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Andrade-Collantes E, Landeros-Rivera B, Sixto-López Y, Bello-Rios C, Contreras-García J, Tiznado JAG, Pedroza-Torres A, Camacho-Pérez B, Montaño S. Molecular insight into endosulfan degradation by Ese protein from Arthrobacter: Evidence-based structural bioinformatics and quantum mechanical calculations. Proteins 2024; 92:302-313. [PMID: 37864384 DOI: 10.1002/prot.26610] [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: 02/01/2023] [Revised: 05/22/2023] [Accepted: 09/25/2023] [Indexed: 10/22/2023]
Abstract
Endosulfan is an organochlorine insecticide widely used for agricultural pest control. Many nations worldwide have restricted or completely banned it due to its extreme toxicity to fish and aquatic invertebrates. Arthrobacter sp. strain KW has the ability to degrade α, β endosulfan and its intermediate metabolite endosulfate; this degradation is associated with Ese protein, a two-component flavin-dependent monooxygenase (TC-FDM). Employing in silico tools, we obtained the 3D model of Ese protein, and our results suggest that it belongs to the Luciferase Like Monooxygenase family (LLM). Docking studies showed that the residues V59, V315, D316, and T335 interact with α-endosulfan. The residues: V59, T60, V315, D316, and T335 are implicated in the interacting site with β-endosulfan, and the residues: H17, V315, D316, T335, N364, and Q363 participate in the interaction with endosulfate. Topological analysis of the electron density by means of the Quantum Theory of Atoms in Molecules (QTAIM) and the Non-Covalent Interaction (NCI) index reveals that the Ese-ligands complexes are formed mainly by dispersive forces, where Cl atoms have a predominant role. As Ese is a monooxygenase member, we predict the homodimer formation. However, enzymatic studies must be developed to investigate the Ese protein's enzymatic and catalytic activity.
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Affiliation(s)
- Ernesto Andrade-Collantes
- Laboratorio de Modelado Molecular y Bioinformática, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Sinaloa, Ciudad Universitaria s/n, Culiacán, Sinaloa, Mexico
| | - Bruno Landeros-Rivera
- CNRS, Laboratoire de Chimie Théorique, LCT, Sorbonne Université, Paris, France
- Facultad de Química, Departamento de Química Inorgánica y Nuclear, Universidad Nacional Autónoma de México, Circuito exterior S/N, Ciudad Universitaria, Ciudad de México, Mexico
| | - Yudibeth Sixto-López
- Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, Universidad de Granada, Granada, Spain
| | - Ciresthel Bello-Rios
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Guerrero, Mexico
| | | | - José Antonio Garzón Tiznado
- Laboratorio de Modelado Molecular y Bioinformática, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Sinaloa, Ciudad Universitaria s/n, Culiacán, Sinaloa, Mexico
| | - Abraham Pedroza-Torres
- Cátedra CONACyT-Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Beni Camacho-Pérez
- Instituto Tecnológico y de Estudios Superiores de Occidente, Periférico Sur Manuel Gómez Morín, Tlaquepaque, Jalisco, Mexico
| | - Sarita Montaño
- Laboratorio de Modelado Molecular y Bioinformática, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Sinaloa, Ciudad Universitaria s/n, Culiacán, Sinaloa, Mexico
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2
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Karaiyan P, Chang CCH, Chan ES, Tey BT, Ramanan RN, Ooi CW. In silico screening and heterologous expression of soluble dimethyl sulfide monooxygenases of microbial origin in Escherichia coli. Appl Microbiol Biotechnol 2022; 106:4523-4537. [PMID: 35713659 PMCID: PMC9259527 DOI: 10.1007/s00253-022-12008-8] [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: 02/20/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 11/28/2022]
Abstract
Abstract Sequence-based screening has been widely applied in the discovery of novel microbial enzymes. However, majority of the sequences in the genomic databases were annotated using computational approaches and lacks experimental characterization. Hence, the success in obtaining the functional biocatalysts with improved characteristics requires an efficient screening method that considers a wide array of factors. Recombinant expression of microbial enzymes is often hampered by the undesirable formation of inclusion body. Here, we present a systematic in silico screening method to identify the proteins expressible in soluble form and with the desired biological properties. The screening approach was adopted in the recombinant expression of dimethyl sulfide (DMS) monooxygenase in Escherichia coli. DMS monooxygenase, a two-component enzyme consisting of DmoA and DmoB subunits, was used as a model protein. The success rate of producing soluble and active DmoA is 71% (5 out of 7 genes). Interestingly, the soluble recombinant DmoA enzymes exhibited the NADH:FMN oxidoreductase activity in the absence of DmoB (second subunit), and the cofactor FMN, suggesting that DmoA is also an oxidoreductase. DmoA originated from Janthinobacterium sp. AD80 showed the maximum NADH oxidation activity (maximum reaction rate: 6.6 µM/min; specific activity: 133 µM/min/mg). This novel finding may allow DmoA to be used as an oxidoreductase biocatalyst for various industrial applications. The in silico gene screening methodology established from this study can increase the success rate of producing soluble and functional enzymes while avoiding the laborious trial and error involved in the screening of a large pool of genes available. Key points • A systematic gene screening method was demonstrated. • DmoA is also an oxidoreductase capable of oxidizing NADH and reducing FMN. • DmoA oxidizes NADH in the absence of external FMN. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12008-8.
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Affiliation(s)
- Prasanth Karaiyan
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Catherine Ching Han Chang
- Arkema Thiochemicals Sdn. Bhd., Jalan PJU 1A/7A OASIS Ara Damansara, 47301, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Eng-Seng Chan
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Beng Ti Tey
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.,Advanced Engineering Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Ramakrishnan Nagasundara Ramanan
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia. .,Arkema Thiochemicals Sdn. Bhd., Jalan PJU 1A/7A OASIS Ara Damansara, 47301, Petaling Jaya, Selangor Darul Ehsan, Malaysia.
| | - Chien Wei Ooi
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia. .,Advanced Engineering Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
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3
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Li WL, Dong X, Lu R, Zhou YL, Zheng PF, Feng D, Wang Y. Microbial ecology of sulfur cycling near the sulfate-methane transition of deep-sea cold seep sediments. Environ Microbiol 2021; 23:6844-6858. [PMID: 34622529 DOI: 10.1111/1462-2920.15796] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 11/27/2022]
Abstract
Microbial sulfate reduction is largely associated with anaerobic methane oxidation and alkane degradation in sulfate-methane transition zone (SMTZ) of deep-sea cold seeps. How the sulfur cycling is mediated by microbes near SMTZ has not been fully understood. In this study, we detected a shallow SMTZ in three of eight sediment cores sampled from two cold seep areas in the South China Sea. One hundred ten genomes representing sulfur-oxidizing bacteria (SOB) and sulfur-reducing bacteria (SRB) strains were identified from three SMTZ-bearing cores. In the layers above SMTZ, SOB were mostly constituted by Campylobacterota, Gammaproteobacteria and Alphaproteobacteria that probably depended on nitrogen oxides and/or oxygen for oxidation of sulfide and thiosulfate in near-surface sediment layers. In the layers below the SMTZ, the deltaproteobacterial SRB genomes and metatranscriptomes revealed CO2 fixation by Wood-Ljungdahl pathway, sulfate reduction and nitrogen fixation for syntrophic or fermentative lifestyle. A total of 68% of the metagenome assembled genomes were not adjacent to known species in a phylogenomic tree, indicating a high diversity of bacteria involved in sulfur cycling. With the large number of genomes for SOB and SRB, our study uncovers the microbial populations that potentially mediate sulfur metabolism and associated carbon and nitrogen cycles, which sheds light on complex biogeochemical processes in deep-sea environments.
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Affiliation(s)
- Wen-Li Li
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Rui Lu
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying-Li Zhou
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng-Fei Zheng
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China
| | - Dong Feng
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Yong Wang
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China
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Liew JJM, El Saudi IM, Nguyen SV, Wicht DK, Dowling DP. Structures of the alkanesulfonate monooxygenase MsuD provide insight into C-S bond cleavage, substrate scope, and an unexpected role for the tetramer. J Biol Chem 2021; 297:100823. [PMID: 34029591 PMCID: PMC8234197 DOI: 10.1016/j.jbc.2021.100823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 02/01/2023] Open
Abstract
Bacterial two-component flavin-dependent monooxygenases cleave the stable C-S bond of environmental and anthropogenic organosulfur compounds. The monooxygenase MsuD converts methanesulfonate (MS-) to sulfite, completing the sulfur assimilation process during sulfate starvation, but the mechanism of this conversion remains unclear. To explore the mechanism of C-S bond cleavage, we report a series of crystal structures of MsuD from Pseudomonas fluorescens in different liganded states. This report provides the first crystal structures of an alkanesulfonate monooxygenase with a bound flavin and alkanesulfonate, elucidating the roles of the active site lid, the protein C terminus, and an active site loop in flavin and/or alkanesulfonate binding. These structures position MS- closest to the flavin N5 position, consistent with an N5-(hydro)peroxyflavin mechanism rather than a classical C4a-(hydro)peroxyflavin mechanism. A fully enclosed active site is observed in the ternary complex, mediated by interchain interaction of the C terminus at the tetramer interface. These structures identify an unexpected function of the protein C terminus in this protein family in stabilizing tetramer formation and the alkanesulfonate-binding site. Spurred by interest from the crystal structures, we conducted biochemical assays and molecular docking that redefine MsuD as a small- to medium-chain alkanesulfonate monooxygenase. Functional mutations verify the sulfonate-binding site and reveal the critical importance of the protein C terminus for monooxygenase function. These findings reveal a deeper understanding of MsuD's functionality at the molecular level and consequently how it operates within its role as part of the sulfur assimilation pathway.
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Affiliation(s)
- Jeremy J M Liew
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Israa M El Saudi
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Son V Nguyen
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Denyce K Wicht
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Daniel P Dowling
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA.
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5
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A [6+4]-cycloaddition adduct is the biosynthetic intermediate in streptoseomycin biosynthesis. Nat Commun 2021; 12:2092. [PMID: 33828077 PMCID: PMC8027225 DOI: 10.1038/s41467-021-22395-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/10/2021] [Indexed: 12/14/2022] Open
Abstract
Streptoseomycin (STM, 1) is a bacterial macrolactone that has a unique 5/14/10/6/6-pentacyclic ring with an ether bridge. We have previously identified the biosynthetic gene cluster for 1 and characterized StmD as [6 + 4]- and [4 + 2]-bispericyclase that catalyze a reaction leading to both 6/10/6- and 10/6/6-tricyclic adducts (6 and 7). The remaining steps, especially how to install and stabilize the required 10/6/6-tricyclic core for downstream modifications, remain unknown. In this work, we have identified three oxidoreductases that fix the required 10/6/6-tryciclic core. A pair of flavin-dependent oxidoreductases, StmO1 and StmO2, catalyze the direct hydroxylation at [6 + 4]-adduct (6). Subsequently, a spontaneous [3,3]-Cope rearrangement and an enol-ketone tautomerization result in the formation of 10/6/6-tricyclic intermediate 12b, which can be further converted to a stable 10/6/6-tricyclic alcohol 11 through a ketoreduction by StmK. Crystal structure of the heterodimeric complex NtfO1-NtfO2, homologues of StmO1-StmO2 with equivalent function, reveals protein-protein interactions. Our results demonstrate that the [6 + 4]-adduct instead of [4 + 2]-adduct is the bona fide biosynthetic intermediate.
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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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Hammers DS, Donaghy CM, Heiss SL, Harris LM, Gordon JM, Stevens JW, Murray LP, Schwab AD, Hester BC, Culpepper MA. Identification and Characterization of a DmoB Flavin Oxidoreductase from a Putative Two-Component DMS C-Monooxygenase. ACS OMEGA 2020; 5:9830-9838. [PMID: 32391470 PMCID: PMC7203701 DOI: 10.1021/acsomega.9b04489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/05/2020] [Indexed: 06/11/2023]
Abstract
The compound dimethyl sulfide (DMS) links terrestrial and oceanic sulfur with the atmosphere because of its volatility. Atmospheric DMS is responsible for cloud formation and radiation backscattering and has been implicated in climate control mitigation. The enzyme DMS C-monooxygenase degrades DMS and has been classified as a two-component FMNH2-dependent monooxygenase. This enzyme requires a flavin reductase B subunit to supply electrons to the monooxygenase A subunit where DMS conversion occurs. One form of the enzyme from Hyphomicrobium sulfonivorans has been isolated and characterized. In this work, a putative DMS C-monooxygenase has been identified with bioinformatics in Arthrobacter globiformis. We report the expression, purification, and characterization of the DmoB flavin reductase subunit, termed DmoB, from A. globiformis. Data support DmoB preference and optimal activity for the cosubstrates flavin mononucleotide (FMN) and NADH. FMN binds at a 1:1 stoichiometry with high affinity (K d = 1.11 μM). The reductase is able to generate product with the A subunit from H. sulfonivorans expressed in Escherichia coli, albeit at a lower turnover than the natively expressed enzyme. No static protein-protein interactions were observed under the conditions tested between the two subunits. These results provide new details in the classification of enzymes involved in the sulfur cycling pathway and emerging forms of the enzyme DMS monooxygenase.
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Affiliation(s)
- D. Scott Hammers
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
| | - Caroline M. Donaghy
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
| | - Sarah L. Heiss
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
| | - Lydia M. Harris
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
| | - Jackson M. Gordon
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
| | - John W. Stevens
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
| | - Lucian P. Murray
- Department
of Physics and Astronomy, Appalachian State
University, Boone, North Carolina 28608, United States
| | - Alexander D. Schwab
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
| | - Brooke C. Hester
- Department
of Physics and Astronomy, Appalachian State
University, Boone, North Carolina 28608, United States
| | - Megen A. Culpepper
- Department
of Chemistry and Fermentation Sciences, Appalachian State University, Boone, North Carolina 28608, United States
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