1
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Liu Y, Gu B, Shi J, Fu C, Zhang X, Chen X, Yang R, Lyu X. Inverse metabolic engineering based on metabonomics for efficient production of hydroxytyrosol by Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2024:131187. [PMID: 39094965 DOI: 10.1016/j.biortech.2024.131187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Metabolic engineering provides a powerful approach to efficiently produce valuable compounds, with the aid of emerging gene editing tools and diverse metabolic regulation strategies. However, apart from the current known biochemical pathway information, a variety of unclear constraints commonly limited the optimization space of cell phenotype. Hydroxytyrosol is an important phenolic compound that serves various industries with prominent health-beneficial properties. In this study, the inverse metabolic engineering based on metabolome analysis was customized and implemented to disclose the hidden rate-limiting steps and thus to improve hydroxytyrosol production in Saccharomyces cerevisiae (S. cerevisiae). The potential rate-limiting steps involved three modules that were eliminated individually via reinforcing and balancing metabolic flow, optimizing cofactor supply, and weakening the competitive pathways. Ultimately, a 118.53 % improvement in hydroxytyrosol production (639.84 mg/L) was achieved by inverse metabolic engineering.
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Affiliation(s)
- Yingjie Liu
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Bixuan Gu
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Jiahua Shi
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, QLD, Australia
| | - Changchun Fu
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Xuepeng Zhang
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Xinqi Chen
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Ruijin Yang
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Xiaomei Lyu
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China.
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2
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Knaus T, Macheroux P, Mutti FG. Fus-SMO: Kinetics, Biochemical Characterisation and In Silico Modelling of a Chimeric Styrene Monooxygenase Demonstrating Quantitative Coupling Efficiency. Chembiochem 2024; 25:e202300833. [PMID: 38306174 DOI: 10.1002/cbic.202300833] [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: 12/10/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/03/2024]
Abstract
The styrene monooxygenase, a two-component enzymatic system for styrene epoxidation, was characterised through the study of Fus-SMO - a chimera resulting from the fusion of StyA and StyB using a flexible linker. Notably, it remains debated whether the transfer of FADH2 from StyB to StyA occurs through diffusion, channeling, or a combination of both. Fus-SMO was identified as a trimer with one bound FAD molecule. In silico modelling revealed a well-distanced arrangement (45-50 Å) facilitated by the flexible linker's loopy structure. Pre-steady-state kinetics elucidated the FADox reduction intricacies (kred=110 s-1 for bound FADox), identifying free FADox binding as the rate-determining step. The aerobic oxidation of FADH2 (kox=90 s-1) and subsequent decomposition to FADox and H2O2 demonstrated StyA's protective effect on the bound hydroperoxoflavin (kdec=0.2 s-1) compared to free cofactor (kdec=1.8 s-1). At varied styrene concentrations, kox for FADH2 ranged from 80 to 120 s-1. Studies on NADH consumption vs. styrene epoxidation revealed Fus-SMO's ability to achieve quantitative coupling efficiency in solution, surpassing natural two-component SMOs. The results suggest that Fus-SMO exhibits enhanced FADH2 channelling between subunits. This work contributes to comprehending FADH2 transfer mechanisms in SMO and illustrates how protein fusion can elevate catalytic efficiency for biocatalytic applications.
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Affiliation(s)
- Tanja Knaus
- Van 't Hoff Institute for Molecular Sciences, HIMS-Biocat, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| | - Francesco G Mutti
- Van 't Hoff Institute for Molecular Sciences, HIMS-Biocat, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
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3
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Pierdominici‐Sottile G, Palma J, Ferrelli ML, Sobrado P. The dynamics of the flavin, NADPH, and active site loops determine the mechanism of activation of class B flavin-dependent monooxygenases. Protein Sci 2024; 33:e4935. [PMID: 38501462 PMCID: PMC10962481 DOI: 10.1002/pro.4935] [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: 10/11/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/20/2024]
Abstract
Flavin-dependent monooxygenases (FMOs) constitute a diverse enzyme family that catalyzes crucial hydroxylation, epoxidation, and Baeyer-Villiger reactions across various metabolic pathways in all domains of life. Due to the intricate nature of this enzyme family's mechanisms, some aspects of their functioning remain unknown. Here, we present the results of molecular dynamics computations, supplemented by a bioinformatics analysis, that clarify the early stages of their catalytic cycle. We have elucidated the intricate binding mechanism of NADPH and L-Orn to a class B monooxygenase, the ornithine hydroxylase fromAspergillus $$ Aspergillus $$ fumigatus $$ fumigatus $$ known as SidA. Our investigation involved a comprehensive characterization of the conformational changes associated with the FAD (Flavin Adenine Dinucleotide) cofactor, transitioning from the out to the in position. Furthermore, we explored the rotational dynamics of the nicotinamide ring of NADPH, shedding light on its role in facilitating FAD reduction, supported by experimental evidence. Finally, we also analyzed the extent of conservation of two Tyr-loops that play critical roles in the process.
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Affiliation(s)
- Gustavo Pierdominici‐Sottile
- Departamento de Ciencia y TecnologíaUniversidad Nacional de QuilmesBernalArgentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)CABAArgentina
| | - Juliana Palma
- Departamento de Ciencia y TecnologíaUniversidad Nacional de QuilmesBernalArgentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)CABAArgentina
| | - María Leticia Ferrelli
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)CABAArgentina
- Instituto de Biotecnología y Biología Molecular (IBBM, UNLP‐CONICET), Facultad de Ciencias ExactasUniversidad Nacional de La PlataLa PlataBuenos AiresArgentina
| | - Pablo Sobrado
- Department of BiochemistryVirginia TechBlacksburgVirginiaUSA
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4
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Shi T, Sun X, Yuan Q, Wang J, Shen X. Exploring the role of flavin-dependent monooxygenases in the biosynthesis of aromatic compounds. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:46. [PMID: 38520003 PMCID: PMC10958861 DOI: 10.1186/s13068-024-02490-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 03/13/2024] [Indexed: 03/25/2024]
Abstract
Hydroxylated aromatic compounds exhibit exceptional biological activities. In the biosynthesis of these compounds, three types of hydroxylases are commonly employed: cytochrome P450 (CYP450), pterin-dependent monooxygenase (PDM), and flavin-dependent monooxygenase (FDM). Among these, FDM is a preferred choice due to its small molecular weight, stable expression in both prokaryotic and eukaryotic fermentation systems, and a relatively high concentration of necessary cofactors. However, the catalytic efficiency of many FDMs falls short of meeting the demands of large-scale production. Additionally, challenges arise from the limited availability of cofactors and compatibility issues among enzyme components. Recently, significant progress has been achieved in improving its catalytic efficiency, but have not yet detailed and informative viewed so far. Therefore, this review emphasizes the advancements in FDMs for the biosynthesis of hydroxylated aromatic compounds and presents a summary of three strategies aimed at enhancing their catalytic efficiency: (a) Developing efficient enzyme mutants through protein engineering; (b) enhancing the supply and rapid circulation of critical cofactors; (c) facilitating cofactors delivery for enhancing FDMs catalytic efficiency. Furthermore, the current challenges and further perspectives on improving catalytic efficiency of FDMs are also discussed.
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Affiliation(s)
- Tong Shi
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
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5
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Sutormin OS, Nemtseva EV, Gulnov DV, Sukovatyi LA, Tyrtyshnaya YS, Lisitsa AE, Kratasyuk VA. Coupling of NAD(P)H:FMN-oxidoreductase and luciferase from luminous bacteria in a viscous medium: Finding the weakest link in the chain. Photochem Photobiol 2024; 100:465-476. [PMID: 37583116 DOI: 10.1111/php.13845] [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: 04/16/2023] [Revised: 07/15/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
The study aims at revealing the mechanisms of the viscous medium effects on the kinetic features of NAD(P)H:FMN-oxidoreductase from luminous bacteria (Red), which are exhibited in a single enzyme assay and in coupling with bacterial luciferase (BLuc). Different concentrations of glycerol and sucrose were used to vary the medium viscosity. The activity of Red, alone and in the presence of BLuc, was analyzed, as well as BLuc activity in the presence of Red, whereas in the absence of BLuc, the Red activity was suppressed in viscous medium, and in the presence of BLuc, the increase in Red activity was observed at low glycerol concentrations (5-20 wt%). The interaction of glycerol and sucrose with Red substrates FMN and NADH was studied using absorption spectroscopy and molecular dynamics. Glycerol was found to form hydrogen bonds with the phosphate groups of the substrates, unlike sucrose. A mechanism for the activation of Red in the presence of BLuc in glycerol solutions through the acceleration of FMN reoxidation was proposed. Thus, it was concluded that, under the conditions used, the weakest link of the coupled enzyme system BLuc-Red in viscous medium is the FMN concentration, which depends on Red activity and the medium viscosity.
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Affiliation(s)
- Oleg S Sutormin
- Department of Chemistry, Institute of Natural and Technical Sciences, Surgut State University, Surgut, Russia
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Elena V Nemtseva
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Krasnoyarsk, Russia
| | - Dmitry V Gulnov
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Lev A Sukovatyi
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Yekaterina S Tyrtyshnaya
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Albert E Lisitsa
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Valentina A Kratasyuk
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Krasnoyarsk, Russia
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6
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Phintha A, Chaiyen P. Unifying and versatile features of flavin-dependent monooxygenases: Diverse catalysis by a common C4a-(hydro)peroxyflavin. J Biol Chem 2023; 299:105413. [PMID: 37918809 PMCID: PMC10696468 DOI: 10.1016/j.jbc.2023.105413] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/18/2023] [Accepted: 10/22/2023] [Indexed: 11/04/2023] Open
Abstract
Flavin-dependent monooxygenases (FDMOs) are known for their remarkable versatility and for their crucial roles in various biological processes and applications. Extensive research has been conducted to explore the structural and functional relationships of FDMOs. The majority of reported FDMOs utilize C4a-(hydro)peroxyflavin as a reactive intermediate to incorporate an oxygen atom into a wide range of compounds. This review discusses and analyzes recent advancements in our understanding of the structural and mechanistic features governing the enzyme functions. State-of-the-art discoveries related to common and distinct structural properties governing the catalytic versatility of the C4a-(hydro)peroxyflavin intermediate in selected FDMOs are discussed. Specifically, mechanisms of hydroxylation, dehalogenation, halogenation, and light-emitting reactions by FDMOs are highlighted. We also provide new analysis based on the structural and mechanistic features of these enzymes to gain insights into how the same intermediate can be harnessed to perform a wide variety of reactions. Challenging questions to obtain further breakthroughs in the understanding of FDMOs are also proposed.
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Affiliation(s)
- Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand.
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7
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Mangkalee M, Oonanant W, Aonbangkhen C, Pimviriyakul P, Tinikul R, Chaiyen P, Insin N, Sucharitakul J. Reaction mechanism and kinetics of the two-component flavoprotein dimethyl sulfone monooxygenase system: Using hydrogen peroxide for monooxygenation and substrate cleavage. FEBS J 2023; 290:5171-5195. [PMID: 37522421 DOI: 10.1111/febs.16916] [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: 05/30/2023] [Revised: 07/14/2023] [Accepted: 07/28/2023] [Indexed: 08/01/2023]
Abstract
The dimethyl sulfone monooxygenase system is a two-component flavoprotein, catalyzing the monooxygenation of dimethyl sulfone (DMSO2 ) by oxidative cleavage producing methanesulfinate and formaldehyde. The reductase component (DMSR) is a flavoprotein with FMN as a cofactor, catalyzing flavin reduction using NADH. The monooxygenase (DMSMO) uses reduced flavin from the reductase and oxygen for substrate monooxygenation. DMSMO can bind to FMN and FMNH- with a Kd of 17.4 ± 0.9 μm and 4.08 ± 0.8 μm, respectively. The binding of FMN to DMSMO is required prior to binding DMSO2 . This also applies to the fast binding of reduced FMN to DMSMO followed by DMSO2 . Substituting reduced DMSR with FMNH- demonstrated the same oxidation kinetics, indicating that FMNH- from DMSR was transferred to DMSMO. The oxidation of FMNH- :DMSMO, with and without DMSO2 did not generate any flavin adducts for monooxygenation. Therefore, H2 O2 is likely to be the reactive agent to attack the substrate. The H2 O2 assay results demonstrated production of H2 O2 from the oxidation of FMNH- :DMSMO, whereas H2 O2 was not detected in the presence of DMSO2 , confirming H2 O2 utilization. The rate constant for methanesulfinate formation determined from rapid quenched flow and the rate constant for flavin oxidation were similar, indicating that H2 O2 rapidly reacts with DMSO2 , with flavin oxidation as the rate-limiting step. This is the first report of the kinetic mechanisms of both components using rapid kinetics and of a method for methanesulfinate detection using LC-MS.
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Affiliation(s)
- Montisa Mangkalee
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Research Unit in Integrative Immuno-Microbial Biochemistry and Bioresponsive Nanomaterials, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Worrapoj Oonanant
- Department of Basic Medical Science, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand
| | - Chanat Aonbangkhen
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Numpon Insin
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Research Unit in Integrative Immuno-Microbial Biochemistry and Bioresponsive Nanomaterials, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
- Skeletal Disorders Research Unit, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
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Ashaduzzaman M, Lingkon K, De Silva AJ, Bellizzi JJ. Crystallographic and thermodynamic evidence of negative cooperativity of flavin and tryptophan binding in the flavin-dependent halogenases AbeH and BorH. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554356. [PMID: 37662313 PMCID: PMC10473636 DOI: 10.1101/2023.08.22.554356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The flavin-dependent halogenase AbeH produces 5-chlorotryptophan in the biosynthetic pathway of the chlorinated bisindole alkaloid BE-54017. We report that in vitro, AbeH (assisted by the flavin reductase AbeF) can chlorinate and brominate tryptophan as well as other indole derivatives and substrates with phenyl and quinoline groups. We solved the X-ray crystal structures of AbeH alone and complexed with FAD, as well as crystal structures of the tryptophan-6-halogenase BorH alone, in complex with 6-chlorotryptophan, and in complex with FAD and tryptophan. Partitioning of FAD and tryptophan into different chains of BorH and failure to incorporate tryptophan into AbeH/FAD crystals suggested that flavin and tryptophan binding are negatively coupled in both proteins. ITC and fluorescence quenching experiments confirmed the ability of both AbeH and BorH to form binary complexes with FAD or tryptophan and the inability of tryptophan to bind to AbeH/FAD or BorH/FAD complexes. FAD could not bind to BorH/tryptophan complexes, but FAD appears to displace tryptophan from AbeH/tryptophan complexes in an endothermic entropically-driven process.
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Affiliation(s)
- Md Ashaduzzaman
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo OH 43606
| | - Kazi Lingkon
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo OH 43606
| | - Aravinda J De Silva
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo OH 43606
| | - John J Bellizzi
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo OH 43606
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9
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Ernst S, Mährlein A, Ritzmann NH, Drees SL, Fetzner S. A comparative study of
N
‐hydroxylating flavoprotein monooxygenases reveals differences in kinetics and cofactor binding. FEBS J 2022; 289:5637-5655. [DOI: 10.1111/febs.16444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/21/2022] [Accepted: 03/18/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Simon Ernst
- Institute of Molecular Microbiology and Biotechnology University of Münster Germany
| | - Almuth Mährlein
- Institute of Molecular Microbiology and Biotechnology University of Münster Germany
| | - Niklas H. Ritzmann
- Institute of Molecular Microbiology and Biotechnology University of Münster Germany
| | - Steffen L. Drees
- Institute of Molecular Microbiology and Biotechnology University of Münster Germany
| | - Susanne Fetzner
- Institute of Molecular Microbiology and Biotechnology University of Münster Germany
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10
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Cheng M, Chen D, Parales RE, Jiang J. Oxygenases as Powerful Weapons in the Microbial Degradation of Pesticides. Annu Rev Microbiol 2022; 76:325-348. [PMID: 35650666 DOI: 10.1146/annurev-micro-041320-091758] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Oxygenases, which catalyze the reductive activation of O2 and incorporation of oxygen atoms into substrates, are widely distributed in aerobes. They function by switching the redox states of essential cofactors that include flavin, heme iron, Rieske non-heme iron, and Fe(II)/α-ketoglutarate. This review summarizes the catalytic features of flavin-dependent monooxygenases, heme iron-dependent cytochrome P450 monooxygenases, Rieske non-heme iron-dependent oxygenases, Fe(II)/α-ketoglutarate-dependent dioxygenases, and ring-cleavage dioxygenases, which are commonly involved in pesticide degradation. Heteroatom release (hydroxylation-coupled hetero group release), aromatic/heterocyclic ring hydroxylation to form ring-cleavage substrates, and ring cleavage are the main chemical fates of pesticides catalyzed by these oxygenases. The diversity of oxygenases, specificities for electron transport components, and potential applications of oxygenases are also discussed. This article summarizes our current understanding of the catalytic mechanisms of oxygenases and a framework for distinguishing the roles of oxygenases in pesticide degradation. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Minggen Cheng
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China;
| | - Dian Chen
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, California, USA
| | - Jiandong Jiang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China;
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11
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Properties and Mechanisms of Flavin-Dependent Monooxygenases and Their Applications in Natural Product Synthesis. Int J Mol Sci 2022; 23:ijms23052622. [PMID: 35269764 PMCID: PMC8910399 DOI: 10.3390/ijms23052622] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 11/17/2022] Open
Abstract
Natural products are usually highly complicated organic molecules with special scaffolds, and they are an important resource in medicine. Natural products with complicated structures are produced by enzymes, and this is still a challenging research field, its mechanisms requiring detailed methods for elucidation. Flavin adenine dinucleotide (FAD)-dependent monooxygenases (FMOs) catalyze many oxidation reactions with chemo-, regio-, and stereo-selectivity, and they are involved in the synthesis of many natural products. In this review, we introduce the mechanisms for different FMOs, with the classical FAD (C4a)-hydroperoxide as the major oxidant. We also summarize the difference between FMOs and cytochrome P450 (CYP450) monooxygenases emphasizing the advantages of FMOs and their specificity for substrates. Finally, we present examples of FMO-catalyzed synthesis of natural products. Based on these explanations, this review will expand our knowledge of FMOs as powerful enzymes, as well as implementation of the FMOs as effective tools for biosynthesis.
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12
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Zhang J, Chen J, Wu YF, Wang ZP, Qiu JG, Li XL, Cai F, Xiao KQ, Sun XX, Rosen BP, Zhao FJ. Oxidation of organoarsenicals and antimonite by a novel flavin monooxygenase widely present in soil bacteria. Environ Microbiol 2022; 24:752-761. [PMID: 33769668 PMCID: PMC8862597 DOI: 10.1111/1462-2920.15488] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 02/03/2023]
Abstract
Arsenic can be biomethylated to form a variety of organic arsenicals differing in toxicity and environmental mobility. Trivalent methylarsenite (MAs(III)) produced in the methylation process is more toxic than inorganic arsenite (As(III)). MAs(III) also serves as a primitive antibiotic and, consequently, some environmental microorganisms have evolved mechanisms to detoxify MAs(III). However, the mechanisms of MAs(III) detoxification are not well understood. In this study, we identified an arsenic resistance (ars) operon consisting of three genes, arsRVK, that contribute to MAs(III) resistance in Ensifer adhaerens ST2. ArsV is annotated as an NADPH-dependent flavin monooxygenase with unknown function. Expression of arsV in the arsenic hypersensitive Escherichia coli strain AW3110Δars conferred resistance to MAs(III) and the ability to oxidize MAs(III) to MAs(V). In the presence of NADPH and either FAD or FMN, purified ArsV protein was able to oxidize both MAs(III) to MAs(V) and Sb(III) to Sb(V). Genes with arsV-like sequences are widely present in soils and environmental bacteria. Metagenomic analysis of five paddy soils showed the abundance of arsV-like sequences of 0.12-0.25 ppm. These results demonstrate that ArsV is a novel enzyme for the detoxification of MAs(III) and Sb(III) and the genes encoding ArsV are widely present in soil bacteria.
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Affiliation(s)
- Jun Zhang
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Chen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, 33199
| | - Yi-Fei Wu
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zi-Ping Wang
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ji-Guo Qiu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiao-Long Li
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Cai
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ke-Qing Xiao
- School of Earth and Environment, University of Leeds, Leeds, LS2 9JT, UK
| | - Xiao-Xu Sun
- Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Barry P. Rosen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, 33199
| | - Fang-Jie Zhao
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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13
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Dippe M, Herrmann S, Pecher P, Funke E, Pietzsch M, Wessjohann L. Engineered bacterial flavin-dependent monooxygenases for the regiospecific hydroxylation of polycyclic phenols. Chembiochem 2022; 23:e202100480. [PMID: 34979058 PMCID: PMC9303722 DOI: 10.1002/cbic.202100480] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/06/2021] [Indexed: 11/06/2022]
Abstract
4-Hydroxyphenylacetate 3-hydroxylase (4HPA3H), a flavin-dependent monooxygenase from E. coli that catalyzes the hydroxylation of monophenols to catechols, was modified by rational re-design to convert also more bulky substrates, especially phenolic natural products like phenylpropanoids, flavones or coumarins. Selected amino acid positions in the binding pocket of 4HPA3H were exchanged by residues from the homologous protein from Pseudomonas aeruginosa, yielding variants with improved conversion of spacious substrates such as the flavonoid naringenin or the alkaloid mimetic 2-hydroxycarbazole. Reactions were followed by an adapted Fe(III)-catechol chromogenic assay selective for the products. Especially substitution of the residue Y301 facilitated modulation of substrate specificity: introduction of non-aromatic but hydrophobic (iso)leucine resulted in the preference of the substrate ferulic acid (having a guaiacyl (guajacyl) moiety, part of the vanilloid motif) over unsubstituted monophenols. The in vivo (whole-cell biocatalysts) and in vitro (three-enzyme cascade) transformations of substrates by 4HPA3H and its optimized variants was strictly regiospecific and proceeded without generation of by-products.
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Affiliation(s)
- Martin Dippe
- Leibniz-Institut für Pflanzenbiochemie: Leibniz-Institut fur Pflanzenbiochemie, Bioorganic Chemistry, Weinberg 3, D-06120, Halle/Saale, GERMANY
| | - Susann Herrmann
- Leibniz-Institut für Pflanzenbiochemie: Leibniz-Institut fur Pflanzenbiochemie, Bioorganic Chemistry, Weinberg 3, D-06120, Halle, GERMANY
| | - Pascal Pecher
- Leibniz Institute of Plant Biochemistry: Leibniz-Institut fur Pflanzenbiochemie, Bioorganic Chemistry, GERMANY
| | - Evelyn Funke
- Leibniz-Institut fur Pflanzenbiochemie, Bioorganic Chemistry, GERMANY
| | - Markus Pietzsch
- Martin-Luther-Universität Halle-Wittenberg: Martin-Luther-Universitat Halle-Wittenberg, Institute of Pharmacy, Weinbergweg 22, D-06120, Halle, GERMANY
| | - Ludger Wessjohann
- Leibniz-Institute of Plant Biochemistry, Bioorganic Chemistry, Weinberg 3, 06120, Halle Saale, GERMANY
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14
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The Isoenzymic Diketocamphane Monooxygenases of Pseudomonas putida ATCC 17453-An Episodic History and Still Mysterious after 60 Years. Microorganisms 2021; 9:microorganisms9122593. [PMID: 34946195 PMCID: PMC8706424 DOI: 10.3390/microorganisms9122593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 11/17/2022] Open
Abstract
Researching the involvement of molecular oxygen in the degradation of the naturally occurring bicyclic terpene camphor has generated a six-decade history of fascinating monooxygenase biochemistry. While an extensive bibliography exists reporting the many varied studies on camphor 5-monooxygenase, the initiating enzyme of the relevant catabolic pathway in Pseudomonas putida ATCC 17453, the equivalent recorded history of the isoenzymic diketocamphane monooxygenases, the enzymes that facilitate the initial ring cleavage of the bicyclic terpene, is both less extensive and more enigmatic. First referred to as ‘ketolactonase—an enzyme for cyclic lactonization’—the enzyme now classified as 2,5-diketocamphane 1,2-monooxygenase (EC 1.14.14.108) holds a special place in the history of oxygen-dependent biochemistry, being the first biocatalyst confirmed to undertake a biooxygenation reaction equivalent to the peracid-catalysed Baeyer–Villiger chemical oxidation first reported in the late 19th century. However, following that auspicious beginning, the biochemistry of EC 1.14.14.108, and its isoenzymic partner 3,6-diketocamphane 1,6-monooxygenase (EC 1.14.14.155) was dogged for many years by the mistaken belief that the enzymes were true flavoproteins that function with a tightly-bound flavin cofactor in the active site. This misconception led to a number of erroneous interpretations of relevant experimental data. It is only in the last decade, initially as the result of pure serendipity, that these enzymes have been confirmed to be members of a relatively recently discovered class of oxygen-dependent enzymes, the flavin-dependent two-component monooxygenases. This has promoted a renaissance of interest in the enzymes, resulting in programmes of research that have significantly expanded current knowledge of both their mode of action and regulation in camphor-grown P. putida ATCC 17453. However, some features of the biochemistry of the isoenzymic diketocamphane monooxygenases remain currently unexplained. It is the episodic history of these enzymes and some of what remains unresolved that are the principal subjects of this review.
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15
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Martínez-Montero L, Tischler D, Süss P, Schallmey A, Franssen MCR, Hollmann F, Paul CE. Asymmetric azidohydroxylation of styrene derivatives mediated by a biomimetic styrene monooxygenase enzymatic cascade. Catal Sci Technol 2021; 11:5077-5085. [PMID: 34381590 PMCID: PMC8328376 DOI: 10.1039/d1cy00855b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/13/2021] [Indexed: 12/18/2022]
Abstract
Enantioenriched azido alcohols are precursors for valuable chiral aziridines and 1,2-amino alcohols, however their chiral substituted analogues are difficult to access. We established a cascade for the asymmetric azidohydroxylation of styrene derivatives leading to chiral substituted 1,2-azido alcohols via enzymatic asymmetric epoxidation, followed by regioselective azidolysis, affording the azido alcohols with up to two contiguous stereogenic centers. A newly isolated two-component flavoprotein styrene monooxygenase StyA proved to be highly selective for epoxidation with a nicotinamide coenzyme biomimetic as a practical reductant. Coupled with azide as a nucleophile for regioselective ring opening, this chemo-enzymatic cascade produced highly enantioenriched aromatic α-azido alcohols with up to >99% conversion. A bi-enzymatic counterpart with halohydrin dehalogenase-catalyzed azidolysis afforded the alternative β-azido alcohol isomers with up to 94% diastereomeric excess. We anticipate our biocatalytic cascade to be a starting point for more practical production of these chiral compounds with two-component flavoprotein monooxygenases.
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Affiliation(s)
- Lía Martínez-Montero
- Department of Biotechnology, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Ruhr-Universität Bochum Universitätsstr. 150 44780 Bochum Germany
| | - Philipp Süss
- Enzymicals AG Walther-Rathenau-Straße 49a 17489 Greifswald Germany
| | - Anett Schallmey
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig Spielmannstraße 7 38106 Braunschweig Germany
| | - Maurice C R Franssen
- Laboratory of Organic Chemistry, Wageningen University Stippeneng 4 6708 WE Wageningen The Netherlands
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Caroline E Paul
- Department of Biotechnology, Delft University of Technology Van der Maasweg 9 2629 HZ Delft The Netherlands
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16
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De Silva AJ, Sehgal R, Kim J, Bellizzi JJ. Steady-state kinetic analysis of halogenase-supporting flavin reductases BorF and AbeF reveals different kinetic mechanisms. Arch Biochem Biophys 2021; 704:108874. [PMID: 33862020 DOI: 10.1016/j.abb.2021.108874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/03/2021] [Accepted: 04/05/2021] [Indexed: 11/28/2022]
Abstract
The short-chain flavin reductases BorF and AbeF reduce FAD to FADH2, which is then used by flavin-dependent halogenases (BorH and AbeH respectively) to regioselectively chlorinate tryptophan in the biosynthesis of indolotryptoline natural products. Recombinant AbeF and BorF were overexpressed and purified as homodimers from E. coli, and copurified with substoichiometric amounts of FAD, which could be easily removed. AbeF and BorF can reduce FAD, FMN, and riboflavin in vitro and are selective for NADH over NADPH. Initial velocity studies in the presence and absence of inhibitors showed that BorF proceeds by a sequential ordered kinetic mechanism in which FAD binds first, while AbeF follows a random-ordered sequence of substrate binding. Fluorescence quenching experiments verified that NADH does not bind BorF in the absence of FAD, and that both AbeF and BorF bind FAD with higher affinity than FADH2. pH-rate profiles of BorF and AbeF were bell-shaped with maximum kcat at pH 7.5, and site-directed mutagenesis of BorF implicated His160 and Arg38 as contributing to the catalytic activity and the pH dependence.
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Affiliation(s)
- Aravinda J De Silva
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA
| | - Rippa Sehgal
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA
| | - Jennifer Kim
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA
| | - John J Bellizzi
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA.
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17
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Paul CE, Eggerichs D, Westphal AH, Tischler D, van Berkel WJH. Flavoprotein monooxygenases: Versatile biocatalysts. Biotechnol Adv 2021; 51:107712. [PMID: 33588053 DOI: 10.1016/j.biotechadv.2021.107712] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022]
Abstract
Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.
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Affiliation(s)
- Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniel Eggerichs
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
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18
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Röllig R, Paul CE, Claeys-Bruno M, Duquesne K, Kara S, Alphand V. Divorce in the two-component BVMO family: the single oxygenase for enantioselective chemo-enzymatic Baeyer-Villiger oxidations. Org Biomol Chem 2021; 19:3441-3450. [PMID: 33899864 DOI: 10.1039/d1ob00015b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Two-component flavoprotein monooxygenases consist of a reductase and an oxygenase enzyme. The proof of functionality of the latter without its counterpart as well as the mechanism of flavin transfer remains unanswered beyond doubt. To tackle this question, we utilized a reductase-free reaction system applying purified 2,5-diketocamphane-monooxygenase I (2,5-DKCMO), a FMN-dependent type II Baeyer-Villiger monooxygenase, and synthetic nicotinamide analogues (NCBs) as dihydropyridine derivatives for FMN reduction. This system demonstrated the stand-alone quality of the oxygenase, as well as the mechanism of FMNH2 transport by free diffusion. The efficiency of this reductase-free system strongly relies on the balance of FMN reduction and enzymatic (re)oxidation, since reduced FMN in solution causes undesired side reactions, such as hydrogen peroxide formation. Design of experiments allowed us to (i) investigate the effect of various reaction parameters, underlining the importance to balance the FMN/FMNH2 cycle, (ii) optimize the reaction system for the enzymatic Baeyer-Villiger oxidation of rac-bicyclo[3.2.0]hept-2-en-6-one, rac-camphor, and rac-norcamphor. Finally, this study not only demonstrates the reductase-independence of 2,5-DKCMO, but also revisits the terminology of two-component flavoprotein monooxygenases for this specific case.
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Affiliation(s)
- Robert Röllig
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2 UMR 7313, Marseille, France. and Aarhus University, Denmark
| | | | | | - Katia Duquesne
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2 UMR 7313, Marseille, France.
| | | | - Véronique Alphand
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2 UMR 7313, Marseille, France.
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19
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Li H, Forson B, Eckshtain-Levi M, Valentino H, Martín Del Campo JS, Tanner JJ, Sobrado P. Biochemical Characterization of the Two-Component Flavin-Dependent Monooxygenase Involved in Valanimycin Biosynthesis. Biochemistry 2020; 60:31-40. [PMID: 33350810 DOI: 10.1021/acs.biochem.0c00679] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The flavin reductase (FRED) and isobutylamine N-hydroxylase (IBAH) from Streptomyces viridifaciens constitute a two-component, flavin-dependent monooxygenase system that catalyzes the first step in valanimycin biosynthesis. FRED is an oxidoreductase that provides the reduced flavin to IBAH, which then catalyzes the hydroxylation of isobutylamine (IBA) to isobutylhydroxylamine (IBHA). In this work, we used several complementary methods to investigate FAD binding, steady-state and rapid reaction kinetics, and enzyme-enzyme interactions in the FRED:IBAH system. The affinity of FRED for FADox is higher than its affinity for FADred, consistent with its function as a flavin reductase. Conversely, IBAH binds FADred more tightly than FADox, consistent with its role as a monooxygenase. FRED exhibits a strong preference (28-fold) for NADPH over NADH as the electron source for FAD reduction. Isothermal titration calorimetry was used to study the association of FRED and IBAH. In the presence of FAD, either oxidized or reduced, FRED and IBAH associate with a dissociation constant of 7-8 μM. No interaction was observed in the absence of FAD. These results are consistent with the formation of a protein-protein complex for direct transfer of reduced flavin from the reductase to the monooxygenase in this two-component system.
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Affiliation(s)
- Hao Li
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Benedicta Forson
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Meital Eckshtain-Levi
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Hannah Valentino
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | | | - John J Tanner
- Departments of Biochemistry and Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.,Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
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20
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Abstract
Many flavin-dependent phenolic hydroxylases (monooxygenases) have been extensively investigated. Their crystal structures and reaction mechanisms are well understood. These enzymes belong to groups A and D of the flavin-dependent monooxygenases and can be classified as single-component and two-component flavin-dependent monooxygenases. The insertion of molecular oxygen into the substrates catalyzed by these enzymes is beneficial for modifying the biological properties of phenolic compounds and their derivatives. This chapter provides an in-depth discussion of the structural features of single-component and two-component flavin-dependent phenolic hydroxylases. The reaction mechanisms of selected enzymes, including 3-hydroxy-benzoate 4-hydroxylase (PHBH) and 3-hydroxy-benzoate 6-hydroxylase as representatives of single-component enzymes and 3-hydroxyphenylacetate 4-hydroxylase (HPAH) as a representative of two-component enzymes, are discussed in detail. This chapter comprises the following four main parts: general reaction, structures, reaction mechanisms, and enzyme engineering for biocatalytic applications. Enzymes belonging to the same group catalyze similar reactions but have different unique structural features to control their reactivity to substrates and the formation and stabilization of C4a-hydroperoxyflavin. Protein engineering has been employed to improve the ability to use these enzymes to synthesize valuable compounds. A thorough understanding of the structural and mechanistic features controlling enzyme reactivity is useful for enzyme redesign and enzyme engineering for future biocatalytic applications.
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Affiliation(s)
- Pirom Chenprakhon
- Institute for Innovative Learning, Mahidol University, Nakhon Pathom, Thailand.
| | - Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand; Department of Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Nakhon Pathom, Thailand
| | - Chanakan Tongsook
- Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
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21
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Abstract
Flavin-dependent enzymes catalyze a wide variety of biological reactions that are important for all types of living organisms. Knowledge gained from studying the chemistry and biological functions of flavins and flavin-dependent enzymes has continuously made significant contributions to the development of the fields of enzymology and metabolism from the 1970s until now. The enzymes have been applied in various applications such as use as biocatalysts in synthetic processes for the chemical and pharmaceutical industries or in the biodetoxification and bioremediation of toxic or unwanted compounds, and as biosensors or biodetection tools for quantifying various agents of interest. Many flavin-dependent enzymes are also prime targets for drug development. Based on their reaction mechanisms, they can be classified into five categories: oxidase, dehydrogenase, monooxygenase, reductase, and redox neutral flavin-dependent enzymes. In this chapter, the general properties of flavin-dependent enzymes and the nature of their chemical reactions are discussed, along with their practical applications.
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22
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Abstract
Bacterial luciferase is a flavin-dependent monooxygenase which is remarkable for its distinctive feature in transforming chemical energy to photons of visible light. The bacterial luciferase catalyzes bioluminescent reaction using reduced flavin mononucleotide, long-chain aldehyde and oxygen to yield oxidized flavin, corresponding acid, water and light at λmax around 490nm. The enzyme comprises of two non-identical α and β subunits, where α subunit is a catalytic center and β subunit is crucially required for maintaining catalytic function of the α subunit. The crystal structure with FMN bound and mutagenesis studies have assigned a number of amino acid residues that are important in coordinating critical reactions and stabilizing intermediates to attain optimum reaction efficiency. The enzyme achieves monooxygenation by generating C4a-hydroperoxyflavin intermediate that later changes its protonation status to become C4a-peroxyflavin, which is necessary for the nucleophilic attacking with aldehyde substrate. The decomposing of C4a-peroxyhemiacetal produces excited C4a-hydroxyflavin and acid product. The chemical basis regrading bioluminophore generation in Lux reaction remains an inconclusive issue. However, current data can, at least, demonstrate the involvement of electron transfer to create radical molecules which is the key step in this mechanism. Lux is a self-sufficient bioluminescent system in which all substrates can be recycled and produced by a group of enzymes from the lux operon. This makes Lux distinctively advantageous over other luciferases for reporter enzyme application. The progression of understanding of Lux catalysis is beneficial to improve light emitting efficiency in order to expand the robustness of Lux application.
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23
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Fang L, Qin H, Shi T, Wu X, Li QX, Hua R. Ortho and para oxydehalogenation of dihalophenols catalyzed by the monooxygenase TcpA and NAD(P)H:FAD reductase Fre. JOURNAL OF HAZARDOUS MATERIALS 2020; 388:121787. [PMID: 31818658 DOI: 10.1016/j.jhazmat.2019.121787] [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: 10/16/2019] [Revised: 11/19/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
Dihalophenols such as dichlorophenols (DCPs) are important industrial chemical intermediates, but also persistent pollutants in the environment. Oxidative dehalogenation by microbes is an efficient biological method to degrade halophenols, but the mechanism is unclear yet. Cupriavidus nantongensis X1T was a type strain of genus Cupriavidus, and could degrade 2,4-dichlorophenol of 50 mg/L within 12 h. The degradation rate constant was approximately 84 fold greater than that by Bacillus endophyticus CP1R43, a well-studied 2,4-DCP-degrading bacterial strain. The genes encoding 2,4,6-trichlorophenol monooxygenase (TcpA) and NAD(P)H:FAD reductase (Fre) from strain X1T were cloned and expressed. The expressed TcpA Fre were purified. The molecular docking of TcpA with DCPs and point mutation experiments showed that the degradation activity of TcpA was associated with the length of the hydrogen bond between the substrates and the amino acids in the active pocket. DCPs were degraded via a stepwise oxidative dechlorination in a positive relationship between the oxidation ability and the electron-withdrawing potential of the p-position group. In addition, TcpA has dual dehalogenation and denitration functions. The results demonstrate that either strain X1T or TcpA and Fre can effectively dehalogenate dihalophenols, which can be useful for the treatment of dihalophenols in wastewaters and remediation of DCP-contaminated environments.
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Affiliation(s)
- Liancheng Fang
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Han Qin
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Taozhong Shi
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xiangwei Wu
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, HI 96822, United States.
| | - Rimao Hua
- Key Laboratory for Agri-Food Safety, School of Resource & Environment, Anhui Agricultural University, Hefei, Anhui 230036, China.
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24
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Phonbuppha J, Tinikul R, Wongnate T, Intasian P, Hollmann F, Paul CE, Chaiyen P. A Minimized Chemoenzymatic Cascade for Bacterial Luciferase in Bioreporter Applications. Chembiochem 2020; 21:2073-2079. [PMID: 32187433 DOI: 10.1002/cbic.202000100] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Indexed: 12/17/2022]
Abstract
Bacterial luciferase (Lux) catalyzes a bioluminescence reaction by using long-chain aldehyde, reduced flavin and molecular oxygen as substrates. The reaction can be applied in reporter gene systems for biomolecular detection in both prokaryotic and eukaryotic organisms. Because reduced flavin is unstable under aerobic conditions, another enzyme, flavin reductase, is needed to supply reduced flavin to the Lux-catalyzed reaction. To create a minimized cascade for Lux that would have greater ease of use, a chemoenzymatic reaction with a biomimetic nicotinamide (BNAH) was used in place of the flavin reductase reaction in the Lux system. The results showed that the minimized cascade reaction can be applied to monitor bioluminescence of the Lux reporter in eukaryotic cells effectively, and that it can achieve higher efficiencies than the system with flavin reductase. This development is useful for future applications as high-throughput detection tools for drug screening applications.
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Affiliation(s)
- Jittima Phonbuppha
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1, Payupnai, Wangchan, Rayong, 21210, Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1, Payupnai, Wangchan, Rayong, 21210, Thailand
| | - Pattarawan Intasian
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1, Payupnai, Wangchan, Rayong, 21210, Thailand
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft (The, Netherlands
| | - Caroline E Paul
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft (The, Netherlands
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1, Payupnai, Wangchan, Rayong, 21210, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
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25
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Maenpuen S, Pongsupasa V, Pensook W, Anuwan P, Kraivisitkul N, Pinthong C, Phonbuppha J, Luanloet T, Wijma HJ, Fraaije MW, Lawan N, Chaiyen P, Wongnate T. Creating Flavin Reductase Variants with Thermostable and Solvent-Tolerant Properties by Rational-Design Engineering. Chembiochem 2020; 21:1481-1491. [PMID: 31886941 DOI: 10.1002/cbic.201900737] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Indexed: 02/06/2023]
Abstract
We have employed computational approaches-FireProt and FRESCO-to predict thermostable variants of the reductase component (C1 ) of (4-hydroxyphenyl)acetate 3-hydroxylase. With the additional aid of experimental results, two C1 variants, A166L and A58P, were identified as thermotolerant enzymes, with thermostability improvements of 2.6-5.6 °C and increased catalytic efficiency of 2- to 3.5-fold. After heat treatment at 45 °C, both of the thermostable C1 variants remain active and generate reduced flavin mononucleotide (FMNH- ) for reactions catalyzed by bacterial luciferase and by the monooxygenase C2 more efficiently than the wild type (WT). In addition to thermotolerance, the A166L and A58P variants also exhibited solvent tolerance. Molecular dynamics (MD) simulations (6 ns) at 300-500 K indicated that mutation of A166 to L and of A58 to P resulted in structural changes with increased stabilization of hydrophobic interactions, and thus in improved thermostability. Our findings demonstrated that improvements in the thermostability of C1 enzyme can lead to broad-spectrum uses of C1 as a redox biocatalyst for future industrial applications.
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Affiliation(s)
- Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, 169 Long-Hard Bangsaen Road, Chonburi, 20131, Thailand
| | - Vinutsada Pongsupasa
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand
| | - Wiranee Pensook
- Department of Biochemistry, Faculty of Science, Burapha University, 169 Long-Hard Bangsaen Road, Chonburi, 20131, Thailand
| | - Piyanuch Anuwan
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand
| | | | - Chatchadaporn Pinthong
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, 114 Sukhumvit 23 Road, Bangkok, 10110, Thailand
| | - Jittima Phonbuppha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand
| | - Thikumporn Luanloet
- Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Hein J Wijma
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Narin Lawan
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huaykaew Road, Suthep, Chiang Mai, 50200, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand.,Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), 555 Moo 1 Payupnai, Wangchan, Rayong, 21210, Thailand
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Pitsawong W, Chenprakhon P, Dhammaraj T, Medhanavyn D, Sucharitakul J, Tongsook C, van Berkel WJH, Chaiyen P, Miller AF. Tuning of p Ka values activates substrates in flavin-dependent aromatic hydroxylases. J Biol Chem 2020; 295:3965-3981. [PMID: 32014994 DOI: 10.1074/jbc.ra119.011884] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/29/2020] [Indexed: 12/31/2022] Open
Abstract
Hydroxylation of substituted phenols by flavin-dependent monooxygenases is the first step of their biotransformation in various microorganisms. The reaction is thought to proceed via electrophilic aromatic substitution, catalyzed by enzymatic deprotonation of substrate, in single-component hydroxylases that use flavin as a cofactor (group A). However, two-component hydroxylases (group D), which use reduced flavin as a co-substrate, are less amenable to spectroscopic investigation. Herein, we employed 19F NMR in conjunction with fluorinated substrate analogs to directly measure pKa values and to monitor protein events in hydroxylase active sites. We found that the single-component monooxygenase 3-hydroxybenzoate 6-hydroxylase (3HB6H) depresses the pKa of the bound substrate analog 4-fluoro-3-hydroxybenzoate (4F3HB) by 1.6 pH units, consistent with previously proposed mechanisms. 19F NMR was applied anaerobically to the two-component monooxygenase 4-hydroxyphenylacetate 3-hydroxylase (HPAH), revealing depression of the pKa of 3-fluoro-4-hydroxyphenylacetate by 2.5 pH units upon binding to the C2 component of HPAH. 19F NMR also revealed a pKa of 8.7 ± 0.05 that we attributed to an active-site residue involved in deprotonating bound substrate, and assigned to His-120 based on studies of protein variants. Thus, in both types of hydroxylases, we confirmed that binding favors the phenolate form of substrate. The 9 and 14 kJ/mol magnitudes of the effects for 3HB6H and HPAH-C2, respectively, are consistent with pKa tuning by one or more H-bonding interactions. Our implementation of 19F NMR in anaerobic samples is applicable to other two-component flavin-dependent hydroxylases and promises to expand our understanding of their catalytic mechanisms.
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Affiliation(s)
- Warintra Pitsawong
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055
| | - Pirom Chenprakhon
- Institute for Innovative Learning, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Taweesak Dhammaraj
- Faculty of Pharmacy, Mahasarakham University, Maha Sarakham 44150, Thailand
| | - Dheeradhach Medhanavyn
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok 10300, Thailand
| | - Chanakan Tongsook
- Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom 73000, Thailand
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wangchan Valley, 555 Moo 1 Payupnai, Wangchan, Rayong 21210, Thailand
| | - Anne-Frances Miller
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055
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Chenprakhon P, Wongnate T, Chaiyen P. Monooxygenation of aromatic compounds by flavin-dependent monooxygenases. Protein Sci 2020; 28:8-29. [PMID: 30311986 DOI: 10.1002/pro.3525] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/08/2018] [Accepted: 10/08/2018] [Indexed: 12/12/2022]
Abstract
Many flavoenzymes catalyze hydroxylation of aromatic compounds especially phenolic compounds have been isolated and characterized. These enzymes can be classified as either single-component or two-component flavin-dependent hydroxylases (monooxygenases). The hydroxylation reactions catalyzed by the enzymes in this group are useful for modifying the biological properties of phenolic compounds. This review aims to provide an in-depth discussion of the current mechanistic understanding of representative flavin-dependent monooxygenases including 3-hydroxy-benzoate 4-hydroxylase (PHBH, a single-component hydroxylase), 3-hydroxyphenylacetate 4-hydroxylase (HPAH, a two-component hydroxylase), and other monooxygenases which catalyze reactions in addition to hydroxylation, including 2-methyl-3-hydroxypyridine-5-carboxylate oxygenase (MHPCO, a single-component enzyme that catalyzes aromatic-ring cleavage), and HadA monooxygenase (a two-component enzyme that catalyzes additional group elimination reaction). These enzymes have different unique structural features which dictate their reactivity toward various substrates and influence their ability to stabilize flavin intermediates such as C4a-hydroperoxyflavin. Understanding the key catalytic residues and the active site environments important for governing enzyme reactivity will undoubtedly facilitate future work in enzyme engineering or enzyme redesign for the development of biocatalytic methods for the synthesis of valuable compounds.
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Affiliation(s)
- Pirom Chenprakhon
- Institute for Innovative Learning, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 14000, Thailand
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28
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Pimviriyakul P, Wongnate T, Tinikul R, Chaiyen P. Microbial degradation of halogenated aromatics: molecular mechanisms and enzymatic reactions. Microb Biotechnol 2020; 13:67-86. [PMID: 31565852 PMCID: PMC6922536 DOI: 10.1111/1751-7915.13488] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/01/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022] Open
Abstract
Halogenated aromatics are used widely in various industrial, agricultural and household applications. However, due to their stability, most of these compounds persist for a long time, leading to accumulation in the environment. Biological degradation of halogenated aromatics provides sustainable, low-cost and environmentally friendly technologies for removing these toxicants from the environment. This minireview discusses the molecular mechanisms of the enzymatic reactions for degrading halogenated aromatics which naturally occur in various microorganisms. In general, the biodegradation process (especially for aerobic degradation) can be divided into three main steps: upper, middle and lower metabolic pathways which successively convert the toxic halogenated aromatics to common metabolites in cells. The most difficult step in the degradation of halogenated aromatics is the dehalogenation step in the middle pathway. Although a variety of enzymes are involved in the degradation of halogenated aromatics, these various pathways all share the common feature of eventually generating metabolites for utilizing in the energy-producing metabolic pathways in cells. An in-depth understanding of how microbes employ various enzymes in biodegradation can lead to the development of new biotechnologies via enzyme/cell/metabolic engineering or synthetic biology for sustainable biodegradation processes.
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Affiliation(s)
- Panu Pimviriyakul
- Department of BiotechnologyFaculty of Engineering and Industrial TechnologySilpakorn UniversityNakhon Pathom73000Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC)Wangchan ValleyRayong21210Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme TechnologyFaculty of ScienceMahidol UniversityBangkok10400Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC)Wangchan ValleyRayong21210Thailand
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29
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30
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Lingkon K, Bellizzi JJ. Structure and Activity of the Thermophilic Tryptophan-6 Halogenase BorH. Chembiochem 2019; 21:1121-1128. [PMID: 31692209 DOI: 10.1002/cbic.201900667] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Indexed: 12/19/2022]
Abstract
Flavin-dependent halogenases carry out regioselective aryl halide synthesis in aqueous solution at ambient temperature and neutral pH using benign halide salts, making them attractive catalysts for green chemistry. BorH and BorF, two proteins encoded by the biosynthetic gene cluster for the chlorinated bisindole alkaloid borregomycin A, are the halogenase and flavin reductase subunits of a tryptophan-6-halogenase. Quantitative conversion of l-tryptophan (Trp) to 6-chlorotryptophan could be achieved using 1.2 mol % BorH and 2 mol % BorF. The optimal reaction temperature for Trp chlorination is 45 °C, and the melting temperatures of BorH and BorF are 48 and 50 °C respectively, which are higher than the thermal parameters for most other halogenases previously studied. Steady-state kinetic analysis of Trp chlorination by BorH determined parameters of kcat =4.42 min-1 , and KM of 9.78 μm at 45 °C. BorH exhibits a broad substrate scope, chlorinating and brominating a variety of aromatic substrates with and without indole groups. Chlorination of Trp at a 100 mg scale with 52 % crude yield, using 0.2 mol % BorH indicates that industrial scale biotransformations using BorH/BorF are feasible. The X-ray crystal structure of BorH with bound Trp provides additional evidence for the model that regioselectivity is determined by substrate positioning in the active site, showing C6 of Trp juxtaposed with the catalytic Lys79 in the same binding pose previously observed in the structure of Thal.
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Affiliation(s)
- Kazi Lingkon
- Department of Chemistry and Biochemistry, The University of Toledo, 2801 W. Bancroft St. MS 602, Toledo, OH, 43606, USA
| | - John J Bellizzi
- Department of Chemistry and Biochemistry, The University of Toledo, 2801 W. Bancroft St. MS 602, Toledo, OH, 43606, USA
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31
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Moritzer A, Niemann HH. Binding of FAD and tryptophan to the tryptophan 6-halogenase Thal is negatively coupled. Protein Sci 2019; 28:2112-2118. [PMID: 31589794 PMCID: PMC6863734 DOI: 10.1002/pro.3739] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 11/08/2022]
Abstract
Flavin-dependent halogenases require reduced flavin adenine dinucleotide (FADH2 ), O2 , and halide salts to halogenate their substrates. We describe the crystal structures of the tryptophan 6-halogenase Thal in complex with FAD or with both tryptophan and FAD. If tryptophan and FAD were soaked simultaneously, both ligands showed impaired binding and in some cases only the adenosine monophosphate or the adenosine moiety of FAD was resolved, suggesting that tryptophan binding increases the mobility mainly of the flavin mononucleotide moiety. This confirms a negative cooperativity between the binding of substrate and cofactor that was previously described for other tryptophan halogenases. Binding of substrate to tryptophan halogenases reduces the affinity for the oxidized cofactor FAD presumably to facilitate the regeneration of FADH2 by flavin reductases.
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Pongpamorn P, Watthaisong P, Pimviriyakul P, Jaruwat A, Lawan N, Chitnumsub P, Chaiyen P. Identification of a Hotspot Residue for Improving the Thermostability of a Flavin‐Dependent Monooxygenase. Chembiochem 2019; 20:3020-3031. [DOI: 10.1002/cbic.201900413] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Pornkanok Pongpamorn
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Pratchaya Watthaisong
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Panu Pimviriyakul
- Department of BiotechnologyFaculty of Engineering and Industrial TechnologySilpakorn University 6 Rajamankha Nai Road Nakornpathom 73000 Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park Paholyothin Road Klong 1 Klong Luang Pathumthani 12120 Thailand
| | - Narin Lawan
- Department of ChemistryFaculty of ScienceChiang Mai University Chiang Mai 50200 Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park Paholyothin Road Klong 1 Klong Luang Pathumthani 12120 Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
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Watthaisong P, Pongpamorn P, Pimviriyakul P, Maenpuen S, Ohmiya Y, Chaiyen P. A Chemo‐Enzymatic Cascade for the Smart Detection of Nitro‐ and Halogenated Phenols. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Pratchaya Watthaisong
- School of Biomolecular Science & Engineering (BSE)Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Pornkanok Pongpamorn
- School of Biomolecular Science & Engineering (BSE)Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Panu Pimviriyakul
- School of Biomolecular Science & Engineering (BSE)Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Somchart Maenpuen
- Department of BiochemistryFaculty of ScienceBurapha University Chonburi 20131 Thailand
| | - Yoshihiro Ohmiya
- National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Ibaraki 305-8566 Japan
| | - Pimchai Chaiyen
- School of Biomolecular Science & Engineering (BSE)Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
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34
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Watthaisong P, Pongpamorn P, Pimviriyakul P, Maenpuen S, Ohmiya Y, Chaiyen P. A Chemo‐Enzymatic Cascade for the Smart Detection of Nitro‐ and Halogenated Phenols. Angew Chem Int Ed Engl 2019; 58:13254-13258. [DOI: 10.1002/anie.201904923] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 06/15/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Pratchaya Watthaisong
- School of Biomolecular Science & Engineering (BSE)Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Pornkanok Pongpamorn
- School of Biomolecular Science & Engineering (BSE)Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Panu Pimviriyakul
- School of Biomolecular Science & Engineering (BSE)Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Somchart Maenpuen
- Department of BiochemistryFaculty of ScienceBurapha University Chonburi 20131 Thailand
| | - Yoshihiro Ohmiya
- National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Ibaraki 305-8566 Japan
| | - Pimchai Chaiyen
- School of Biomolecular Science & Engineering (BSE)Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
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35
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Simulation-based protein engineering of R. erythropolis FMN oxidoreductase (DszD). Heliyon 2019; 5:e02193. [PMID: 31428711 PMCID: PMC6695286 DOI: 10.1016/j.heliyon.2019.e02193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/28/2019] [Accepted: 07/29/2019] [Indexed: 11/23/2022] Open
Abstract
The sulfur contents of fossil fuels have negative impacts on the environment and human health. The bio-catalytic desulfurization strategies and the biological refinement of fossil fuels are a cost-effective process compared to classical chemistry desulfurization. Rhodococcus erythropolis IGTS8 is able to metabolize the organic sulfur compound by the unique genes cluster (i.e. DszA, B, C and D genes) in the 4S metabolic pathway. The dszD gene codes a key enzyme for sulfur reduction in the gene cluster. In this study, the structure of the DszD enzyme was predicted and then the key residues toward FMN binding were identified which were Thr62, Ser63, Asn77, and Ala79. To investigate the effect of manipulation in key residues on the enzymatic activity of the DszD, different mutations were performed on key residues. The molecular docking simulation showed that A79I and A79N mutants have the lowest binding free energies compared to the wild-type enzyme in binding with FMN substrate. A 50 ns molecular dynamics (MD) simulation performed using GROMACS software. The RMSD and RMSF analysis showed that two mutants are more stable than the wild-type enzyme during MD simulation. The binding free energies between FMN substrate and complexes were calculated and analyzed by the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) method. The experimental results showed that the enzyme activity for the oxidoreductase process toward biodesulfurization increased 1.9 and 2.3 fold for A79I and A79N mutants, respectively.
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Sedláček V, Kučera I. Functional and mechanistic characterization of an atypical flavin reductase encoded by the pden_5119 gene in Paracoccus denitrificans. Mol Microbiol 2019; 112:166-183. [PMID: 30977245 DOI: 10.1111/mmi.14260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2019] [Indexed: 01/25/2023]
Abstract
Pden_5119, annotated as an NADPH-dependent FMN reductase, shows homology to proteins assisting in utilization of alkanesulfonates in other bacteria. Here, we report that inactivation of the pden_5119 gene increased susceptibility to oxidative stress, decreased growth rate and increased growth yield; growth on lower alkanesulfonates as sulfur sources was not specifically influenced. Pden_5119 transcript rose in response to oxidative stressors, respiratory chain inhibitors and terminal oxidase downregulation. Kinetic analysis of a fusion protein suggested a sequential mechanism in which FMN binds first, followed by NADH. The affinity of flavin toward the protein decreased only slightly upon reduction. The observed strong viscosity dependence of kcat demonstrated that reduced FMN formed tends to remain bound to the enzyme where it can be re-oxidized by oxygen or, less efficiently, by various artificial electron acceptors. Stopped flow data were consistent with the enzyme-FMN complex being a functional oxidase that conducts the reduction of oxygen by NADH. Hydrogen peroxide was identified as the main product. As shown by isotope effects, hydride transfer occurs from the pro-S C4 position of the nicotinamide ring and partially limits the overall turnover rate. Collectively, our results point to a role for the Pden_5119 protein in maintaining the cellular redox state.
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Affiliation(s)
- Vojtěch Sedláček
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Igor Kučera
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
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37
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Yun X, Zhang Q, Lv M, Deng H, Deng Z, Yu Y. In vitro reconstitution of the biosynthetic pathway of 3-hydroxypicolinic acid. Org Biomol Chem 2019; 17:454-460. [PMID: 30565646 DOI: 10.1039/c8ob02972e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
3-Hydroxypicolinic acid (3-HPA) is an important pyridine building block of bacterial secondary metabolites. Although the main biosynthetic pathways of these metabolites have been identified and well characterized, the enzymatic mechanism underlying the biosynthesis of 3-HPA has yet to be elucidated. In this work, we successfully reconstituted the complete biosynthetic pathway of 3-HPA in vitro. We showed that an l-lysine 2-aminotransferase, a two-component monooxygenase, and a FAD-dependent dehydrogenase are required to convert l-lysine to 3-HPA. We further demonstrated that 3-HPA does not derive from the direct hydroxylation of the picolinic acid at C-3, but from a successive process of C-3 hydroxylation of the piperideine-2-carboxylic acid and tautomerization of the produced 3-hydroxyl dihydropicolinic acid. Therefore, this study unveils the unusual assembly logic of 3-HPA and sheds light on the potential of engineering the 3-HPA pathway for generating novel pyridine-based building blocks.
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Affiliation(s)
- Xuan Yun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, P. R. China.
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Willetts A. Characterised Flavin-Dependent Two-Component Monooxygenases from the CAM Plasmid of Pseudomonas putida ATCC 17453 (NCIMB 10007): ketolactonases by Another Name. Microorganisms 2018; 7:E1. [PMID: 30577535 PMCID: PMC6352141 DOI: 10.3390/microorganisms7010001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/15/2018] [Accepted: 12/16/2018] [Indexed: 11/17/2022] Open
Abstract
The CAM plasmid-coded isoenzymic diketocamphane monooxygenases induced in Pseudomonas putida ATCC 17453 (NCIMB 10007) by growth of the bacterium on the bicyclic monoterpene (rac)-camphor are notable both for their interesting history, and their strategic importance in chemoenzymatic syntheses. Originally named 'ketolactonase-an enzyme system for cyclic lactonization' because of its characterised mode of action, (+)-camphor-induced 2,5-diketocamphane 1,2-monooxygenase was the first example of a Baeyer-Villiger monooxygenase activity to be confirmed in vitro. Both this enzyme and the enantiocomplementary (-)-camphor-induced 3,6-diketocamphane 1,6-monooxygenase were mistakenly classified and studied as coenzyme-containing flavoproteins for nearly 40 years before being correctly recognised and reinvestigated as FMN-dependent two-component monooxygenases. As has subsequently become evident, both the nature and number of flavin reductases able to supply the requisite reduced flavin co-substrate for the monooxygenases changes progressively throughout the different phases of camphor-dependent growth. Highly purified preparations of the enantiocomplementary monooxygenases have been exploited successfully for undertaking both nucleophilic and electrophilic biooxidations generating various enantiopure lactones and sulfoxides of value as chiral synthons and auxiliaries, respectively. In this review the chequered history, current functional understanding, and scope and value as biocatalysts of the diketocamphane monooxygenases are discussed.
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Affiliation(s)
- Andrew Willetts
- College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QG, UK.
- Curnow Consultancies, Helston TR13 9PQ, UK.
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Pimviriyakul P, Surawatanawong P, Chaiyen P. Oxidative dehalogenation and denitration by a flavin-dependent monooxygenase is controlled by substrate deprotonation. Chem Sci 2018; 9:7468-7482. [PMID: 30319747 PMCID: PMC6180312 DOI: 10.1039/c8sc01482e] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 08/08/2018] [Indexed: 12/19/2022] Open
Abstract
Enzymes that are capable of detoxifying halogenated phenols (HPs) and nitrophenols (NPs) are valuable for bioremediation and waste biorefining. HadA monooxygenase was found to perform dual functions of oxidative dehalogenation (hydroxylation plus halide elimination) and denitration (hydroxylation plus nitro elimination). Rate constants associated with individual steps of HadA reactions with phenol, halogenated phenols and nitrophenols were measured using combined transient kinetic approaches of stopped-flow absorbance/fluorescence and rapid-quench flow techniques. Density functional theory was used to calculate the thermodynamic and electronic parameters associated with hydroxylation and group elimination steps. These parameters were correlated with the rate constants of hydroxylation, group elimination, and overall product formation to identify factors controlling individual steps. The results indicated that the hydroxylation rate constant is higher when the pK a of the phenolic group is lower, i.e. it is more easily deprotonated, but not higher when the energy gap between the E LUMO of the C4a-hydroperoxy-FAD intermediate and the E HOMO of the phenolate substrate is lower. These data suggest that the substrate deprotonation has a higher energy barrier than the -OH transfer, and thus controls the hydroxylation step. For the group elimination, the process is controlled by the ability of the C-X bond to break. For the overall product formation (hydroxylation and group elimination combined), this analysis showed that the rate constant of product formation is dependent on the pK a value of the substrate, indicating that the overall reaction is controlled by substrate deprotonation. This step also likely has the highest energy barrier and thus controls the overall process of oxidative dehalogenation and denitration by HadA. This report is the first to identify a key mechanistic factor controlling the enzymatic processes of oxidative dehalogenation and denitration.
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Affiliation(s)
- Panu Pimviriyakul
- School of Biomolecular Science and Engineering , Vidyasirimedhi Institute of Science and Technology (VISTEC) , Wangchan Valley , Rayong , 21210 , Thailand .
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology , Faculty of Science , Mahidol University , Bangkok , 10400 , Thailand
| | - Panida Surawatanawong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry , Faculty of Science , Mahidol University , Bangkok , 10400 , Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering , Vidyasirimedhi Institute of Science and Technology (VISTEC) , Wangchan Valley , Rayong , 21210 , Thailand .
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Pimviriyakul P, Chaiyen P. A complete bioconversion cascade for dehalogenation and denitration by bacterial flavin-dependent enzymes. J Biol Chem 2018; 293:18525-18539. [PMID: 30282807 DOI: 10.1074/jbc.ra118.005538] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 09/29/2018] [Indexed: 12/17/2022] Open
Abstract
Halogenated phenol and nitrophenols are toxic compounds that are widely accumulated in the environment. Enzymes in the had operon from the bacterium Ralstonia pickettii DTP0602 have the potential for application as biocatalysts in the degradation of many of these toxic chemicals. HadA monooxygenase previously was identified as a two-component reduced FAD (FADH-)-utilizing monooxygenase with dual activities of dehalogenation and denitration. However, the partner enzymes of HadA, that is, the flavin reductase and quinone reductase that provide the FADH- for HadA and reduce quinone to hydroquinone, remain to be identified. In this report, we overexpressed and purified the flavin reductases, HadB and HadX, to investigate their functional and catalytic properties. Our results indicated that HadB is an FMN-dependent quinone reductase that converts the quinone products from HadA to hydroquinone compounds that are more stable and can be assimilated by downstream enzymes in the pathway. Transient kinetics indicated that HadB prefers NADH and menadione as the electron donor and acceptor, respectively. We found that HadX is an FAD-bound flavin reductase, which can generate FADH- for HadA to catalyze dehalogenation or denitration reactions. Thermodynamic and transient kinetic experiments revealed that HadX prefers to bind FAD over FADH- and that HadX can transfer FADH- from HadX to HadA via free diffusion. Moreover, HadX rapidly catalyzed NADH-mediated reduction of flavin and provided the FADH- for a monooxygenase of a different system. Combination of all three flavin-dependent enzymes, i.e. HadA/HadB/HadX, reconstituted an effective dehalogenation and denitration cascade, which may be useful for future bioremediation applications.
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Affiliation(s)
- Panu Pimviriyakul
- From the School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210 and.,the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 14000, Thailand
| | - Pimchai Chaiyen
- From the School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210 and
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41
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Szaleniec M, Wojtkiewicz AM, Bernhardt R, Borowski T, Donova M. Bacterial steroid hydroxylases: enzyme classes, their functions and comparison of their catalytic mechanisms. Appl Microbiol Biotechnol 2018; 102:8153-8171. [PMID: 30032434 PMCID: PMC6153880 DOI: 10.1007/s00253-018-9239-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 12/22/2022]
Abstract
The steroid superfamily includes a wide range of compounds that are essential for living organisms of the animal and plant kingdoms. Structural modifications of steroids highly affect their biological activity. In this review, we focus on hydroxylation of steroids by bacterial hydroxylases, which take part in steroid catabolic pathways and play an important role in steroid degradation. We compare three distinct classes of metalloenzymes responsible for aerobic or anaerobic hydroxylation of steroids, namely: cytochrome P450, Rieske-type monooxygenase 3-ketosteroid 9α-hydroxylase, and molybdenum-containing steroid C25 dehydrogenases. We analyze the available literature data on reactivity, regioselectivity, and potential application of these enzymes in organic synthesis of hydroxysteroids. Moreover, we describe mechanistic hypotheses proposed for all three classes of enzymes along with experimental and theoretical evidences, which have provided grounds for their formulation. In case of the 3-ketosteroid 9α-hydroxylase, such a mechanistic hypothesis is formulated for the first time in the literature based on studies conducted for other Rieske monooxygenases. Finally, we provide comparative analysis of similarities and differences in the reaction mechanisms utilized by bacterial steroid hydroxylases.
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Affiliation(s)
- Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Kraków, Poland.
| | - Agnieszka M Wojtkiewicz
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Kraków, Poland
| | - Rita Bernhardt
- Lehrstuhl für Biochemie, Universität des Saarlandes, Campus B2 2, 66123, Saarbrücken, Germany
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Kraków, Poland
| | - Marina Donova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Oblast, 142290, Russia
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Heine T, van Berkel WJH, Gassner G, van Pée KH, Tischler D. Two-Component FAD-Dependent Monooxygenases: Current Knowledge and Biotechnological Opportunities. BIOLOGY 2018; 7:biology7030042. [PMID: 30072664 PMCID: PMC6165268 DOI: 10.3390/biology7030042] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 12/11/2022]
Abstract
Flavoprotein monooxygenases create valuable compounds that are of high interest for the chemical, pharmaceutical, and agrochemical industries, among others. Monooxygenases that use flavin as cofactor are either single- or two-component systems. Here we summarize the current knowledge about two-component flavin adenine dinucleotide (FAD)-dependent monooxygenases and describe their biotechnological relevance. Two-component FAD-dependent monooxygenases catalyze hydroxylation, epoxidation, and halogenation reactions and are physiologically involved in amino acid metabolism, mineralization of aromatic compounds, and biosynthesis of secondary metabolites. The monooxygenase component of these enzymes is strictly dependent on reduced FAD, which is supplied by the reductase component. More and more representatives of two-component FAD-dependent monooxygenases have been discovered and characterized in recent years, which has resulted in the identification of novel physiological roles, functional properties, and a variety of biocatalytic opportunities.
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Affiliation(s)
- Thomas Heine
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - George Gassner
- Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA.
| | - Karl-Heinz van Pée
- Allgemeine Biochemie, Technische Universität Dresden, 01062 Dresden, Germany.
| | - Dirk Tischler
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
- Microbial Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44780 Bochum, Germany.
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Yuenyao A, Petchyam N, Kamonsutthipaijit N, Chaiyen P, Pakotiprapha D. Crystal structure of the flavin reductase of Acinetobacter baumannii p-hydroxyphenylacetate 3-hydroxylase (HPAH) and identification of amino acid residues underlying its regulation by aromatic ligands. Arch Biochem Biophys 2018; 653:24-38. [PMID: 29940152 DOI: 10.1016/j.abb.2018.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/07/2018] [Accepted: 06/21/2018] [Indexed: 10/28/2022]
Abstract
The first step in the degradation of p-hydroxyphenylacetic acid (HPA) is catalyzed by the two-component enzyme p-hydroxyphenylacetate 3-hydroxylase (HPAH). The two components of Acinetobacter baumannii HPAH are known as C1 and C2, respectively. C1 is a flavin reductase that uses NADH to generate reduced flavin mononucleotide (FMNH-), which is used by C2 in the hydroxylation of HPA. Interestingly, although HPA is not directly involved in the reaction catalyzed by C1, the presence of HPA dramatically increases the FMN reduction rate. Amino acid sequence analysis revealed that C1 contains two domains: an N-terminal flavin reductase domain, and a C-terminal MarR domain. Although MarR proteins typically function as transcription regulators, the MarR domain of C1 was found to play an auto-inhibitory role. Here, we report a crystal structure of C1 and small-angle X-ray scattering (SAXS) studies that revealed that C1 undergoes a substantial conformational change in the presence of HPA, concomitant with the increase in the rate of flavin reduction. Amino acid residues that are important for HPA binding and regulation of C1 activity were identified by site-directed mutagenesis. Amino acid sequence similarity analysis revealed several as yet uncharacterized flavin reductases with N- or C-terminal fusions.
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Affiliation(s)
- Anan Yuenyao
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Nopphon Petchyam
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | | | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science, Mahidol University, Bangkok, 10400, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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Drees SL, Ernst S, Belviso BD, Jagmann N, Hennecke U, Fetzner S. PqsL uses reduced flavin to produce 2-hydroxylaminobenzoylacetate, a preferred PqsBC substrate in alkyl quinolone biosynthesis in Pseudomonas aeruginosa. J Biol Chem 2018; 293:9345-9357. [PMID: 29669807 DOI: 10.1074/jbc.ra117.000789] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 04/06/2018] [Indexed: 01/05/2023] Open
Abstract
Alkyl hydroxyquinoline N-oxides (AQNOs) are antibiotic compounds produced by the opportunistic bacterial pathogen Pseudomonas aeruginosa They are products of the alkyl quinolone (AQ) biosynthetic pathway, which also generates the quorum-sensing molecules 2-heptyl-4(1H)-quinolone (HHQ) and 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS). Although the enzymatic synthesis of HHQ and PQS had been elucidated, the route by which AQNOs are synthesized remained elusive. Here, we report on PqsL, the key enzyme for AQNO production, which structurally resembles class A flavoprotein monooxygenases such as p-hydroxybenzoate 3-hydroxylase (pHBH) and 3-hydroxybenzoate 6-hydroxylase. However, we found that unlike related enzymes, PqsL hydroxylates a primary aromatic amine group, and it does not use NAD(P)H as cosubstrate, but unexpectedly required reduced flavin as electron donor. We also observed that PqsL is active toward 2-aminobenzoylacetate (2-ABA), the central intermediate of the AQ pathway, and forms the unstable compound 2-hydroxylaminobenzoylacetate, which was preferred over 2-ABA as substrate of the downstream enzyme PqsBC. In vitro reconstitution of the PqsL/PqsBC reaction was feasible by using the FAD reductase HpaC, and we noted that the AQ:AQNO ratio is increased in an hpaC-deletion mutant of P. aeruginosa PAO1 compared with the ratio in the WT strain. A structural comparison with pHBH, the model enzyme of class A flavoprotein monooxygenases, revealed that structural features associated with NAD(P)H binding are missing in PqsL. Our study completes the AQNO biosynthetic pathway in P. aeruginosa, indicating that PqsL produces the unstable product 2-hydroxylaminobenzoylacetate from 2-ABA and depends on free reduced flavin as electron donor instead of NAD(P)H.
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Affiliation(s)
| | - Simon Ernst
- From the Institute for Molecular Microbiology and Biotechnology and
| | - Benny Danilo Belviso
- the Institute of Crystallography, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
| | - Nina Jagmann
- From the Institute for Molecular Microbiology and Biotechnology and
| | - Ulrich Hennecke
- Organic Chemistry Institute, University of Münster, D-48149 Münster, Germany and
| | - Susanne Fetzner
- From the Institute for Molecular Microbiology and Biotechnology and
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Teanphonkrang S, Janke S, Chaiyen P, Sucharitakul J, Suginta W, Khunkaewla P, Schuhmann W, Ruff A, Schulte A. Tuned Amperometric Detection of Reduced β-Nicotinamide Adenine Dinucleotide by Allosteric Modulation of the Reductase Component of the p-Hydroxyphenylacetate Hydroxylase Immobilized within a Redox Polymer. Anal Chem 2018; 90:5703-5711. [PMID: 29633834 DOI: 10.1021/acs.analchem.7b05467] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report the fabrication of an amperometric NADH biosensor system that employs an allosterically modulated bacterial reductase in an adapted osmium(III)-complex-modified redox polymer film for analyte quantification. Chains of complexed Os(III) centers along matrix polymer strings make electrical connection between the immobilized redox protein and a graphite electrode disc, transducing enzymatic oxidation of NADH into a biosensor current. Sustainable anodic signaling required (1) a redox polymer with a formal potential that matched the redox switch of the embedded reductase and avoided interfering redox interactions and (2) formation of a cross-linked enzyme/polymer film for stable biocatalyst entrapment. The activity of the chosen reductase is enhanced upon binding of an effector, i.e. p-hydroxy-phenylacetic acid ( p-HPA), allowing the acceleration of the substrate conversion rate on the sensor surface by in situ addition or preincubation with p-HPA. Acceleration of NADH oxidation amplified the response of the biosensor, with a 1.5-fold increase in the sensitivity of analyte detection, compared to operation without the allosteric modulator. Repetitive quantitative testing of solutions of known NADH concentration verified the performance in terms of reliability and analyte recovery. We herewith established the use of allosteric enzyme modulation and redox polymer-based enzyme electrode wiring for substrate biosensing, a concept that may be applicable to other allosteric enzymes.
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Affiliation(s)
- Somjai Teanphonkrang
- School of Chemistry, Institute of Science, Biochemistry-Electrochemistry Research Unit (BECRU) , Suranaree University of Technology , 30000 Nakhon Ratchasima , Thailand
| | - Salome Janke
- Analytical Chemistry, Center for Electrochemical Sciences (CES) , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering (BSE) , Vidyasirimedhi Institute of Science and Technology (VISTEC) , 21210 Rayong , Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry , Chulalongkorn University , 10330 Bangkok , Thailand
| | - Wipa Suginta
- School of Chemistry, Institute of Science, Biochemistry-Electrochemistry Research Unit (BECRU) , Suranaree University of Technology , 30000 Nakhon Ratchasima , Thailand.,Center of Excellence (CoE) in Advanced Functional Materials, Institute of Science , Suranaree University of Technology , Nakhon Ratchasima 30000 , Thailand
| | - Panida Khunkaewla
- School of Chemistry, Institute of Science, Biochemistry-Electrochemistry Research Unit (BECRU) , Suranaree University of Technology , 30000 Nakhon Ratchasima , Thailand
| | - Wolfgang Schuhmann
- Analytical Chemistry, Center for Electrochemical Sciences (CES) , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Adrian Ruff
- Analytical Chemistry, Center for Electrochemical Sciences (CES) , Ruhr-University Bochum , 44780 Bochum , Germany
| | - Albert Schulte
- School of Biomolecular Science and Engineering (BSE) , Vidyasirimedhi Institute of Science and Technology (VISTEC) , 21210 Rayong , Thailand
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Romero E, Gómez Castellanos JR, Gadda G, Fraaije MW, Mattevi A. Same Substrate, Many Reactions: Oxygen Activation in Flavoenzymes. Chem Rev 2018; 118:1742-1769. [DOI: 10.1021/acs.chemrev.7b00650] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Elvira Romero
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - J. Rubén Gómez Castellanos
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Giovanni Gadda
- Departments of Chemistry and Biology, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
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48
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Sobrado P, Gadda G. Introduction to flavoproteins: Beyond the classical paradigms. Arch Biochem Biophys 2017; 632:1-3. [DOI: 10.1016/j.abb.2017.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2017] [Indexed: 02/08/2023]
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49
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Chenprakhon P, Dhammaraj T, Chantiwas R, Chaiyen P. Hydroxylation of 4-hydroxyphenylethylamine derivatives by R263 variants of the oxygenase component of p -hydroxyphenylacetate-3-hydroxylase. Arch Biochem Biophys 2017; 620:1-11. [DOI: 10.1016/j.abb.2017.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 11/29/2022]
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50
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Pimviriyakul P, Thotsaporn K, Sucharitakul J, Chaiyen P. Kinetic Mechanism of the Dechlorinating Flavin-dependent Monooxygenase HadA. J Biol Chem 2017; 292:4818-4832. [PMID: 28159841 DOI: 10.1074/jbc.m116.774448] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 01/30/2017] [Indexed: 01/26/2023] Open
Abstract
The accumulation of chlorophenols (CPs) in the environment, due to their wide use as agrochemicals, has become a serious environmental problem. These organic halides can be degraded by aerobic microorganisms, where the initial steps of various biodegradation pathways include an oxidative dechlorinating process in which chloride is replaced by a hydroxyl substituent. Harnessing these dechlorinating processes could provide an opportunity for environmental remediation, but detailed catalytic mechanisms for these enzymes are not yet known. To close this gap, we now report transient kinetics and product analysis of the dechlorinating flavin-dependent monooxygenase, HadA, from the aerobic organism Ralstonia pickettii DTP0602, identifying several mechanistic properties that differ from other enzymes in the same class. We first overexpressed and purified HadA to homogeneity. Analyses of the products from single and multiple turnover reactions demonstrated that HadA prefers 4-CP and 2-CP over CPs with multiple substituents. Stopped-flow and rapid-quench flow experiments of HadA with 4-CP show the involvement of specific intermediates (C4a-hydroperoxy-FAD and C4a-hydroxy-FAD) in the reaction, define rate constants and the order of substrate binding, and demonstrate that the hydroxylation step occurs prior to chloride elimination. The data also identify the non-productive and productive paths of the HadA reactions and demonstrate that product formation is the rate-limiting step. This is the first elucidation of the kinetic mechanism of a two-component flavin-dependent monooxygenase that can catalyze oxidative dechlorination of various CPs, and as such it will serve as the basis for future investigation of enzyme variants that will be useful for applications in detoxifying chemicals hazardous to human health.
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Affiliation(s)
- Panu Pimviriyakul
- From the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400 and
| | - Kittisak Thotsaporn
- the Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok 10300, Thailand
| | - Jeerus Sucharitakul
- the Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok 10300, Thailand
| | - Pimchai Chaiyen
- From the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400 and
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