzN. Our results highlight a robust inverse 15N/14N fractionation pattern for identifying microbial s-triazine hydrolysis in the environment caused by multiple protonation options in TrzN.
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Affiliation(s)
- Heide K V Schürner
- †Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Bavaria, Germany
| | - Jennifer L Seffernick
- ‡Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Anna Grzybkowska
- §Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Agnieszka Dybala-Defratyka
- §Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Lawrence P Wackett
- ‡Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Martin Elsner
- †Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Bavaria, Germany
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Peat TS, Newman J, Balotra S, Lucent D, Warden AC, Scott C. The structure of the hexameric atrazine chlorohydrolase AtzA. ACTA ACUST UNITED AC 2015; 71:710-20. [PMID: 25760618 PMCID: PMC4356373 DOI: 10.1107/s1399004715000619] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/12/2015] [Indexed: 12/05/2022]
Abstract
The structure of atrazine chlorohydrolase (AtzA) is presented and is used to reinterpret data from genetic, biochemical and evolutionary studies, providing insight into why this recently evolved enzyme appears to be poorly adapted for its physiological substrate compared with the alternative metal-dependent atrazine dechlorinase TrzN. Atrazine chlorohydrolase (AtzA) was discovered and purified in the early 1990s from soil that had been exposed to the widely used herbicide atrazine. It was subsequently found that this enzyme catalyzes the first and necessary step in the breakdown of atrazine by the soil organism Pseudomonas sp. strain ADP. Although it has taken 20 years, a crystal structure of the full hexameric form of AtzA has now been obtained. AtzA is less well adapted to its physiological role (i.e. atrazine dechlorination) than the alternative metal-dependent atrazine chlorohydrolase (TrzN), with a substrate-binding pocket that is under considerable strain and for which the substrate is a poor fit.
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Affiliation(s)
- T S Peat
- CSIRO Biomedical Manufacturing, Parkville, Australia
| | - J Newman
- CSIRO Biomedical Manufacturing, Parkville, Australia
| | - S Balotra
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - D Lucent
- Division of Engineering and Physics, Wilkes University, Wilkes-Barr, Pennsylvania, USA
| | - A C Warden
- CSIRO Land and Water Flagship, Black Mountain, Canberra, Australia
| | - C Scott
- CSIRO Biomedical Manufacturing, Parkville, Australia
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X-ray structure of the amidase domain of AtzF, the allophanate hydrolase from the cyanuric acid-mineralizing multienzyme complex. Appl Environ Microbiol 2014; 81:470-80. [PMID: 25362066 DOI: 10.1128/aem.02783-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The activity of the allophanate hydrolase from Pseudomonas sp. strain ADP, AtzF, provides the final hydrolytic step for the mineralization of s-triazines, such as atrazine and cyanuric acid. Indeed, the action of AtzF provides metabolic access to two of the three nitrogens in each triazine ring. The X-ray structure of the N-terminal amidase domain of AtzF reveals that it is highly homologous to allophanate hydrolases involved in a different catabolic process in other organisms (i.e., the mineralization of urea). The smaller C-terminal domain does not appear to have a physiologically relevant catalytic function, as reported for the allophanate hydrolase of Kluyveromyces lactis, when purified enzyme was tested in vitro. However, the C-terminal domain does have a function in coordinating the quaternary structure of AtzF. Interestingly, we also show that AtzF forms a large, ca. 660-kDa, multienzyme complex with AtzD and AtzE that is capable of mineralizing cyanuric acid. The function of this complex may be to channel substrates from one active site to the next, effectively protecting unstable metabolites, such as allophanate, from solvent-mediated decarboxylation to a dead-end metabolic product.
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Aerobic biodegradation of 2,4-Dinitroanisole by Nocardioides sp. strain JS1661. Appl Environ Microbiol 2014; 80:7725-31. [PMID: 25281383 DOI: 10.1128/aem.02752-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2,4-Dinitroanisole (DNAN) is an insensitive munition ingredient used in explosive formulations as a replacement for 2,4,6-trinitrotoluene (TNT). Little is known about the environmental behavior of DNAN. There are reports of microbial transformation to dead-end products, but no bacteria with complete biodegradation capability have been reported. Nocardioides sp. strain JS1661 was isolated from activated sludge based on its ability to grow on DNAN as the sole source of carbon and energy. Enzyme assays indicated that the first reaction involves hydrolytic release of methanol to form 2,4-dinitrophenol (2,4-DNP). Growth yield and enzyme assays indicated that 2,4-DNP underwent subsequent degradation by a previously established pathway involving formation of a hydride-Meisenheimer complex and release of nitrite. Identification of the genes encoding the key enzymes suggested recent evolution of the pathway by recruitment of a novel hydrolase to extend the well-characterized 2,4-DNP pathway.
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300-Fold increase in production of the Zn2+-dependent dechlorinase TrzN in soluble form via apoenzyme stabilization. Appl Environ Microbiol 2014; 80:4003-11. [PMID: 24771025 DOI: 10.1128/aem.00916-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial metalloenzymes constitute a large library of biocatalysts, a number of which have already been shown to catalyze the breakdown of toxic chemicals or industrially relevant chemical transformations. However, while there is considerable interest in harnessing these catalysts for biotechnology, for many of the enzymes, their large-scale production in active, soluble form in recombinant systems is a significant barrier to their use. In this work, we demonstrate that as few as three mutations can result in a 300-fold increase in the expression of soluble TrzN, an enzyme from Arthrobacter aurescens with environmental applications that catalyzes the hydrolysis of triazine herbicides, in Escherichia coli. Using a combination of X-ray crystallography, kinetic analysis, and computational simulation, we show that the majority of the improvement in expression is due to stabilization of the apoenzyme rather than the metal ion-bound holoenzyme. This provides a structural and mechanistic explanation for the observation that many compensatory mutations can increase levels of soluble-protein production without increasing the stability of the final, active form of the enzyme. This study provides a molecular understanding of the importance of the stability of metal ion free states to the accumulation of soluble protein and shows that differences between apoenzyme and holoenzyme structures can result in mutations affecting the stability of either state differently.
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Rehan M, Kluge M, Fränzle S, Kellner H, Ullrich R, Hofrichter M. Degradation of atrazine by Frankia alni ACN14a: gene regulation, dealkylation, and dechlorination. Appl Microbiol Biotechnol 2014; 98:6125-35. [DOI: 10.1007/s00253-014-5665-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 03/04/2014] [Accepted: 03/05/2014] [Indexed: 11/29/2022]
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Benassi E, Di Foggia M, Bonora S. Accurate computational prediction of the structural and vibrational properties of s-triazine derivatives in vacuo. A DFT approach. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ongoing functional evolution of the bacterial atrazine chlorohydrolase AtzA. Biodegradation 2013; 25:21-30. [DOI: 10.1007/s10532-013-9637-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 04/03/2013] [Indexed: 10/27/2022]
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Udiković-Kolić N, Scott C, Martin-Laurent F. Evolution of atrazine-degrading capabilities in the environment. Appl Microbiol Biotechnol 2012; 96:1175-89. [DOI: 10.1007/s00253-012-4495-0] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/02/2012] [Accepted: 10/03/2012] [Indexed: 11/30/2022]
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Reátegui E, Reynolds E, Kasinkas L, Aggarwal A, Sadowsky MJ, Aksan A, Wackett LP. Silica gel-encapsulated AtzA biocatalyst for atrazine biodegradation. Appl Microbiol Biotechnol 2012; 96:231-40. [DOI: 10.1007/s00253-011-3821-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 11/29/2011] [Accepted: 12/05/2011] [Indexed: 11/30/2022]
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