1
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Wang C, Calcaterra J, Anderson B, Rydel T, Wang R, Bertho L, Saracco SA, Hodge-Bell K, Burzio L, White T, Li B. Risk assessment of homologous variants of biotech trait proteins using a bridging approach. GM CROPS & FOOD 2024; 15:336-351. [PMID: 39520709 PMCID: PMC11552266 DOI: 10.1080/21645698.2024.2420412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 10/09/2024] [Accepted: 10/18/2024] [Indexed: 11/16/2024]
Abstract
A transgenic protein is frequently expressed as different homologous variants in genetically modified crops due to differential processing of targeting peptides or optimization of activity and specificity. The aim of this study was to develop a science-based approach for risk assessment of homologous protein variants using dicamba mono-oxygenase (DMO) as a case study. In this study, DMO expressed in the next-generation dicamba-tolerant maize, sugar beet and soybean crops exhibited up to 27 amino acid sequence differences in the N-terminus. Structure modeling using AlphaFold, ESMFold and OpenFold demonstrates that these small N-terminal extensions lack an ordered secondary structure and do not disrupt the DMO functional structure. Three DMO variants were demonstrated to have equivalent immunoreactivity and functional activity ranging from 214 to 331 nmol/min/mg. Repeated toxicity studies using each DMO variant found no test substance-related adverse effects. These results support that homologous protein variants, which have demonstrated physicochemical and functional equivalence, can leverage existing safety data from one variant without requiring additional de novo safety assessments.
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Affiliation(s)
- Cunxi Wang
- Regulatory Science, Bayer Crop Science, Chesterfield, MO, USA
| | | | | | - Timothy Rydel
- Plant Biotechnology, Bayer Crop Science, Chesterfield, MO, USA
| | - Rong Wang
- Regulatory Science, Bayer Crop Science, Chesterfield, MO, USA
| | - Lieselot Bertho
- Regulatory Science, Bayer Crop Science, Chesterfield, MO, USA
| | | | | | - Luis Burzio
- Regulatory Science, Bayer Crop Science, Chesterfield, MO, USA
- Bill & Melinda Gates Agricultural Innovations, St. Louis, MO, USA
| | - Tommi White
- Plant Biotechnology, Bayer Crop Science, Chesterfield, MO, USA
| | - Bin Li
- Regulatory Science, Bayer Crop Science, Chesterfield, MO, USA
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2
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Guerrero Ramírez JR, Ibarra Muñoz LA, Balagurusamy N, Frías Ramírez JE, Alfaro Hernández L, Carrillo Campos J. Microbiology and Biochemistry of Pesticides Biodegradation. Int J Mol Sci 2023; 24:15969. [PMID: 37958952 PMCID: PMC10649977 DOI: 10.3390/ijms242115969] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/17/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Pesticides are chemicals used in agriculture, forestry, and, to some extent, public health. As effective as they can be, due to the limited biodegradability and toxicity of some of them, they can also have negative environmental and health impacts. Pesticide biodegradation is important because it can help mitigate the negative effects of pesticides. Many types of microorganisms, including bacteria, fungi, and algae, can degrade pesticides; microorganisms are able to bioremediate pesticides using diverse metabolic pathways where enzymatic degradation plays a crucial role in achieving chemical transformation of the pesticides. The growing concern about the environmental and health impacts of pesticides is pushing the industry of these products to develop more sustainable alternatives, such as high biodegradable chemicals. The degradative properties of microorganisms could be fully exploited using the advances in genetic engineering and biotechnology, paving the way for more effective bioremediation strategies, new technologies, and novel applications. The purpose of the current review is to discuss the microorganisms that have demonstrated their capacity to degrade pesticides and those categorized by the World Health Organization as important for the impact they may have on human health. A comprehensive list of microorganisms is presented, and some metabolic pathways and enzymes for pesticide degradation and the genetics behind this process are discussed. Due to the high number of microorganisms known to be capable of degrading pesticides and the low number of metabolic pathways that are fully described for this purpose, more research must be conducted in this field, and more enzymes and genes are yet to be discovered with the possibility of finding more efficient metabolic pathways for pesticide biodegradation.
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Affiliation(s)
- José Roberto Guerrero Ramírez
- Instituto Tecnológico de Torreón, Tecnológico Nacional de México, Torreon 27170, Coahuila, Mexico; (J.R.G.R.); (J.E.F.R.); (L.A.H.)
| | - Lizbeth Alejandra Ibarra Muñoz
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreon 27275, Coahuila, Mexico; (L.A.I.M.); (N.B.)
| | - Nagamani Balagurusamy
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreon 27275, Coahuila, Mexico; (L.A.I.M.); (N.B.)
| | - José Ernesto Frías Ramírez
- Instituto Tecnológico de Torreón, Tecnológico Nacional de México, Torreon 27170, Coahuila, Mexico; (J.R.G.R.); (J.E.F.R.); (L.A.H.)
| | - Leticia Alfaro Hernández
- Instituto Tecnológico de Torreón, Tecnológico Nacional de México, Torreon 27170, Coahuila, Mexico; (J.R.G.R.); (J.E.F.R.); (L.A.H.)
| | - Javier Carrillo Campos
- Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua 31453, Chihuahua, Mexico
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3
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Runda ME, de Kok NAW, Schmidt S. Rieske Oxygenases and Other Ferredoxin-Dependent Enzymes: Electron Transfer Principles and Catalytic Capabilities. Chembiochem 2023; 24:e202300078. [PMID: 36964978 DOI: 10.1002/cbic.202300078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/27/2023]
Abstract
Enzymes that depend on sophisticated electron transfer via ferredoxins (Fds) exhibit outstanding catalytic capabilities, but despite decades of research, many of them are still not well understood or exploited for synthetic applications. This review aims to provide a general overview of the most important Fd-dependent enzymes and the electron transfer processes involved. While several examples are discussed, we focus in particular on the family of Rieske non-heme iron-dependent oxygenases (ROs). In addition to illustrating their electron transfer principles and catalytic potential, the current state of knowledge on structure-function relationships and the mode of interaction between the redox partner proteins is reviewed. Moreover, we highlight several key catalyzed transformations, but also take a deeper dive into their engineerability for biocatalytic applications. The overall findings from these case studies highlight the catalytic capabilities of these biocatalysts and could stimulate future interest in developing additional Fd-dependent enzyme classes for synthetic applications.
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Affiliation(s)
- Michael E Runda
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Niels A W de Kok
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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4
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Tian J, Garcia AA, Donnan PH, Bridwell-Rabb J. Leveraging a Structural Blueprint to Rationally Engineer the Rieske Oxygenase TsaM. Biochemistry 2023. [PMID: 37188334 DOI: 10.1021/acs.biochem.3c00150] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Rieske nonheme iron oxygenases use two metallocenters, a Rieske-type [2Fe-2S] cluster and a mononuclear iron center, to catalyze oxidation reactions on a broad range of substrates. These enzymes are widely used by microorganisms to degrade environmental pollutants and to build complexity in a myriad of biosynthetic pathways that are industrially interesting. However, despite the value of this chemistry, there is a dearth of understanding regarding the structure-function relationships in this enzyme class, which limits our ability to rationally redesign, optimize, and ultimately exploit the chemistry of these enzymes. Therefore, in this work, by leveraging a combination of available structural information and state-of-the-art protein modeling tools, we show that three "hotspot" regions can be targeted to alter the site selectivity, substrate preference, and substrate scope of the Rieske oxygenase p-toluenesulfonate methyl monooxygenase (TsaM). Through mutation of six to 10 residues distributed between three protein regions, TsaM was engineered to behave as either vanillate monooxygenase (VanA) or dicamba monooxygenase (DdmC). This engineering feat means that TsaM was rationally engineered to catalyze an oxidation reaction at the meta and ortho positions of an aromatic substrate, rather than its favored native para position, and that TsaM was redesigned to perform chemistry on dicamba, a substrate that is not natively accepted by the enzyme. This work thus contributes to unlocking our understanding of structure-function relationships in the Rieske oxygenase enzyme class and expands foundational principles for future engineering of these metalloenzymes.
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Affiliation(s)
- Jiayi Tian
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Patrick H Donnan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer Bridwell-Rabb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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5
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Zhu D, Qaria MA, Zhu B, Sun J, Yang B. Extremophiles and extremozymes in lignin bioprocessing. RENEWABLE AND SUSTAINABLE ENERGY REVIEWS 2022; 157:112069. [DOI: 10.1016/j.rser.2021.112069] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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6
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Qamar Z, Nasir IA, Abouhaidar MG, Hefferon KL, Rao AQ, Latif A, Ali Q, Anwar S, Rashid B, Shahid AA. Novel approaches to circumvent the devastating effects of pests on sugarcane. Sci Rep 2021; 11:12428. [PMID: 34127751 PMCID: PMC8203629 DOI: 10.1038/s41598-021-91985-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/21/2021] [Indexed: 02/05/2023] Open
Abstract
Sugarcane (Saccharum officinarum L.) is a cash crop grown commercially for its higher amounts of sucrose, stored within the mature internodes of the stem. Numerous studies have been done for the resistance development against biotic and abiotic stresses to save the sucrose yields. Quality and yield of sugarcane production is always threatened by the damages of cane borers and weeds. In current study two problems were better addressed through the genetic modification of sugarcane for provision of resistance against insects and weedicide via the expression of two modified cane borer resistant CEMB-Cry1Ac (1.8 kb), CEMB-Cry2A (1.9 kb) and one glyphosate tolerant CEMB-GTGene (1.4 kb) genes, driven by maize Ubiquitin Promoter and nos terminator. Insect Bio-toxicity assays were carried out for the assessment of Cry proteins through mortality percent of shoot borer Chilo infuscatellus at 2nd instar larvae stage. During V0, V1 and V2 generations young leaves from the transgenic sugarcane plants were collected at plant age of 20, 40, 60, 80 days and fed to the Chilo infuscatellus larvae. Up to 100% mortality of Chilo infuscatellus from 80 days old transgenic plants of V2 generation indicated that these transgenic plants were highly resistant against shoot borer and the gene expression level is sufficient to provide complete resistance against target pests. Glyphosate spray assay was carried out for complete removal of weeds. In V1-generation, 70-76% transgenic sugarcane plants were found tolerant against glyphosate spray (3000 mL/ha) under field conditions. While in V2-generation, the replicates of five selected lines 4L/2, 5L/5, 6L/5, L8/4, and L9/6 were found 100% tolerant against 3000 mL/ha glyphosate spray. It is evident from current study that CEMB-GTGene, CEMB-Cry1Ac and CEMB-Cry2A genes expression in sugarcane variety CPF-246 showed an efficient resistance against cane borers (Chilo infuscatellus) and was also highly tolerant against glyphosate spray. The selected transgenic sugarcane lines showed sustainable resistance against cane borer and glyphosate spray can be further exploited at farmer's field level after fulfilling the biosafety requirements to boost the sugarcane production in the country.
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Affiliation(s)
- Zahida Qamar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | - Idrees Ahmad Nasir
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mounir G Abouhaidar
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | | | - Abdul Qayyum Rao
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ayesha Latif
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Qurban Ali
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Saima Anwar
- Pakistan Biomedical Engineering Centre University of Engineering and Technology, New Campus, Lahore, Pakistan
| | - Bushra Rashid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ahmad Ali Shahid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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7
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Egea TC, da Silva R, Boscolo M, Rigonato J, Monteiro DA, Grünig D, da Silva H, van der Wielen F, Helmus R, Parsons JR, Gomes E. Diuron degradation by bacteria from soil of sugarcane crops. Heliyon 2017; 3:e00471. [PMID: 29322098 PMCID: PMC5753625 DOI: 10.1016/j.heliyon.2017.e00471] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/24/2017] [Accepted: 11/24/2017] [Indexed: 12/03/2022] Open
Abstract
The isolation of microorganisms from soil impacted by xenobiotic chemicals and exposing them in the laboratory to the contaminant can provide important information about their response to the contaminants. The purpose of this study was to isolate bacteria from soil with historical application of herbicides and to evaluate their potential to degrade diuron. The isolation media contained either glucose or diuron as carbon source. A total of 400 bacteria were isolated, with 68% being Gram-positive and 32% Gram-negative. Most isolates showed potential to degrade between 10 and 30% diuron after five days of cultivation; however Stenotrophomonas acidophila TD4.7 and Bacillus cereus TD4.31 were able to degrade 87% and 68%, respectively. The degradation of diuron resulted in the formation of the metabolites DCPMU, DCPU, DCA, 3,4-CAC, 4-CA, 4-CAC and aniline. Based on these results it was proposed that Pseudomonas aeruginosa TD2.3, Stenotrophomonas acidaminiphila TD4.7, B. cereus TD4.31 and Alcaligenes faecalis TG 4.48, act on 3,4-DCA and 4-CA by alkylation and dealkylation while Micrococcus luteus and Achromobacter sp follow dehalogenation directly to aniline. Growth on aniline as sole carbon source demonstrates the capacity of strains to open the aromatic ring. In conclusion, the results show that the role of microorganisms in the degradation of xenobiotics in the environment depends on their own metabolism and also on their synergistic interactions.
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Affiliation(s)
- Tassia C. Egea
- Ibilce-Universidade Estadual Paulista-UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Roberto da Silva
- Ibilce-Universidade Estadual Paulista-UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Maurício Boscolo
- Ibilce-Universidade Estadual Paulista-UNESP, São José do Rio Preto, São Paulo, Brazil
| | | | - Diego A. Monteiro
- Ibilce-Universidade Estadual Paulista-UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Danilo Grünig
- Faculty of Science Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Netherlands
| | - Humberto da Silva
- Ibilce-Universidade Estadual Paulista-UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Frans van der Wielen
- Faculty of Science Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Netherlands
| | - Rick Helmus
- Faculty of Science Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Netherlands
| | - John R. Parsons
- Faculty of Science Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Netherlands
| | - Eleni Gomes
- Ibilce-Universidade Estadual Paulista-UNESP, São José do Rio Preto, São Paulo, Brazil
- Corresponding author.
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8
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Wang C, Glenn KC, Kessenich C, Bell E, Burzio LA, Koch MS, Li B, Silvanovich A. Safety assessment of dicamba mono-oxygenases that confer dicamba tolerance to various crops. Regul Toxicol Pharmacol 2016; 81:171-182. [PMID: 27575686 DOI: 10.1016/j.yrtph.2016.08.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/22/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
Abstract
Dicamba tolerant (DT) soybean, cotton and maize were developed through constitutive expression of dicamba mono-oxygenase (DMO) in chloroplasts. DMO expressed in three DT crops exhibit 91.6-97.1% amino acid sequence identity to wild type DMO. All DMO forms maintain the characteristics of Rieske oxygenases that have a history of safe use. Additionally, they are all functionally similar in vivo since the three DT crops are all tolerant to dicamba treatment. None of these DMO sequences were found to have similarity to any known allergens or toxins. Herein, to further understand the safety of these DMO variants, a weight of evidence approach was employed. Each purified DMO protein was found to be completely deactivated in vitro by heating at temperatures 55 °C and above, and all were completely digested within 30 s or 5 min by pepsin and pancreatin, respectively. Mice orally dosed with each of these DMO proteins showed no adverse effects as evidenced by analysis of body weight gain, food consumption and clinical observations. Therefore, the weight of evidence from all these protein safety studies support the conclusion that the various forms of DMO proteins introduced into DT soybean, cotton and maize are safe for food and feed consumption, and the small amino acid sequence differences outside the active site of DMO do not raise any additional safety concerns.
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MESH Headings
- Administration, Oral
- Amino Acid Sequence
- Animals
- Computational Biology
- Consumer Product Safety
- Crops, Agricultural/enzymology
- Crops, Agricultural/genetics
- Crops, Agricultural/toxicity
- Databases, Protein
- Dicamba/pharmacology
- Drug Resistance/genetics
- Enzyme Stability
- Female
- Food Safety
- Food, Genetically Modified/parasitology
- Food, Genetically Modified/toxicity
- Gene Expression Regulation, Plant
- Gossypium/enzymology
- Gossypium/genetics
- Gossypium/toxicity
- Herbicides/pharmacology
- Humans
- Male
- Mice
- Mixed Function Oxygenases/administration & dosage
- Mixed Function Oxygenases/genetics
- Mixed Function Oxygenases/metabolism
- Mixed Function Oxygenases/toxicity
- Oxidoreductases, O-Demethylating/toxicity
- Pancreatin/metabolism
- Pepsin A/metabolism
- Plants, Genetically Modified/enzymology
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/toxicity
- Protein Denaturation
- Proteolysis
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Recombinant Proteins/toxicity
- Risk Assessment
- Glycine max/enzymology
- Glycine max/genetics
- Glycine max/toxicity
- Stenotrophomonas maltophilia/enzymology
- Stenotrophomonas maltophilia/genetics
- Temperature
- Toxicity Tests, Acute
- Zea mays/enzymology
- Zea mays/genetics
- Zea mays/toxicity
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Affiliation(s)
- Cunxi Wang
- Monsanto Company, 800 North Lindbergh Blvd, St. Louis, MO 63167, USA.
| | - Kevin C Glenn
- Monsanto Company, 800 North Lindbergh Blvd, St. Louis, MO 63167, USA
| | - Colton Kessenich
- Monsanto Company, 800 North Lindbergh Blvd, St. Louis, MO 63167, USA
| | - Erin Bell
- Monsanto Company, 800 North Lindbergh Blvd, St. Louis, MO 63167, USA
| | - Luis A Burzio
- Monsanto Company, 800 North Lindbergh Blvd, St. Louis, MO 63167, USA
| | - Michael S Koch
- Monsanto Company, 800 North Lindbergh Blvd, St. Louis, MO 63167, USA
| | - Bin Li
- Monsanto Company, 800 North Lindbergh Blvd, St. Louis, MO 63167, USA
| | - Andre Silvanovich
- Monsanto Company, 800 North Lindbergh Blvd, St. Louis, MO 63167, USA
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9
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The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part III. {[Fe2S2](Cys)3(X)} (X=Asp, Arg, His) and {[Fe2S2](Cys)2(His)2} proteins. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Yoshikata T, Suzuki K, Kamimura N, Namiki M, Hishiyama S, Araki T, Kasai D, Otsuka Y, Nakamura M, Fukuda M, Katayama Y, Masai E. Three-Component O-Demethylase System Essential for Catabolism of a Lignin-Derived Biphenyl Compound in Sphingobium sp. Strain SYK-6. Appl Environ Microbiol 2014; 80:7142-53. [PMID: 25217011 PMCID: PMC4249175 DOI: 10.1128/aem.02236-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 09/05/2014] [Indexed: 11/20/2022] Open
Abstract
Sphingobium sp. strain SYK-6 is able to assimilate lignin-derived biaryls, including a biphenyl compound, 5,5'-dehydrodivanillate (DDVA). Previously, ligXa (SLG_07770), which is similar to the gene encoding oxygenase components of Rieske-type nonheme iron aromatic-ring-hydroxylating oxygenases, was identified to be essential for the conversion of DDVA; however, the genes encoding electron transfer components remained unknown. Disruption of putative electron transfer component genes scattered through the SYK-6 genome indicated that SLG_08500 and SLG_21200, which showed approximately 60% amino acid sequence identities with ferredoxin and ferredoxin reductase of dicamba O-demethylase, were essential for the normal growth of SYK-6 on DDVA. LigXa and the gene products of SLG_08500 (LigXc) and SLG_21200 (LigXd) were purified and were estimated to be a trimer, a monomer, and a monomer, respectively. LigXd contains FAD as the prosthetic group and showed much higher reductase activity toward 2,6-dichlorophenolindophenol with NADH than with NADPH. A mixture of purified LigXa, LigXc, and LigXd converted DDVA into 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl in the presence of NADH, indicating that DDVA O-demethylase is a three-component monooxygenase. This enzyme requires Fe(II) for its activity and is highly specific for DDVA, with a Km value of 63.5 μM and kcat of 6.1 s(-1). Genome searches in six other sphingomonads revealed genes similar to ligXc and ligXd (>58% amino acid sequence identities) with a limited number of electron transfer component genes, yet a number of diverse oxygenase component genes were found. This fact implies that these few electron transfer components are able to interact with numerous oxygenase components and the conserved LigXc and LigXd orthologs are important in sphingomonads.
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Affiliation(s)
- Taichi Yoshikata
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Kazuya Suzuki
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Masahiro Namiki
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Shojiro Hishiyama
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Takuma Araki
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Yuichiro Otsuka
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Masaya Nakamura
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Masao Fukuda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Yoshihiro Katayama
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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11
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Jiang WZ, Adamec J, Weeks DP. A small-scale, inexpensive method for detecting formaldehyde or methanol in biochemical reactions containing interfering substances. Anal Biochem 2013; 442:146-8. [PMID: 23938775 DOI: 10.1016/j.ab.2013.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 07/31/2013] [Accepted: 08/02/2013] [Indexed: 11/30/2022]
Abstract
A simple, inexpensive microdistillation device is described for capturing methanol or formaldehyde as end products of biochemical reactions or in environmental samples. We demonstrate that the microdistillation protocol, coupled with the use of alcohol oxidase and the formaldehyde-sensitive reagent Purpald (4-amino-3-hydrazino-5-mercapto-1,2,4-triazole), serves as a quick and inexpensive alternative to chromatographic and mass spectrometer analyses for determining if formaldehyde or methanol is a product of reactions that contain substances that interfere with the Purpald reaction. These techniques were used to affirm formaldehyde as the end product of the dicamba monooxygenase-catalyzed O-demethylation of the herbicide dicamba (2-methoxy-3,6-dichlorobenzoic acid).
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Affiliation(s)
- Wen Zhi Jiang
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588-0664, USA
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12
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Jiang W, Wilson MA, Weeks DP. O-Demethylations catalyzed by Rieske nonheme iron monooxygenases involve the difficult oxidation of a saturated C-H bond. ACS Chem Biol 2013; 8:1687-91. [PMID: 23719540 DOI: 10.1021/cb400154a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dicamba monooxygenase (DMO) catalyzes the O-demethylation of dicamba (3,6-dichloro-2-methoxybenzoate) to produce 3,6-dichlorosalicylate and formaldehyde. Recent crystallographic studies suggest that DMO catalyzes the challenging oxidation of a saturated C-H bond within the methyl group of dicamba to form a hemiacetal intermediate. Testing of this hypothesis was made possible by our development of two new independent techniques. As a novel method to allow use of (18)O2 to follow reaction products, bisulfite was used to trap newly formed (18)O-formaldehyde in the stable adduct, hydroxymethanesulfonate (HMS(-)), and thereby prevent the rapid exchange of (18)O in formaldehyde with (16)O in water. The second technique utilized unique properties of Pseudomonas putida formaldehyde dehydrogenase that allow rapid conversion of (18)O-formaldehyde into stable and easily detectable (18)O-formic acid. Experiments using these two new techniques provided compelling evidence for DMO-catalyzed oxidation of the methyl group of dicamba, thus validating a mechanism for DMO [and for vanillate monooxygenase, a related Rieske nonheme iron monooxygenase] that involves the difficult oxidation of a saturated C-H bond.
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Affiliation(s)
- Wenzhi Jiang
- Department
of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United
States
| | - Mark A. Wilson
- Department
of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United
States
| | - Donald P. Weeks
- Department
of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United
States
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13
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Structural and molecular genetic analyses of the bacterial carbazole degradation system. Biosci Biotechnol Biochem 2012; 76:1-18. [PMID: 22232235 DOI: 10.1271/bbb.110620] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Carbazole degradation by several bacterial strains, including Pseudomonas resinovorans CA10, has been investigated over the last two decades. As the initial reaction in degradation pathways, carbazole is commonly oxygenated at angular (C9a) and adjacent (C1) carbons as two hydroxyl groups in a cis configuration. This type of dioxygenation is termed "angular dioxygenation," and is catalyzed by carbazole 1,9a-dioxygenase (CARDO), consisting of terminal oxygenase, ferredoxin, and ferredoxin reductase components. The crystal structures of all components and the electron transfer complex between terminal oxygenase and ferredoxin indicate substrate recognition mechanisms suitable for angular dioxygenation and specific electron transfer among the three components. In contrast, the carbazole degradative car operon of CA10 is located on IncP-7 conjugative plasmid pCAR1. Together with conventional molecular genetic and biochemical investigations, recent genome sequencing and RNA mapping studies have clarified that transcriptional cross-regulation via nucleoid-associated proteins is established between pCAR1 and the host chromosome.
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14
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Cao M, Sato SJ, Behrens M, Jiang WZ, Clemente TE, Weeks DP. Genetic engineering of maize (Zea mays) for high-level tolerance to treatment with the herbicide dicamba. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:5830-5834. [PMID: 21133415 DOI: 10.1021/jf104233h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Herbicide-tolerant crops have been widely and rapidly adopted by farmers in several countries due to enhanced weed control, lower labor and production costs, increased environmental benefits, and gains in profitability. Soon to be introduced transgenic soybean and cotton varieties tolerant to treatments with the herbicide dicamba offer prospects for excellent broadleaf weed control in these broadleaf crops. Because monocots such as maize (Zea mays) can be treated with dicamba only during a limited window of crop development and because crop injury is sometimes observed when conditions are unfavorable, transgenic maize plants have been produced and tested for higher levels of tolerance to treatment with dicamba. Maize plants expressing the gene encoding dicamba monooxygenase (DMO) linked with an upstream chloroplast transit peptide (CTP) display greatly enhanced tolerance to dicamba applied either pre-emergence or postemergence. Comparisons of DMO coupled to CTPs derived from the Rubisco small subunit from either Arabidopsis thaliana or Z. mays showed that both allowed production of transgenic maize plants tolerant to treatment with levels of dicamba (i.e., 27 kg/ha) greatly exceeding the highest recommended rate of 0.56 kg/ha.
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Affiliation(s)
- Mingxia Cao
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0665, USA
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15
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Scott C, Begley C, Taylor MJ, Pandey G, Momiroski V, French N, Brearley C, Kotsonis SE, Selleck MJ, Carino FA, Bajet CM, Clarke C, Oakeshott JG, Russell RJ. Free-Enzyme Bioremediation of Pesticides. ACS SYMPOSIUM SERIES 2011. [DOI: 10.1021/bk-2011-1075.ch011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Colin Scott
- CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
- Orica Australia Pty Ltd., 1 Nicholson Street, Melbourne Victoria 3000, Australia
- Institute of Chemistry, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Pesticide Toxicology and Chemistry Laboratory, National Crop Protection Center, University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Cameron Begley
- CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
- Orica Australia Pty Ltd., 1 Nicholson Street, Melbourne Victoria 3000, Australia
- Institute of Chemistry, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Pesticide Toxicology and Chemistry Laboratory, National Crop Protection Center, University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Matthew J. Taylor
- CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
- Orica Australia Pty Ltd., 1 Nicholson Street, Melbourne Victoria 3000, Australia
- Institute of Chemistry, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Pesticide Toxicology and Chemistry Laboratory, National Crop Protection Center, University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Gunjan Pandey
- CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
- Orica Australia Pty Ltd., 1 Nicholson Street, Melbourne Victoria 3000, Australia
- Institute of Chemistry, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Pesticide Toxicology and Chemistry Laboratory, National Crop Protection Center, University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Vinko Momiroski
- CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
- Orica Australia Pty Ltd., 1 Nicholson Street, Melbourne Victoria 3000, Australia
- Institute of Chemistry, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Pesticide Toxicology and Chemistry Laboratory, National Crop Protection Center, University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Nigel French
- CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
- Orica Australia Pty Ltd., 1 Nicholson Street, Melbourne Victoria 3000, Australia
- Institute of Chemistry, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Pesticide Toxicology and Chemistry Laboratory, National Crop Protection Center, University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Clint Brearley
- CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
- Orica Australia Pty Ltd., 1 Nicholson Street, Melbourne Victoria 3000, Australia
- Institute of Chemistry, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Pesticide Toxicology and Chemistry Laboratory, National Crop Protection Center, University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Steve E. Kotsonis
- CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
- Orica Australia Pty Ltd., 1 Nicholson Street, Melbourne Victoria 3000, Australia
- Institute of Chemistry, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Pesticide Toxicology and Chemistry Laboratory, National Crop Protection Center, University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Michael J. Selleck
- CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
- Orica Australia Pty Ltd., 1 Nicholson Street, Melbourne Victoria 3000, Australia
- Institute of Chemistry, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Pesticide Toxicology and Chemistry Laboratory, National Crop Protection Center, University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Flerida A. Carino
- CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
- Orica Australia Pty Ltd., 1 Nicholson Street, Melbourne Victoria 3000, Australia
- Institute of Chemistry, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Pesticide Toxicology and Chemistry Laboratory, National Crop Protection Center, University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Cristina M. Bajet
- CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
- Orica Australia Pty Ltd., 1 Nicholson Street, Melbourne Victoria 3000, Australia
- Institute of Chemistry, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Pesticide Toxicology and Chemistry Laboratory, National Crop Protection Center, University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Craig Clarke
- CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
- Orica Australia Pty Ltd., 1 Nicholson Street, Melbourne Victoria 3000, Australia
- Institute of Chemistry, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Pesticide Toxicology and Chemistry Laboratory, National Crop Protection Center, University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - John G. Oakeshott
- CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
- Orica Australia Pty Ltd., 1 Nicholson Street, Melbourne Victoria 3000, Australia
- Institute of Chemistry, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Pesticide Toxicology and Chemistry Laboratory, National Crop Protection Center, University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Robyn J. Russell
- CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia
- Orica Australia Pty Ltd., 1 Nicholson Street, Melbourne Victoria 3000, Australia
- Institute of Chemistry, University of the Philippines, Diliman, Quezon City 1101, Philippines
- Pesticide Toxicology and Chemistry Laboratory, National Crop Protection Center, University of the Philippines, Los Banos, Laguna 4031, Philippines
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16
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Evidence that ubiquinone is a required intermediate for rhodoquinone biosynthesis in Rhodospirillum rubrum. J Bacteriol 2009; 192:436-45. [PMID: 19933361 DOI: 10.1128/jb.01040-09] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhodoquinone (RQ) is an important cofactor used in the anaerobic energy metabolism of Rhodospirillum rubrum. RQ is structurally similar to ubiquinone (coenzyme Q or Q), a polyprenylated benzoquinone used in the aerobic respiratory chain. RQ is also found in several eukaryotic species that utilize a fumarate reductase pathway for anaerobic respiration, an important example being the parasitic helminths. RQ is not found in humans or other mammals, and therefore inhibition of its biosynthesis may provide a parasite-specific drug target. In this report, we describe several in vivo feeding experiments with R. rubrum used for the identification of RQ biosynthetic intermediates. Cultures of R. rubrum were grown in the presence of synthetic analogs of ubiquinone and the known Q biosynthetic precursors demethylubiquinone, demethoxyubiquinone, and demethyldemethoxyubiquinone, and assays were monitored for the formation of RQ(3). Data from time course experiments and S-adenosyl-l-methionine-dependent O-methyltransferase inhibition studies are discussed. Based on the results presented, we have demonstrated that Q is a required intermediate for the biosynthesis of RQ in R. rubrum.
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17
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D'Ordine RL, Rydel TJ, Storek MJ, Sturman EJ, Moshiri F, Bartlett RK, Brown GR, Eilers RJ, Dart C, Qi Y, Flasinski S, Franklin SJ. Dicamba monooxygenase: structural insights into a dynamic Rieske oxygenase that catalyzes an exocyclic monooxygenation. J Mol Biol 2009; 392:481-97. [PMID: 19616009 DOI: 10.1016/j.jmb.2009.07.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2009] [Revised: 07/08/2009] [Accepted: 07/09/2009] [Indexed: 11/29/2022]
Abstract
Dicamba (2-methoxy-3,6-dichlorobenzoic acid) O-demethylase (DMO) is the terminal Rieske oxygenase of a three-component system that includes a ferredoxin and a reductase. It catalyzes the NADH-dependent oxidative demethylation of the broad leaf herbicide dicamba. DMO represents the first crystal structure of a Rieske non-heme iron oxygenase that performs an exocyclic monooxygenation, incorporating O(2) into a side-chain moiety and not a ring system. The structure reveals a 3-fold symmetric trimer (alpha(3)) in the crystallographic asymmetric unit with similar arrangement of neighboring inter-subunit Rieske domain and non-heme iron site enabling electron transport consistent with other structurally characterized Rieske oxygenases. While the Rieske domain is similar, differences are observed in the catalytic domain, which is smaller in sequence length than those described previously, yet possessing an active-site cavity of larger volume when compared to oxygenases with larger substrates. Consistent with the amphipathic substrate, the active site is designed to interact with both the carboxylate and aromatic ring with both key polar and hydrophobic interactions observed. DMO structures were solved with and without substrate (dicamba), product (3,6-dichlorosalicylic acid), and either cobalt or iron in the non-heme iron site. The substitution of cobalt for iron revealed an uncommon mode of non-heme iron binding trapped by the non-catalytic Co(2+), which, we postulate, may be transiently present in the native enzyme during the catalytic cycle. Thus, we present four DMO structures with resolutions ranging from 1.95 to 2.2 A, which, in sum, provide a snapshot of a dynamic enzyme where metal binding and substrate binding are coupled to observed structural changes in the non-heme iron and catalytic sites.
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18
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Crystal structure of dicamba monooxygenase: a Rieske nonheme oxygenase that catalyzes oxidative demethylation. J Mol Biol 2009; 392:498-510. [PMID: 19616011 DOI: 10.1016/j.jmb.2009.07.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Revised: 07/04/2009] [Accepted: 07/09/2009] [Indexed: 11/20/2022]
Abstract
Dicamba (3,6-dichloro-2-methoxybenzoic acid) is a widely used herbicide that is efficiently degraded by soil microbes. These microbes use a novel Rieske nonheme oxygenase, dicamba monooxygenase (DMO), to catalyze the oxidative demethylation of dicamba to 3,6-dichlorosalicylic acid (DCSA) and formaldehyde. We have determined the crystal structures of DMO in the free state, bound to its substrate dicamba, and bound to the product DCSA at 2.10-1.75 A resolution. The structures show that the DMO active site uses a combination of extensive hydrogen bonding and steric interactions to correctly orient chlorinated, ortho-substituted benzoic-acid-like substrates for catalysis. Unlike other Rieske aromatic oxygenases, DMO oxygenates the exocyclic methyl group, rather than the aromatic ring, of its substrate. This first crystal structure of a Rieske demethylase shows that the Rieske oxygenase structural scaffold can be co-opted to perform varied types of reactions on xenobiotic substrates.
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19
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Behrens MR, Mutlu N, Chakraborty S, Dumitru R, Jiang WZ, Lavallee BJ, Herman PL, Clemente TE, Weeks DP. Dicamba resistance: enlarging and preserving biotechnology-based weed management strategies. Science 2007; 316:1185-8. [PMID: 17525337 DOI: 10.1126/science.1141596] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The advent of biotechnology-derived, herbicide-resistant crops has revolutionized farming practices in many countries. Facile, highly effective, environmentally sound, and profitable weed control methods have been rapidly adopted by crop producers who value the benefits associated with biotechnology-derived weed management traits. But a rapid rise in the populations of several troublesome weeds that are tolerant or resistant to herbicides currently used in conjunction with herbicide-resistant crops may signify that the useful lifetime of these economically important weed management traits will be cut short. We describe the development of soybean and other broadleaf plant species resistant to dicamba, a widely used, inexpensive, and environmentally safe herbicide. The dicamba resistance technology will augment current herbicide resistance technologies and extend their effective lifetime. Attributes of both nuclear- and chloroplast-encoded dicamba resistance genes that affect the potency and expected durability of the herbicide resistance trait are examined.
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Affiliation(s)
- Mark R Behrens
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
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20
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Urata M, Uchimura H, Noguchi H, Sakaguchi T, Takemura T, Eto K, Habe H, Omori T, Yamane H, Nojiri H. Plasmid pCAR3 contains multiple gene sets involved in the conversion of carbazole to anthranilate. Appl Environ Microbiol 2006; 72:3198-205. [PMID: 16672458 PMCID: PMC1472349 DOI: 10.1128/aem.72.5.3198-3205.2006] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The carbazole degradative car-I gene cluster (carAaIBaIBbICIAcI) of Sphingomonas sp. strain KA1 is located on the 254-kb circular plasmid pCAR3. Carbazole conversion to anthranilate is catalyzed by carbazole 1,9a-dioxygenase (CARDO; CarAaIAcI), meta-cleavage enzyme (CarBaIBbI), and hydrolase (CarCI). CARDO is a three-component dioxygenase, and CarAaI and CarAcI are its terminal oxygenase and ferredoxin components. The car-I gene cluster lacks the gene encoding the ferredoxin reductase component of CARDO. In the present study, based on the draft sequence of pCAR3, we found multiple carbazole degradation genes dispersed in four loci on pCAR3, including a second copy of the car gene cluster (carAaIIBaIIBbIICIIAcII) and the ferredoxin/reductase genes fdxI-fdrI and fdrII. Biotransformation experiments showed that FdrI (or FdrII) could drive the electron transfer chain from NAD(P)H to CarAaI (or CarAaII) with the aid of ferredoxin (CarAcI, CarAcII, or FdxI). Because this electron transfer chain showed phylogenetic relatedness to that consisting of putidaredoxin and putidaredoxin reductase of the P450cam monooxygenase system of Pseudomonas putida, CARDO systems of KA1 can be classified in the class IIA Rieske non-heme iron oxygenase system. Reverse transcription-PCR (RT-PCR) and quantitative RT-PCR analyses revealed that two car gene clusters constituted operons, and their expression was induced when KA1 was exposed to carbazole, although the fdxI-fdrI and fdrII genes were expressed constitutively. Both terminal oxygenases of KA1 showed roughly the same substrate specificity as that from the well-characterized carbazole degrader Pseudomonas resinovorans CA10, although slight differences were observed.
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Affiliation(s)
- Masaaki Urata
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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21
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Abstract
Molecular paramagnetism pervades the bioinorganic chemistry of V, Mn, Fe, Co, Ni, Cu, Mo, W, and of a number of non-biological transition elements. To date we can look back at half a century of fruitful EPR studies on metalloproteins, and against this background evaluate the significance of modern EPR spectroscopy from the perspective of a biochemist, making a distinction between conventional continuous wave X-band spectroscopy as a reliable work horse with broad, established applicability even on crude preparations, vs. a diffuse set of "advanced EPR" technologies whose practical application typically calls for narrowly focused research hypotheses and very high quality samples. The type of knowledge on metalloproteins that is readily obtainable with EPR spectroscopy, is explained with illustrative examples, as is the relation between experimental complexity and the spin value of the system.
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Affiliation(s)
- Wilfred R Hagen
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628, BC Delft, The Netherlands.
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22
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Herman PL, Behrens M, Chakraborty S, Chrastil BM, Barycki J, Weeks DP. A three-component dicamba O-demethylase from Pseudomonas maltophilia, strain DI-6: gene isolation, characterization, and heterologous expression. J Biol Chem 2005; 280:24759-67. [PMID: 15855162 DOI: 10.1074/jbc.m500597200] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dicamba O-demethylase is a multicomponent enzyme from Pseudomonas maltophilia, strain DI-6, that catalyzes the conversion of the widely used herbicide dicamba (2-methoxy-3,6-dichlorobenzoic acid) to DCSA (3,6-dichlorosalicylic acid). We recently described the biochemical characteristics of the three components of this enzyme (i.e. reductase(DIC), ferredoxin(DIC), and oxygenase(DIC)) and classified the oxygenase component of dicamba O-demethylase as a member of the Rieske non-heme iron family of oxygenases. In the current study, we used N-terminal and internal amino acid sequence information from the purified proteins to clone the genes that encode dicamba O-demethylase. Two reductase genes (ddmA1 and ddmA2) with predicted amino acid sequences of 408 and 409 residues were identified. The open reading frames encode 43.7- and 43.9-kDa proteins that are 99.3% identical to each other and homologous to members of the FAD-dependent pyridine nucleotide reductase family. The ferredoxin coding sequence (ddmB) specifies an 11.4-kDa protein composed of 105 residues with similarity to the adrenodoxin family of [2Fe-2S] bacterial ferredoxins. The oxygenase gene (ddmC) encodes a 37.3-kDa protein composed of 339 amino acids that is homologous to members of the Phthalate family of Rieske non-heme iron oxygenases that function as monooxygenases. Southern analysis localized the oxygenase gene to a megaplasmid in cells of P. maltophilia. Mixtures of the three highly purified recombinant dicamba O-demethylase components overexpressed in Escherichia coli converted dicamba to DCSA with an efficiency similar to that of the native enzyme, suggesting that all of the components required for optimal enzymatic activity have been identified. Computer modeling suggests that oxygenase(DIC) has strong similarities with the core alphasubunits of naphthalene 1,2-dioxygenase. Nonetheless, the present studies point to dicamba O-demethylase as an enzyme system with its own unique combination of characteristics.
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Affiliation(s)
- Patricia L Herman
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 65888-0664, USA
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