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Xu J, Hao J, Bu C, Meng Y, Xiao H, Zhang M, Li C. XMECP: Reaching State-of-the-Art MECP Optimization in Multiscale Complex Systems. J Chem Theory Comput 2024; 20:3590-3600. [PMID: 38651739 DOI: 10.1021/acs.jctc.4c00033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The Python-based program, XMECP, is developed for realizing robust, efficient, and state-of-the-art minimum energy crossing point (MECP) optimization in multiscale complex systems. This article introduces the basic capabilities of the XMECP program by theoretically investigating the MECP mechanism of several example systems including (1) the photosensitization mechanism of benzophenone, (2) photoinduced proton-coupled electron transfer in the cytosine-guanine base pair in DNA, (3) the spin-flip process in oxygen activation catalyzed by an iron-containing 2-oxoglutarate-dependent oxygenase (Fe/2OGX), and (4) the photochemical pathway of flavoprotein adjusted by the intensity of an external electric field. MECPs related to multistate reaction and multistate reactivity in large-scale complex biochemical systems can be well-treated by workflows suggested by the XMECP program. The branching plane updating the MECP optimization algorithm is strongly recommended as it provides derivative coupling vector (DCV) with explicit calculation and can equivalently evaluate contributions from non-QM residues to DCV, which can be nonadiabatic coupling or spin-orbit coupling in different cases. In the discussed QM/MM examples, we also found that the influence on the QM region by DCV can occur through noncovalent interactions and decay with distance. In the example of DNA base pairs, the nonadiabatic coupling occurs across the π-π stacking structure formed in the double-helix system. In contrast to general intuition, in the example of Fe/2OGX, the central ferrous and oxygen part contribute little to the spin-orbit coupling; however, a nearby arginine residue, which is treated by molecular mechanics in the QM/MM method, contributes significantly via two hydrogen bonds formed with α-ketoglutarate (α-KG). This indicates that the arginine residue plays a significant role in oxygen activation, driving the initial triplet state toward the productive quintet state, which is more than the previous knowledge that the arginine residue can bind α-KG at the reaction site by hydrogen bonds.
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Affiliation(s)
- Jiawei Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jian Hao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Caijie Bu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350117, Fujian, P. R. China
| | - Yajie Meng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Han Xiao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
| | - Minyi Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
| | - Chunsen Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, Fujian, P. R. China
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Teufel R. Oxygen-transfer reactions by enzymatic flavin-N 5 oxygen adducts-Oxidation is not a must. Curr Opin Chem Biol 2024; 80:102464. [PMID: 38739969 DOI: 10.1016/j.cbpa.2024.102464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
Flavoenzymes catalyze numerous redox reactions including the transfer of an O2-derived oxygen atom to organic substrates, while the other one is reduced to water. Investigation of some of these monooxygenases led to a detailed understanding of their catalytic cycle, which involves the flavin-C4α-(hydro)peroxide as hallmark oxygenating species, and newly discovered flavoprotein monooxygenases were generally assumed to operate similarly. However, discoveries in recent years revealed a broader mechanistic versatility, including enzymes that utilize flavin-N5 oxygen adducts for catalysis in the form of the flavin-N5-(hydro)peroxide and the flavin-N5-oxide species. In this review, I will highlight recent developments in that area, including noncanonical flavoenzymes from natural product biosynthesis and sulfur metabolism that provide first insights into the chemical properties of these species. Remarkably, some enzymes may even combine the flavin-N5-peroxide and the flavin-N5-oxide species for consecutive oxygen-transfers to the same substrate and thereby in essence operate as dioxygenases.
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Affiliation(s)
- Robin Teufel
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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Qiu L, Jiang H, Cho K, Yu Y, Jones LA, Huang T, Perlmutter JS, Gropler RJ, Brier MR, Patti GJ, Benzinger TLS, Tu Z. Metabolite Study and Structural Authentication for the First-in-Human Use Sphingosine-1-phosphate Receptor 1 Radiotracer. ACS Chem Neurosci 2024; 15:1882-1892. [PMID: 38634759 DOI: 10.1021/acschemneuro.4c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
The sphingosine-1-phosphate receptor 1 (S1PR1) radiotracer [11C]CS1P1 has shown promise in proof-of-concept PET imaging of neuroinflammation in multiple sclerosis (MS). Our HPLC radiometabolite analysis of human plasma samples collected during PET scans with [11C]CS1P1 detected a radiometabolite peak that is more lipophilic than [11C]CS1P1. Radiolabeled metabolites that cross the blood-brain barrier complicate quantitative modeling of neuroimaging tracers; thus, characterizing such radiometabolites is important. Here, we report our detailed investigation of the metabolite profile of [11C]CS1P1 in rats, nonhuman primates, and humans. CS1P1 is a fluorine-containing ligand that we labeled with C-11 or F-18 for preclinical studies; the brain uptake was similar for both radiotracers. The same lipophilic radiometabolite found in human studies also was observed in plasma samples of rats and NHPs for CS1P1 labeled with either C-11 or F-18. We characterized the metabolite in detail using rats after injection of the nonradioactive CS1P1. To authenticate the molecular structure of this radiometabolite, we injected rats with 8 mg/kg of CS1P1 to collect plasma for solvent extraction and HPLC injection, followed by LC/MS analysis of the same metabolite. The LC/MS data indicated in vivo mono-oxidation of CS1P1 produces the metabolite. Subsequently, we synthesized three different mono-oxidized derivatives of CS1P1 for further investigation. Comparing the retention times of the mono-oxidized derivatives with the metabolite observed in rats injected with CS1P1 identified the metabolite as N-oxide 1, also named TZ82121. The MS fragmentation pattern of N-oxide 1 also matched that of the major metabolite in rat plasma. To confirm that metabolite TZ82121 does not enter the brain, we radiosynthesized [18F]TZ82121 by the oxidation of [18F]FS1P1. Radio-HPLC analysis confirmed that [18F]TZ82121 matched the radiometabolite observed in rat plasma post injection of [18F]FS1P1. Furthermore, the acute biodistribution study in SD rats and PET brain imaging in a nonhuman primate showed that [18F]TZ82121 does not enter the rat or nonhuman primate brain. Consequently, we concluded that the major lipophilic radiometabolite N-oxide [11C]TZ82121, detected in human plasma post injection of [11C]CS1P1, does not enter the brain to confound quantitative PET data analysis. [11C]CS1P1 is a promising S1PR1 radiotracer for detecting S1PR1 expression in the CNS.
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Affiliation(s)
- Lin Qiu
- Department of Radiology, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Hao Jiang
- Department of Radiology, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Kevin Cho
- Center for Mass Spectrometry and Metabolic Tracing, Department of Chemistry, Department of Medicine, Washington University, Saint Louis, Missouri 63130, United States
| | - Yanbo Yu
- Department of Radiology, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Lynne A Jones
- Department of Radiology, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Tianyu Huang
- Department of Radiology, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Joel S Perlmutter
- Department of Radiology, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
- Departments of Neurology, Neuroscience, Physical Therapy and Occupational Therapy, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Robert J Gropler
- Department of Radiology, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Matthew R Brier
- Departments of Neurology, Neuroscience, Physical Therapy and Occupational Therapy, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Gary J Patti
- Center for Mass Spectrometry and Metabolic Tracing, Department of Chemistry, Department of Medicine, Washington University, Saint Louis, Missouri 63130, United States
| | - Tammie L S Benzinger
- Department of Radiology, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Zhude Tu
- Department of Radiology, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
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Rehpenn A, Hindelang S, Truong KN, Pöthig A, Storch G. Enhancing Flavins Photochemical Activity in Hydrogen Atom Abstraction and Triplet Sensitization through Ring-Contraction. Angew Chem Int Ed Engl 2024; 63:e202318590. [PMID: 38339882 DOI: 10.1002/anie.202318590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
The isoalloxazine heterocycle of flavin cofactors reacts with various nucleophiles to form covalent adducts with important functions in enzymes. Molecular flavin models allow for the characterization of such adducts and the study of their properties. A fascinating set of reactions occurs when flavins react with hydroxide base, which leads to imidazolonequinoxalines, ring-contracted flavins, with so far unexplored activity. We report a systematic study of the photophysical properties of this new chromophore by absorption and emission spectroscopy as well as cyclic voltammetry. Excited, ring-contracted flavins are significantly stronger hydrogen atom abstractors when compared to the parent flavins, which allowed the direct trifluoromethylthiolation of aliphatic methine positions (bond dissociation energy (BDE) of 400.8 kJ mol-1). In an orthogonal activity, their increased triplet energy (E(S0←T1)=244 kJ mol-1) made sensitized reactions possible which exceeded the power of standard flavins. Combining both properties, ring-contracted flavin catalysts enabled the one-pot, five-step transformation of α-tropolone into trans-3,4-disubstituted cyclopentanones. We envision this new class of flavin-derived chromophores to open up new modes of reactivity that are currently impossible with unmodified flavins.
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Affiliation(s)
- Andreas Rehpenn
- Technical University of Munich (TUM), School of Natural Sciences and Catalysis Research Center (CRC), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Stephan Hindelang
- Technical University of Munich (TUM), School of Natural Sciences and Catalysis Research Center (CRC), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Khai-Nghi Truong
- Rigaku Europe SE, Hugenottenallee 167, 63263, Neu-Isenburg, Germany
| | - Alexander Pöthig
- Technical University of Munich (TUM), School of Natural Sciences and Catalysis Research Center (CRC), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Golo Storch
- Technical University of Munich (TUM), School of Natural Sciences and Catalysis Research Center (CRC), Lichtenbergstr. 4, 85747, Garching, Germany
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Prakinee K, Lawan N, Phintha A, Visitsatthawong S, Chitnumsub P, Jitkaroon W, Chaiyen P. On the Mechanisms of Hypohalous Acid Formation and Electrophilic Halogenation by Non-Native Halogenases. Angew Chem Int Ed Engl 2024:e202403858. [PMID: 38606607 DOI: 10.1002/anie.202403858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/13/2024]
Abstract
Enzymatic electrophilic halogenation is a mild tool for functionalization of diverse organic compounds. Only a few groups of native halogenases are capable of catalyzing such a reaction. In this study, we used a mechanism-guided strategy to discover the electrophilic halogenation activity catalyzed by non-native halogenases. As the ability to form a hypohalous acid (HOX) is key for halogenation, flavin-dependent monooxygenases/oxidases capable of forming C4a-hydroperoxyflavin (FlC4a-OOH), such as dehalogenase, hydroxylases, luciferase and pyranose-2-oxidase (P2O), and flavin reductase capable of forming H2O2 were explored for their abilities to generate HOX in situ. Transient kinetic analyses using stopped-flow spectrophotometry/fluorometry and product analysis indicate that FlC4a-OOH in dehalogenases, selected hydroxylases and luciferases, but not in P2O can form HOX; however, the HOX generated from FlC4a-OOH cannot halogenate their substrates. Remarkably, in situ H2O2 generated by P2O can form HOI and also iodinate various compounds. Because not all enzymes capable of forming FlC4a-OOH can react with halides to form HOX, QM/MM calculations, site-directed mutagenesis and structural analysis were carried out to elucidate the mechanism underlying HOX formation and characterize the active site environment. Our findings shed light on identifying new halogenase scaffolds besides the currently known enzymes and have invoked a new mode of chemoenzymatic halogenation.
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Affiliation(s)
- Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
| | - Narin Lawan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
| | - Surawit Visitsatthawong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
| | - Penchit Chitnumsub
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA) Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Watcharapa Jitkaroon
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, 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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Zhang Q, Chen Q, Shaik S, Wang B. Flavin-N5OOH Functions as both a Powerful Nucleophile and a Base in the Superfamily of Flavoenzymes. Angew Chem Int Ed Engl 2024; 63:e202318629. [PMID: 38299700 DOI: 10.1002/anie.202318629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024]
Abstract
Flavoenzymes can mediate a large variety of oxidation reactions through the activation of oxygen. However, the O2 activation chemistry of flavin enzymes is not yet fully exploited. Normally, the O2 activation occurs at the C4a site of the flavin cofactor, yielding the flavin C4a-(hydro)hydroperoxyl species in monooxygenases or oxidases. Using extensive MD simulations, QM/MM calculations and QM calculations, our studies reveal the formation of the common nucleophilic species, Flavin-N5OOH, in two distinct flavoenzymes (RutA and EncM). Our studies show that Flavin-N5OOH acts as a powerful nucleophile that promotes C-N cleavage of uracil in RutA, and a powerful base in the deprotonation of substrates in EncM. We reason that Flavin-N5OOH can be a common reactive species in the superfamily of flavoenzymes, which accomplish generally selective general base catalysis and C-X (X=N, S, Cl, O) cleavage reactions that are otherwise challenging with solvated hydroxide ion base. These results expand our understanding of the chemistry and catalysis of flavoenzymes.
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Affiliation(s)
- Qiaoyu Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Qianqian Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
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Ferizhendi KK, Simon P, Pelosi L, Séchet E, Arulanandam R, Chehade MH, Rey M, Onal D, Flandrin L, Chreim R, Faivre B, Vo SCDT, Arias-Cartin R, Barras F, Fontecave M, Bouveret E, Lombard M, Pierrel F. An organic O donor for biological hydroxylation reactions. Proc Natl Acad Sci U S A 2024; 121:e2321242121. [PMID: 38507448 PMCID: PMC10990095 DOI: 10.1073/pnas.2321242121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 02/08/2024] [Indexed: 03/22/2024] Open
Abstract
All biological hydroxylation reactions are thought to derive the oxygen atom from one of three inorganic oxygen donors, O2, H2O2, or H2O. Here, we have identified the organic compound prephenate as the oxygen donor for the three hydroxylation steps of the O2-independent biosynthetic pathway of ubiquinone, a widely distributed lipid coenzyme. Prephenate is an intermediate in the aromatic amino acid pathway and genetic experiments showed that it is essential for ubiquinone biosynthesis in Escherichia coli under anaerobic conditions. Metabolic labeling experiments with 18O-shikimate, a precursor of prephenate, demonstrated the incorporation of 18O atoms into ubiquinone. The role of specific iron-sulfur enzymes belonging to the widespread U32 protein family is discussed. Prephenate-dependent hydroxylation reactions represent a unique biochemical strategy for adaptation to anaerobic environments.
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Affiliation(s)
| | - Philippe Simon
- Laboratoire de Chimie des Processus Biologiques, Institut de Chimie, Collège de France, CNRS UMR 8229, PSL Research University, Sorbonne Université, Paris75005, France
| | - Ludovic Pelosi
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Grenoble38000, France
| | - Emmanuel Séchet
- SAMe Unit, Département de Microbiologie, Institut Pasteur, Université Paris-Cité, UMR CNRS 6047, ParisF-75015, France
| | - Roache Arulanandam
- Laboratoire de Chimie des Processus Biologiques, Institut de Chimie, Collège de France, CNRS UMR 8229, PSL Research University, Sorbonne Université, Paris75005, France
| | - Mahmoud Hajj Chehade
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Grenoble38000, France
| | - Martial Rey
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Mass Spectrometry for Biology, ParisF-75015, France
| | - Deniz Onal
- Laboratoire de Chimie des Processus Biologiques, Institut de Chimie, Collège de France, CNRS UMR 8229, PSL Research University, Sorbonne Université, Paris75005, France
| | - Laura Flandrin
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Grenoble38000, France
| | - Rouba Chreim
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Grenoble38000, France
| | - Bruno Faivre
- Laboratoire de Chimie des Processus Biologiques, Institut de Chimie, Collège de France, CNRS UMR 8229, PSL Research University, Sorbonne Université, Paris75005, France
| | - Samuel Chau-Duy-Tam Vo
- Laboratoire de Chimie des Processus Biologiques, Institut de Chimie, Collège de France, CNRS UMR 8229, PSL Research University, Sorbonne Université, Paris75005, France
| | - Rodrigo Arias-Cartin
- SAMe Unit, Département de Microbiologie, Institut Pasteur, Université Paris-Cité, UMR CNRS 6047, ParisF-75015, France
| | - Frédéric Barras
- SAMe Unit, Département de Microbiologie, Institut Pasteur, Université Paris-Cité, UMR CNRS 6047, ParisF-75015, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Institut de Chimie, Collège de France, CNRS UMR 8229, PSL Research University, Sorbonne Université, Paris75005, France
| | - Emmanuelle Bouveret
- SAMe Unit, Département de Microbiologie, Institut Pasteur, Université Paris-Cité, UMR CNRS 6047, ParisF-75015, France
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, Institut de Chimie, Collège de France, CNRS UMR 8229, PSL Research University, Sorbonne Université, Paris75005, France
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Grenoble38000, France
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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. Biotechnol Biofuels Bioprod 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ouyang X, Liu G, Guo L, Wu G, Xu P, Zhao YL, Tang H. A multifunctional flavoprotein monooxygenase HspB for hydroxylation and C-C cleavage of 6-hydroxy-3-succinoyl-pyridine. Appl Environ Microbiol 2024; 90:e0225523. [PMID: 38415602 PMCID: PMC10952382 DOI: 10.1128/aem.02255-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/26/2024] [Indexed: 02/29/2024] Open
Abstract
Flavoprotein monooxygenases catalyze reactions, including hydroxylation and epoxidation, involved in the catabolism, detoxification, and biosynthesis of natural substrates and industrial contaminants. Among them, the 6-hydroxy-3-succinoyl-pyridine (HSP) monooxygenase (HspB) from Pseudomonas putida S16 facilitates the hydroxylation and C-C bond cleavage of the pyridine ring in nicotine. However, the mechanism for biodegradation remains elusive. Here, we refined the crystal structure of HspB and elucidated the detailed mechanism behind the oxidative hydroxylation and C-C cleavage processes. Leveraging structural information about domains for binding the cofactor flavin adenine dinucleotide (FAD) and HSP substrate, we used molecular dynamics simulations and quantum/molecular mechanics calculations to demonstrate that the transfer of an oxygen atom from the reactive FAD peroxide species (C4a-hydroperoxyflavin) to the C3 atom in the HSP substrate constitutes a rate-limiting step, with a calculated reaction barrier of about 20 kcal/mol. Subsequently, the hydrogen atom was rebounded to the FAD cofactor, forming C4a-hydroxyflavin. The residue Cys218 then catalyzed the subsequent hydrolytic process of C-C cleavage. Our findings contribute to a deeper understanding of the versatile functions of flavoproteins in the natural transformation of pyridine and HspB in nicotine degradation.IMPORTANCEPseudomonas putida S16 plays a pivotal role in degrading nicotine, a toxic pyridine derivative that poses significant environmental challenges. This study highlights a key enzyme, HspB (6-hydroxy-3-succinoyl-pyridine monooxygenase), in breaking down nicotine through the pyrrolidine pathway. Utilizing dioxygen and a flavin adenine dinucleotide cofactor, HspB hydroxylates and cleaves the substrate's side chain. Structural analysis of the refined HspB crystal structure, combined with state-of-the-art computations, reveals its distinctive mechanism. The crucial function of Cys218 was never discovered in its homologous enzymes. Our findings not only deepen our understanding of bacterial nicotine degradation but also open avenues for applications in both environmental cleanup and pharmaceutical development.
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Affiliation(s)
- Xingyu Ouyang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Gongquan Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lihua Guo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Geng Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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10
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Gonzalez L, Chau-Duy Tam Vo S, Faivre B, Pierrel F, Fontecave M, Hamdane D, Lombard M. Activation of Coq6p, a FAD Monooxygenase Involved in Coenzyme Q Biosynthesis, by Adrenodoxin Reductase/Ferredoxin. Chembiochem 2024; 25:e202300738. [PMID: 38141230 DOI: 10.1002/cbic.202300738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 12/25/2023]
Abstract
Adrenodoxin reductase (AdxR) plays a pivotal role in electron transfer, shuttling electrons between NADPH and iron/sulfur adrenodoxin proteins in mitochondria. This electron transport system is essential for P450 enzymes involved in various endogenous biomolecules biosynthesis. Here, we present an in-depth examination of the kinetics governing the reduction of human AdxR by NADH or NADPH. Our results highlight the efficiency of human AdxR when utilizing NADPH as a flavin reducing agent. Nevertheless, akin to related flavoenzymes such as cytochrome P450 reductase, we observe that low NADPH concentrations hinder flavin reduction due to intricate equilibrium reactions between the enzyme and its substrate/product. Remarkably, the presence of MgCl2 suppresses this complex kinetic behavior by decreasing NADPH binding to oxidized AdxR, effectively transforming AdxR into a classical Michaelis-Menten enzyme. We propose that the addition of MgCl2 may be adapted for studying the reductive half-reactions of other flavoenzymes with NADPH. Furthermore, in vitro experiments provide evidence that the reduction of the yeast flavin monooxygenase Coq6p relies on an electron transfer chain comprising NADPH-AdxR-Yah1p-Coq6p, where Yah1p shuttles electrons between AdxR and Coq6p. This discovery explains the previous in vivo observation that Yah1p and the AdxR homolog, Arh1p, are required for the biosynthesis of coenzyme Q in yeast.
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Affiliation(s)
- Lucie Gonzalez
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Sorbonne Université, CNRS UMR8229, PSL Research University, Sorbonne Université, 11 place Marcelin Berthelot, 75 005, Paris, France
| | - Samuel Chau-Duy Tam Vo
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Sorbonne Université, CNRS UMR8229, PSL Research University, Sorbonne Université, 11 place Marcelin Berthelot, 75 005, Paris, France
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bruno Faivre
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Sorbonne Université, CNRS UMR8229, PSL Research University, Sorbonne Université, 11 place Marcelin Berthelot, 75 005, Paris, France
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000, Grenoble, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Sorbonne Université, CNRS UMR8229, PSL Research University, Sorbonne Université, 11 place Marcelin Berthelot, 75 005, Paris, France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Sorbonne Université, CNRS UMR8229, PSL Research University, Sorbonne Université, 11 place Marcelin Berthelot, 75 005, Paris, France
- Institut de Biologie Paris-Seine, Biology of Aging and Adaptation, UMR 8256, Sorbonne Université, 7 quai Saint-Bernard, 75 252, Paris, France
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Sorbonne Université, CNRS UMR8229, PSL Research University, Sorbonne Université, 11 place Marcelin Berthelot, 75 005, Paris, France
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11
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Schittich AR, Fenner K, Stedmon CA, Xu J, McKnight US, Smets BF. Coupling pathway prediction and fluorescence spectroscopy to assess the impact of auxiliary substrates on micropollutant biodegradation. Environ Microbiol 2024; 26:e16560. [PMID: 38234207 DOI: 10.1111/1462-2920.16560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/08/2023] [Indexed: 01/19/2024]
Abstract
Some bacteria can degrade organic micropollutants (OMPs) as primary carbon sources. Due to typically low OMP concentrations, these bacteria may benefit from supplemental assimilation of natural substrates present in the pool of dissolved organic matter (DOM). The biodegradability of such auxiliary substrates and the impacts on OMP removal are tightly linked to biotransformation pathways. Here, we aimed to elucidate the biodegradability and effect of different DOM constituents for the carbofuran degrader Novosphingobium sp. KN65.2, using a novel approach that combines pathway prediction, laboratory experiments, and fluorescence spectroscopy. Pathway prediction suggested that ring hydroxylation reactions catalysed by Rieske-type dioxygenases and flavin-dependent monooxygenases determine the transformability of the 11 aromatic compounds used as model DOM constituents. Our approach further identified two groups with distinct transformation mechanisms amongst the four growth-supporting compounds selected for mixed substrate biodegradation experiments with the pesticide carbofuran (Group 1: 4-hydroxybenzoic acid, 4-hydroxybenzaldehyde; Group 2: p-coumaric acid, ferulic acid). Carbofuran biodegradation kinetics were stable in the presence of both Group 1 and Group 2 auxiliary substrates. However, Group 2 substrates would be preferable for bioremediation processes, as they showed constant biodegradation kinetics under different experimental conditions (pre-growing KN65.2 on carbofuran vs. DOM constituent). Furthermore, Group 2 substrates were utilisable by KN65.2 in the presence of a competitor (Pseudomonas fluorescens sp. P17). Our study thus presents a simple and cost-efficient approach that reveals mechanistic insights into OMP-DOM biodegradation.
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Affiliation(s)
- Anna-Ricarda Schittich
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
- Sino-Danish Center for Education and Research, Denmark
- Department of Civil and Environmental Engineering, University of California Berkeley, Berkeley, California, USA
| | - Kathrin Fenner
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- University of Zürich, Department of Chemistry, Zürich, Switzerland
| | - Colin A Stedmon
- National Institute of Aquatic Research, Technical University of Denmark, Lyngby, Denmark
| | - Jianxin Xu
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Ursula S McKnight
- Swedish Meteorological and Hydrological Institute, Norrköping, Sweden
| | - Barth F Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
- Sino-Danish Center for Education and Research, Denmark
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12
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Turlington ZR, Vaz Ferreira de Macedo S, Perry K, Belsky SL, Faust JA, Snider MJ, Hicks KA. Ligand bound structure of a 6-hydroxynicotinic acid 3-monooxygenase provides mechanistic insights. Arch Biochem Biophys 2024; 752:109859. [PMID: 38104959 DOI: 10.1016/j.abb.2023.109859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
6-Hydroxynicotinic acid 3-monooxygenase (NicC) is a bacterial enzyme involved in the degradation of nicotinic acid. This enzyme is a Class A flavin-dependent monooxygenase that catalyzes a unique decarboxylative hydroxylation. The unliganded structure of this enzyme has previously been reported and studied using steady- and transient-state kinetics to support a comprehensive kinetic mechanism. Here we report the crystal structure of the H47Q NicC variant in both a ligand-bound (solved to 2.17 Å resolution) and unliganded (1.51 Å resolution) form. Interestingly, in the liganded form, H47Q NicC is bound to 2-mercaptopyridine (2-MP), a contaminant present in the commercial stock of 6-mercaptopyridine-3-carboxylic acid(6-MNA), a substrate analogue. 2-MP binds weakly to H47Q NicC and is not a substrate for the enzyme. Based on kinetic and thermodynamic characterization, we have fortuitously captured a catalytically inactive H47Q NicC•2-MP complex in our crystal structure. This complex reveals interesting mechanistic details about the reaction catalyzed by 6-hydroxynicotinic acid 3-monooxygenase.
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Affiliation(s)
- Zachary R Turlington
- Department of Chemistry, State University of New York at Cortland, Cortland, NY, 13045, United States
| | | | - Kay Perry
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL, United States
| | - Sam L Belsky
- Department of Chemistry, The College of Wooster, Wooster, OH, 44691, United States
| | - Jennifer A Faust
- Department of Chemistry, The College of Wooster, Wooster, OH, 44691, United States
| | - Mark J Snider
- Department of Chemistry, The College of Wooster, Wooster, OH, 44691, United States
| | - Katherine A Hicks
- Department of Chemistry, State University of New York at Cortland, Cortland, NY, 13045, United States.
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13
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Sun P, Xu S, Tian Y, Chen P, Wu D, Zheng P. 4-Hydroxyphenylacetate 3-Hydroxylase (4HPA3H): A Vigorous Monooxygenase for Versatile O-Hydroxylation Applications in the Biosynthesis of Phenolic Derivatives. Int J Mol Sci 2024; 25:1222. [PMID: 38279222 PMCID: PMC10816480 DOI: 10.3390/ijms25021222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
4-Hydroxyphenylacetate 3-hydroxylase (4HPA3H) is a long-known class of two-component flavin-dependent monooxygenases from bacteria, including an oxygenase component (EC 1.14.14.9) and a reductase component (EC 1.5.1.36), with the latter being accountable for delivering the cofactor (reduced flavin) essential for o-hydroxylation. 4HPA3H has a broad substrate spectrum involved in key biological processes, including cellular catabolism, detoxification, and the biosynthesis of bioactive molecules. Additionally, it specifically hydroxylates the o-position of the C4 position of the benzene ring in phenolic compounds, generating high-value polyhydroxyphenols. As a non-P450 o-hydroxylase, 4HPA3H offers a viable alternative for the de novo synthesis of valuable natural products. The enzyme holds the potential to replace plant-derived P450s in the o-hydroxylation of plant polyphenols, addressing the current significant challenge in engineering specific microbial strains with P450s. This review summarizes the source distribution, structural properties, and mechanism of 4HPA3Hs and their application in the biosynthesis of natural products in recent years. The potential industrial applications and prospects of 4HPA3H biocatalysts are also presented.
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Affiliation(s)
| | | | | | | | | | - Pu Zheng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (P.S.); (Y.T.); (P.C.); (D.W.)
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14
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Martins TM, Bento A, Martins C, Tomé AS, Moreira CJS, Silva Pereira C. Bringing up to date the toolkit for the catabolism of aromatic compounds in fungi: The unexpected 1,2,3,5-tetrahydroxybenzene central pathway. Microb Biotechnol 2024; 17:e14371. [PMID: 38064205 PMCID: PMC10832562 DOI: 10.1111/1751-7915.14371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/04/2023] [Accepted: 11/01/2023] [Indexed: 02/03/2024] Open
Abstract
Saprophytic fungi are able to catabolize many plant-derived aromatics, including, for example, gallate. The catabolism of gallate in fungi is assumed to depend on the five main central pathways, i.e., of the central intermediates' catechol, protocatechuate, hydroxyquinol, homogentisate and gentisate, but a definitive demonstration is lacking. To shed light on this process, we analysed the transcriptional reprogramming of the growth of Aspergillus terreus on gallate compared with acetate as the control condition. Surprisingly, the results revealed that the five main central pathways did not exhibit significant positive regulation. Instead, an in-depth analysis identified four highly expressed and upregulated genes that are part of a conserved gene cluster found in numerous species of fungi, though not in Aspergilli. The cluster comprises a monooxygenase gene and a fumarylacetoacetate hydrolase-like gene, which are recognized as key components of catabolic pathways responsible for aromatic compound degradation. The other two genes encode proteins with no reported enzymatic activities. Through functional analyses of gene deletion mutants in Aspergillus nidulans, the conserved short protein with no known domains could be linked to the conversion of the novel metabolite 5-hydroxydienelatone, whereas the DUF3500 gene likely encodes a ring-cleavage enzyme for 1,2,3,5-tetrahydroxybenzene. These significant findings establish the existence of a new 1,2,3,5-tetrahydroxybenzene central pathway for the catabolism of gallate and related compounds (e.g. 2,4,6-trihydroxybenzoate) in numerous fungi where this catabolic gene cluster was observed.
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Affiliation(s)
- Tiago M. Martins
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de Lisboa (ITQB NOVA)OeirasPortugal
| | - Artur Bento
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de Lisboa (ITQB NOVA)OeirasPortugal
| | - Celso Martins
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de Lisboa (ITQB NOVA)OeirasPortugal
- Present address:
Center for Integrative Genomics, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Ana S. Tomé
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de Lisboa (ITQB NOVA)OeirasPortugal
| | - Carlos J. S. Moreira
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de Lisboa (ITQB NOVA)OeirasPortugal
| | - Cristina Silva Pereira
- Instituto de Tecnologia Química e Biológica António XavierUniversidade Nova de Lisboa (ITQB NOVA)OeirasPortugal
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15
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Boonkumkrong R, Chunthaboon P, Munkajohnpong P, Watthaisong P, Pimviriyakul P, Maenpuen S, Chaiyen P, Tinikul R. A high catalytic efficiency and chemotolerant formate dehydrogenase from Bacillus simplex. Biotechnol J 2024; 19:e2300330. [PMID: 38180313 DOI: 10.1002/biot.202300330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 01/06/2024]
Abstract
NAD+ -dependent formate dehydrogenase (FDH) catalyzes the conversion of formate and NAD+ to produce carbon dioxide and NADH. The reaction is biotechnologically important because FDH is widely used for NADH regeneration in various enzymatic syntheses. However, major drawbacks of this versatile enzyme in industrial applications are its low activity, requiring its utilization in large amounts to achieve optimal process conditions. Here, FDH from Bacillus simplex (BsFDH) was characterized for its biochemical and catalytic properties in comparison to FDH from Pseudomonas sp. 101 (PsFDH), a commonly used FDH in various biocatalytic reactions. The data revealed that BsFDH possesses high formate oxidizing activity with a kcat value of 15.3 ± 1.9 s-1 at 25°C compared to 7.7 ± 1.0 s-1 for PsFDH. At the optimum temperature (60°C), BsFDH exhibited 6-fold greater activity than PsFDH. The BsFDH displayed higher pH stability and a superior tolerance toward sodium azide and H2 O2 inactivation, showing a 200-fold higher Ki value for azide inhibition and remaining stable in the presence of 0.5% H2 O2 compared to PsFDH. The application of BsFDH as a cofactor regeneration system for the detoxification of 4-nitrophenol by the reaction of HadA, which produced a H2 O2 byproduct was demonstrated. The biocatalytic cascades using BsFDH demonstrated a distinct superior conversion activity because the system tolerated H2 O2 well. Altogether, the data showed that BsFDH is a robust enzyme suitable for future application in industrial biotechnology.
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Affiliation(s)
- Rattima Boonkumkrong
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Paweenapon Chunthaboon
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pobthum Munkajohnpong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
| | - Pratchaya Watthaisong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
| | - Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
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16
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Liu Y, Zhou H, Zhao S, Hao X, Dai G, Zhong L, Ren X, Sui H, Zhang Y, Yan F, Bian X. Biosynthesis of trans-AT PKS-Derived Shuangdaolides Featuring a trans-acting Enzyme for Online Epoxidation. ACS Chem Biol 2023; 18:2474-2484. [PMID: 37992317 DOI: 10.1021/acschembio.3c00368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) synthesize natural products with intricate structures and potent biological activities. They generally contain various unusual modules or trans-acting enzymes. Herein, we report the trans-AT PKS-derived biosynthetic pathway of the shuangdaolide with a rare internal 2-hydroxycyclopentenone moiety. The multidomain protein SdlR catalyzes the synthesis of 16,17-epoxide during polyketide chain elongation. The SdlR contains a ketoreductase, an acyl carrier protein, a flavoprotein monooxygenase, and a serine hydrolase domain. This online epoxidation occurs at unusual positions away from the thioester. Then, two tailoring enzymes, SdlB and SdlQ, convert a methylene to a carbonyl group and oxidize a hydroxyl group to a carbonyl group, respectively. The following spontaneous opening of 16,17-epoxide induces the formation of a new C-C bond to generate the 2-hydroxycyclopentenone moiety. The characterization of the shuangdaolide pathway extends the understanding of the trans-AT PKSs, facilitating the mining and identification of this class of natural products.
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Affiliation(s)
- Yang Liu
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Shuang Zhao
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xingkun Hao
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Guangzhi Dai
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Lin Zhong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiangmei Ren
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Haiyan Sui
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fu Yan
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
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17
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Zubova E, Pokluda A, Dvořáková H, Krupička M, Cibulka R. Exploring the Reactivity of Flavins with Nucleophiles Using a Theoretical and Experimental Approach. Chempluschem 2023:e202300547. [PMID: 38064649 DOI: 10.1002/cplu.202300547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/30/2023] [Indexed: 01/13/2024]
Abstract
Covalent adducts of flavin cofactors with nucleophiles play an important role in non-canonical function of flavoenzymes as well as in flavin-based catalysis. Herein, the interaction of flavin derivatives including substituted flavins (isoalloxazines), 1,10-ethylene-bridged flavinium salts, and non-substituted alloxazine and deazaflavin with selected nucleophiles was investigated using an experimental and computational approach. Triphenylphosphine or trimethylphosphine, 1-nitroethan-1-ide, and methoxide were selected as representatives of neutral soft, anionic soft, and hard nucleophiles, respectively. The interactions were investigated using UV/Vis and 1 H NMR spectroscopy as well as by DFT calculations. The position of nucleophilic attack estimated using the calculated Gibbs free energy values was found to correspond with the experimental data, favouring the addition of phosphine and 1-nitroethan-1-ide into position N(5) and methoxide into position C(10a) of 1,10-ethylene-bridged flavinium salts. The calculated Gibbs free energy values were found to correlate with the experimental redox potentials of the flavin derivatives tested. These findings can be utilized as valuable tools for the design of artificial flavin-based catalytic systems or investigating the mechanism of flavoenzymes.
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Affiliation(s)
- Ekaterina Zubova
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Adam Pokluda
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Hana Dvořáková
- Central Laboratories, University of Chemistry and Technology, Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Martin Krupička
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Radek Cibulka
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28, Prague, Czech Republic
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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Grandi E, Feyza Özgen F, Schmidt S, Poelarends GJ. Enzymatic Oxy- and Amino-Functionalization in Biocatalytic Cascade Synthesis: Recent Advances and Future Perspectives. Angew Chem Int Ed Engl 2023; 62:e202309012. [PMID: 37639631 DOI: 10.1002/anie.202309012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
Biocatalytic cascades are a powerful tool for building complex molecules containing oxygen and nitrogen functionalities. Moreover, the combination of multiple enzymes in one pot offers the possibility to minimize downstream processing and waste production. In this review, we illustrate various recent efforts in the development of multi-step syntheses involving C-O and C-N bond-forming enzymes to produce high value-added compounds, such as pharmaceuticals and polymer precursors. Both in vitro and in vivo examples are discussed, revealing the respective advantages and drawbacks. The use of engineered enzymes to boost the cascades outcome is also addressed and current co-substrate and cofactor recycling strategies are presented, highlighting the importance of atom economy. Finally, tools to overcome current challenges for multi-enzymatic oxy- and amino-functionalization reactions are discussed, including flow systems with immobilized biocatalysts and cascades in confined nanomaterials.
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Affiliation(s)
- Eleonora Grandi
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Fatma Feyza Özgen
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Gerrit J Poelarends
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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20
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Nicoll C, Mascotti M. Investigating the biochemical signatures and physiological roles of the FMO family using molecular phylogeny. BBA Adv 2023; 4:100108. [PMID: 38034983 PMCID: PMC10682829 DOI: 10.1016/j.bbadva.2023.100108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023] Open
Abstract
Group B flavin-dependent monooxygenases are employed in swathes of different physiological functions. Despite their collectively large substrate profile, they all harness a flavin-based C4a-(hydro)peroxy intermediate for function. Within this class are the flavin-containing monooxygenases (FMOs), representing an integral component within the secondary metabolism of all living things - xenobiotic detoxification. Their broad substrate profile makes them ideal candidates for detoxifying procedures as they can tackle a range of compounds. Recent studies have illustrated that several FMOs, however, have unique substrate profiles and differing physiological functions that implicate new roles within secondary and primary metabolism. Herein this article, by employing phylogenetic approaches, and inspecting structures of AlphaFold generated models, we have constructed a biochemical blueprint of the FMO family. FMOs are clustered in four distinct groups, with two being predominantly dedicated to xenobiotic detoxification. Furthermore, we observe that differing enzymatic activities are not constricted to a 'golden' set of residues but instead an intricate constellation of primary and secondary sphere residues. We believe that this work delineates the core phylogeny of the Group B monooxygenases and will prove useful for classifying newly sequenced genes and provide directions to future biochemical investigations.
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Affiliation(s)
- C.R. Nicoll
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - M.L. Mascotti
- Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG Groningen, The Netherlands
- IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, Ejercito de los Andes 950, D5700HHW, San Luis, Argentina
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21
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Wang Q, Liu N, Deng Y, Guan Y, Xiao H, Nitka TA, Yang H, Yadav A, Vukovic L, Mathews II, Chen X, Kim CY. Triepoxide formation by a flavin-dependent monooxygenase in monensin biosynthesis. Nat Commun 2023; 14:6273. [PMID: 37805629 PMCID: PMC10560226 DOI: 10.1038/s41467-023-41889-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 09/18/2023] [Indexed: 10/09/2023] Open
Abstract
Monensin A is a prototypical natural polyether polyketide antibiotic. It acts by binding a metal cation and facilitating its transport across the cell membrane. Biosynthesis of monensin A involves construction of a polyene polyketide backbone, subsequent epoxidation of the alkenes, and, lastly, formation of cyclic ethers via epoxide-opening cyclization. MonCI, a flavin-dependent monooxygenase, is thought to transform all three alkenes in the intermediate polyketide premonensin A into epoxides. Our crystallographic study has revealed that MonCI's exquisite stereocontrol is due to the preorganization of the active site residues which allows only one specific face of the alkene to approach the reactive C(4a)-hydroperoxyflavin moiety. Furthermore, MonCI has an unusually large substrate-binding cavity that can accommodate premonensin A in an extended or folded conformation which allows any of the three alkenes to be placed next to C(4a)-hydroperoxyflavin. MonCI, with its ability to perform multiple epoxidations on the same substrate in a stereospecific manner, demonstrates the extraordinary versatility of the flavin-dependent monooxygenase family of enzymes.
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Affiliation(s)
- Qian Wang
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Avenue, El Paso, TX, 79968, USA
| | - Ning Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710127, Xi'an, China
| | - Yaming Deng
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710127, Xi'an, China
| | - Yuze Guan
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710127, Xi'an, China
| | - Hongli Xiao
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710127, Xi'an, China
| | - Tara A Nitka
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Avenue, El Paso, TX, 79968, USA
| | - Hui Yang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710127, Xi'an, China
| | - Anju Yadav
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Avenue, El Paso, TX, 79968, USA
| | - Lela Vukovic
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Avenue, El Paso, TX, 79968, USA
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 95124, USA
| | - Xi Chen
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710127, Xi'an, China.
| | - Chu-Young Kim
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 West University Avenue, El Paso, TX, 79968, USA.
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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22
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Nonaka K, Osamura T, Takahashi F. A 4-hydroxybenzoate 3-hydroxylase mutant enables 4-amino-3-hydroxybenzoic acid production from glucose in Corynebacterium glutamicum. Microb Cell Fact 2023; 22:168. [PMID: 37644492 PMCID: PMC10466732 DOI: 10.1186/s12934-023-02179-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Microbial production of aromatic chemicals is an attractive method for obtaining high-performance materials from biomass resources. A non-proteinogenic amino acid, 4-amino-3-hydroxybenzoic acid (4,3-AHBA), is expected to be a precursor of highly functional polybenzoxazole polymers; however, methods for its microbial production have not been reported. In this study, we attempted to produce 4,3-AHBA from glucose by introducing 3-hydroxylation of 4-aminobenzoic acid (4-ABA) into the metabolic pathway of an industrially relevant bacterium, Corynebacterium glutamicum. RESULTS Six different 4-hydroxybenzoate 3-hydroxylases (PHBHs) were heterologously expressed in C. glutamicum strains, which were then screened for the production of 4,3-AHBA by culturing with glucose as a carbon source. The highest concentration of 4,3-AHBA was detected in the strain expressing PHBH from Caulobacter vibrioides (CvPHBH). A combination of site-directed mutagenesis in the active site and random mutagenesis via laccase-mediated colorimetric assay allowed us to obtain CvPHBH mutants that enhanced 4,3-AHBA productivity under deep-well plate culture conditions. The recombinant C. glutamicum strain expressing CvPHBHM106A/T294S and having an enhanced 4-ABA biosynthetic pathway produced 13.5 g/L (88 mM) 4,3-AHBA and 0.059 g/L (0.43 mM) precursor 4-ABA in fed-batch culture using a nutrient-rich medium. The culture of this strain in the chemically defined CGXII medium yielded 9.8 C-mol% of 4,3-AHBA from glucose, corresponding to 12.8% of the theoretical maximum yield (76.8 C-mol%) calculated using a genome-scale metabolic model of C. glutamicum. CONCLUSIONS Identification of PHBH mutants that could efficiently catalyze the 3-hydroxylation of 4-ABA in C. glutamicum allowed us to construct an artificial biosynthetic pathway capable of producing 4,3-AHBA on a gram-scale using glucose as the carbon source. These findings will contribute to a better understanding of enzyme-catalyzed regioselective hydroxylation of aromatic chemicals and to the diversification of biomass-derived precursors for high-performance materials.
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Affiliation(s)
- Kyoshiro Nonaka
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640-8580, Japan.
| | - Tatsuya Osamura
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640-8580, Japan
| | - Fumikazu Takahashi
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, Wakayama, 640-8580, Japan
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23
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Hou Y, Zhao W, Ding X, Zhang X, Li Z, Tan Z, Zhou J, Wang H, Jia S. Co-production of 7-chloro-tryptophan and indole pyruvic acid based on an efficient FAD/FADH 2 regeneration system. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12619-9. [PMID: 37354265 DOI: 10.1007/s00253-023-12619-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/26/2023]
Abstract
Efficient FAD/FADH2 regeneration is vital for enzymatic biocatalysis and metabolic pathway optimization. Here, we constructed an efficient and simple FAD/FADH2 regeneration system through a combination of L-amino acid deaminase (L-AAD) and halogenase (CombiAADHa), which was applied for catalyzing the conversion of an L-amino acid to halide and an α-keto acid. For cell-free biotransformation, the optimal activity ratio of L-AAD and halogenase was set between 1:50 and 1:60. Within 6 h, 170 mg/L of 7-chloro-tryptophan (7-Cl-Trp) and 193 mg/L of indole pyruvic acid (IPA) were synthesized in the selected mono-amino acid system. For whole-cell biotransformation, 7-Cl-Trp and IPA synthesis was enhanced by 15% (from 96 to 110 mg/L) and 12% (from 115 to 129 mg/L), respectively, through expression fine-tuning and the strengthening of FAD/FADH2 supply. Finally, ultrasound treatment was applied to improve membrane permeability and adjust the activity ratio, resulting in 1.6-and 1.4-fold higher 7-Cl-Trp and IPA yields. The products were then purified. This system could also be applied to the synthesis of other halides and α-keto acids. KEY POINTS: • In this study, a whole cell FAD/FADH2 regeneration system co-expressing l-AAD and halogenase was constructed • This study found that the activity and ratio of enzyme and the concentration of cofactors had a significant effect on the catalytic process for the efficient co-production of 7-chlorotryptophan and indole pyruvate.
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Affiliation(s)
- Ying Hou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Food Science and Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Wanying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Food Science and Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Xincheng Ding
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Food Science and Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Xuan Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Food Science and Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Zhibin Li
- College of Agronomy and Resources Environment, Tianjin Agricultural University, Tianjin, 300384, People's Republic of China
| | - Zhilei Tan
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Food Science and Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, People's Republic of China
| | - Hongxing Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Food Science and Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Shiru Jia
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Food Science and Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
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24
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Abstract
Flavoenzymes are highly versatile and participate in the catalysis of a wide range of reactions, including key reactions in the metabolism of sulfur-containing compounds. S-Alkyl cysteine is formed primarily by the degradation of S-alkyl glutathione generated during electrophile detoxification. A recently discovered S-alkyl cysteine salvage pathway uses two flavoenzymes (CmoO and CmoJ) to dealkylate this metabolite in soil bacteria. CmoO catalyzes a stereospecific sulfoxidation, and CmoJ catalyzes the cleavage of one of the sulfoxide C-S bonds in a new reaction of unknown mechanism. In this paper, we investigate the mechanism of CmoJ. We provide experimental evidence that eliminates carbanion and radical intermediates and conclude that the reaction proceeds via an unprecedented enzyme-mediated modified Pummerer rearrangement. The elucidation of the mechanism of CmoJ adds a new motif to the flavoenzymology of sulfur-containing natural products and demonstrates a new strategy for the enzyme-catalyzed cleavage of C-S bonds.
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Affiliation(s)
- Sohan Hazra
- Department of Chemistry, Texas A&M University, College
Station, Texas 77843, United States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College
Station, Texas 77843, United States
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25
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Nishida I, Ohmori Y, Yanai R, Nishihara S, Matsuo Y, Kaino T, Hirata D, Kawamukai M. Identification of novel coenzyme Q 10 biosynthetic proteins Coq11 and Coq12 in Schizosaccharomyces pombe. J Biol Chem 2023; 299:104797. [PMID: 37156397 PMCID: PMC10279924 DOI: 10.1016/j.jbc.2023.104797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023] Open
Abstract
Coenzyme Q (CoQ) is an essential component of the electron transport system in aerobic organisms. CoQ10 has ten isoprene units in its quinone structure and is especially valuable as a food supplement. However, the CoQ biosynthetic pathway has not been fully elucidated, including synthesis of the p-hydroxybenzoic acid (PHB) precursor to form a quinone backbone. To identify the novel components of CoQ10 synthesis, we investigated CoQ10 production in 400 Schizosaccharomyces pombe gene-deleted strains in which individual mitochondrial proteins were lost. We found that deletion of coq11 (an S. cerevisiae COQ11 homolog) and a novel gene designated coq12 lowered CoQ levels to ∼4% of that of the WT strain. Addition of PHB or p-hydroxybenzaldehyde restored the CoQ content and growth and lowered hydrogen sulfide production of the Δcoq12 strain, but these compounds did not affect the Δcoq11 strain. The primary structure of Coq12 has a flavin reductase motif coupled with an NAD+ reductase domain. We determined that purified Coq12 protein from S. pombe displayed NAD+ reductase activity when incubated with ethanol-extracted substrate of S. pombe. Because purified Coq12 from Escherichia coli did not exhibit reductase activity under the same conditions, an extra protein is thought to be necessary for its activity. Analysis of Coq12-interacting proteins by LC-MS/MS revealed interactions with other Coq proteins, suggesting formation of a complex. Thus, our analysis indicates that Coq12 is required for PHB synthesis, and it has diverged among species.
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Affiliation(s)
- Ikuhisa Nishida
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Matsue, Japan; Sakeology Center, Niigata University, Niigata, Japan
| | - Yuki Ohmori
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Matsue, Japan
| | - Ryota Yanai
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Matsue, Japan
| | - Shogo Nishihara
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Matsue, Japan
| | - Yasuhiro Matsuo
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Matsue, Japan; Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Japan
| | - Tomohiro Kaino
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Matsue, Japan; Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Japan
| | - Dai Hirata
- Sakeology Center, Niigata University, Niigata, Japan
| | - Makoto Kawamukai
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Matsue, Japan; Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Japan.
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26
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Perkins SW, Hlaing MZ, Hicks KA, Rajakovich LJ, Snider MJ. Mechanism of the Multistep Catalytic Cycle of 6-Hydroxynicotinate 3-Monooxygenase Revealed by Global Kinetic Analysis. Biochemistry 2023; 62:1553-1567. [PMID: 37130364 DOI: 10.1021/acs.biochem.2c00514] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The class A flavoenzyme 6-hydroxynicotinate 3-monooxygenase (NicC) catalyzes a rare decarboxylative hydroxylation reaction in the degradation of nicotinate by aerobic bacteria. While the structure and critical residues involved in catalysis have been reported, the mechanism of this multistep enzyme has yet to be determined. A kinetic understanding of the NicC mechanism would enable comparison to other phenolic hydroxylases and illuminate its bioengineering potential for remediation of N-heterocyclic aromatic compounds. Toward these goals, transient state kinetic analyses by stopped-flow spectrophotometry were utilized to follow rapid changes in flavoenzyme absorbance spectra during all three stages of NicC catalysis: (1) 6-HNA binding; (2) NADH binding and FAD reduction; and (3) O2 binding with C4a-adduct formation, substrate hydroxylation, and FAD regeneration. Global kinetic simulations by numeric integration were used to supplement analytical fitting of time-resolved data and establish a kinetic mechanism. Results indicate that 6-HNA binding is a two-step process that substantially increases the affinity of NicC for NADH and enables the formation of a charge-transfer-complex intermediate to enhance the rate of flavin reduction. Singular value decomposition of the time-resolved spectra during the reaction of the substrate-bound, reduced enzyme with dioxygen provides evidence for the involvement of C4a-hydroperoxy-flavin and C4a-hydroxy-flavin intermediates in NicC catalysis. Global analysis of the full kinetic mechanism suggests that steady-state catalytic turnover is partially limited by substrate hydroxylation and C4a-hydroxy-flavin dehydration to regenerate the flavoenzyme. Insights gleaned from the kinetic model and determined microscopic rate constants provide a fundamental basis for understanding NicC's substrate specificity and reactivity.
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Affiliation(s)
- Scott W Perkins
- Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
| | - May Z Hlaing
- Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
| | - Katherine A Hicks
- Department of Chemistry, The State University of New York College at Cortland, Cortland, New York 13045, United States
| | - Lauren J Rajakovich
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mark J Snider
- Department of Chemistry, The College of Wooster, Wooster, Ohio 44691, United States
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27
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Stewart A, Dershwitz P, Stewart C, Sawaya MR, Yeates TO, Semrau JD, Zischka H, DiSpirito AA, Bobik TA. Crystal structure of MbnF: an NADPH-dependent flavin monooxygenase from Methylocystis strain SB2. Acta Crystallogr F Struct Biol Commun 2023; 79:111-118. [PMID: 37158309 PMCID: PMC10167746 DOI: 10.1107/s2053230x23003035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/02/2023] [Indexed: 05/10/2023] Open
Abstract
Methanobactins (MBs) are ribosomally produced and post-translationally modified peptides (RiPPs) that are used by methanotrophs for copper acquisition. The signature post-translational modification of MBs is the formation of two heterocyclic groups, either an oxazolone, pyrazinedione or imidazolone group, with an associated thioamide from an X-Cys dipeptide. The precursor peptide (MbnA) for MB formation is found in a gene cluster of MB-associated genes. The exact biosynthetic pathway of MB formation is not yet fully understood, and there are still uncharacterized proteins in some MB gene clusters, particularly those that produce pyrazinedione or imidazolone rings. One such protein is MbnF, which is proposed to be a flavin monooxygenase (FMO) based on homology. To help to elucidate its possible function, MbnF from Methylocystis sp. strain SB2 was recombinantly produced in Escherichia coli and its X-ray crystal structure was resolved to 2.6 Å resolution. Based on its structural features, MbnF appears to be a type A FMO, most of which catalyze hydroxylation reactions. Preliminary functional characterization shows that MbnF preferentially oxidizes NADPH over NADH, supporting NAD(P)H-mediated flavin reduction, which is the initial step in the reaction cycle of several type A FMO enzymes. It is also shown that MbnF binds the precursor peptide for MB, with subsequent loss of the leader peptide sequence as well as the last three C-terminal amino acids, suggesting that MbnF might be needed for this process to occur. Finally, molecular-dynamics simulations revealed a channel in MbnF that is capable of accommodating the core MbnA fragment minus the three C-terminal amino acids.
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Affiliation(s)
- Andrew Stewart
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011-3260, USA
| | - Philip Dershwitz
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011-3260, USA
| | - Charles Stewart
- Macromolecular X-ray Crystallography Facility, Office of Biotechnology, Iowa State University, Ames, IA 50011-3260, USA
| | - Michael R Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095-1570, USA
| | - Todd O Yeates
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095-1570, USA
| | - Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
| | - Hans Zischka
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011-3260, USA
| | - Thomas A Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011-3260, USA
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Ma Q, Meng N, Su J, Li Y, Gu J, Wang Y, Wang J, Qu Y, Zhao Z, Sun Y. Unraveling the skatole biodegradation process in an enrichment consortium using integrated omics and culture-dependent strategies. J Environ Sci (China) 2023; 127:688-699. [PMID: 36522097 DOI: 10.1016/j.jes.2022.06.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 06/17/2023]
Abstract
3-Methylindole (skatole) is regarded as one of the most offensive compounds in odor emission. Biodegradation is feasible for skatole removal but the functional species and genes responsible for skatole degradation remain enigmatic. In this study, an efficient aerobic skatole-degrading consortium was obtained. Rhodococcus and Pseudomonas were identified as the two major and active populations by integrated metagenomic and metatranscriptomic analyses. Bioinformatic analyses indicated that the skatole downstream degradation was mainly via the catechol pathway, and upstream degradation was likely catalyzed by the aromatic ring-hydroxylating oxygenase and flavin monooxygenase. Genome binning and gene analyses indicated that Pseudomonas, Pseudoclavibacter, and Raineyella should cooperate with Rhodococcus for the skatole degradation process. Moreover, a pure strain Rhodococcus sp. DMU1 was successfully obtained which could utilize skatole as the sole carbon source. Complete genome sequencing showed that strain DMU1 was the predominant population in the consortium. Further crude enzyme and RT-qPCR assays indicated that strain DMU1 degraded skatole through the catechol ortho-cleavage pathway. Collectively, our results suggested that synergistic degradation of skatole in the consortium should be performed by diverse bacteria with Rhodococcus as the primary degrader, and the degradation mainly proceeded via the catechol pathway.
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Affiliation(s)
- Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China.
| | - Nan Meng
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jiancheng Su
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yujie Li
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jiazheng Gu
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yidi Wang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jingwei Wang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zelong Zhao
- Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China.
| | - Yeqing Sun
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
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29
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Kurt Z, Qu Y, Spain JC. Novel catabolic pathway for 4-Nitroaniline in a Rhodococcus sp. strain JS360. J Hazard Mater 2023; 454:131473. [PMID: 37146325 DOI: 10.1016/j.jhazmat.2023.131473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/03/2023] [Accepted: 04/21/2023] [Indexed: 05/07/2023]
Abstract
4-Nitroaniline (4NA), the starting material for the first synthesized azo dye, is a toxic compound found in industrial wastewaters. Several bacterial strains capable of 4NA biodegradation were previously reported but the details of the catabolic pathway were not established. To search for novel metabolic diversity, we isolated a Rhodococcus sp. Strain JS360 by selective enrichment from 4NA-contaminated soil. When grown on 4NA the isolate accumulated biomass released stoichiometric amounts of nitrite and released less than stoichiometric amounts of ammonia, indicating that 4NA was used as sole carbon and nitrogen source to support growth and mineralization. Enzyme assays coupled with respirometry provided preliminary evidence that the first and second steps of 4NA degradation involve monooxygenase-catalyzed reactions followed by ring cleavage prior to deamination. Sequencing and annotation of the whole genome revealed candidate monooxygenases that were subsequently cloned and expressed in E.coli. Heterologously expressed 4NA monooxygenase (NamA) and 4-aminophenol (4AP) monooxygenase (NamB) transformed 4NA to 4AP and 4AP to 4-aminoresorcinol (4AR) respectively. The results revealed a novel pathway for nitroanilines and defined two monooxygenase mechanisms likely to be involved in the biodegradation of similar compounds.
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Affiliation(s)
- Zohre Kurt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0512, Georgia; Middle East Technical University, Ankara, Turkey; Florida State University Panamá, Panama.
| | - Yi Qu
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0512, Georgia
| | - Jim C Spain
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0512, Georgia; Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, FL 32514-5751, United States
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Xiang L, Shi J, Zhu A, Xu ZF, Liu SH, Wang YS, Guo ZK, Jiao RH, Tan RX, Ge HM. Total Biosynthesis of Mutaxanthene Unveils a Flavoprotein Monooxygenase Catalyzing Xanthene Ring Formation. Angew Chem Int Ed Engl 2023; 62:e202218660. [PMID: 36727486 DOI: 10.1002/anie.202218660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/03/2023]
Abstract
Flavoprotein monooxygenases (FPMOs) play important roles in generating structural complexity and diversity in natural products biosynthesized by type II polyketide synthases (PKSs). In this study, we used genome mining to discover novel mutaxanthene analogues and investigated the biosynthesis of these aromatic polyketides and their unusual xanthene framework. We determined the complete biosynthetic pathway of mutaxathene through in vivo gene deletion and in vitro biochemical experiments. We show that a multifunctional FPMO, MtxO4, catalyzes ring rearrangement and generates the required xanthene ring through a multistep transformation. In addition, we successfully obtained all necessary enzymes for in vitro reconstitution and completed the total biosynthesis of mutaxanthene in a stepwise manner. Our results revealed the formation of a rare xanthene ring in type II polyketide biosynthesis, and demonstrate the potential of using total biosynthesis for the discovery of natural products synthesized by type II PKSs.
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Affiliation(s)
- Lang Xiang
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jing Shi
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ao Zhu
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Zi Fei Xu
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Shuang He Liu
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yi Shuang Wang
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Zhi Kai Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Rui Hua Jiao
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
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31
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Kratky J, Eggerichs D, Heine T, Hofmann S, Sowa P, Weiße RH, Tischler D, Sträter N. Structural and Mechanistic Studies on Substrate and Stereoselectivity of the Indole Monooxygenase VpIndA1: New Avenues for Biocatalytic Epoxidations and Sulfoxidations. Angew Chem Int Ed Engl 2023; 62:e202300657. [PMID: 36762980 DOI: 10.1002/anie.202300657] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/11/2023]
Abstract
Flavoprotein monooxygenases are a versatile group of enzymes for biocatalytic transformations. Among these, group E monooxygenases (GEMs) catalyze enantioselective epoxidation and sulfoxidation reactions. Here, we describe the crystal structure of an indole monooxygenase from the bacterium Variovorax paradoxus EPS, a GEM designated as VpIndA1. Complex structures with substrates reveal productive binding modes that, in conjunction with force-field calculations and rapid mixing kinetics, reveal the structural basis of substrate and stereoselectivity. Structure-based redesign of the substrate cavity yielded variants with new substrate selectivity (for sulfoxidation of benzyl phenyl sulfide) or with greatly enhanced stereoselectivity (from 35.1 % to 99.8 % ee for production of (1S,2R)-indene oxide). This first determination of the substrate binding mode of GEMs combined with structure-function relationships opens the door for structure-based design of these powerful biocatalysts.
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Affiliation(s)
- Julia Kratky
- Institute of Bioanalytical Chemistry, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Daniel Eggerichs
- Microbial Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Thomas Heine
- Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Sarah Hofmann
- Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Philipp Sowa
- Microbial Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Renato H Weiße
- Institute of Bioanalytical Chemistry, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Dirk Tischler
- Microbial Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780, Bochum, Germany.,Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
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32
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Yu Z, Huang JP, Yang J, Liu C, Yan Y, Wang L, Zhao J, Chen Y, Xiang W, Huang SX. Discovery and biosynthesis of karnamicins as angiotensin converting enzyme inhibitors. Nat Commun 2023; 14:209. [PMID: 36639377 DOI: 10.1038/s41467-023-35829-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Angiotensin-converting enzyme inhibitors are widely used for treatment of hypertension and related diseases. Here, six karnamicins E1-E6 (1-6), which bear fully substituted hydroxypyridine and thiazole moieties are characterized from the rare actinobacterium Lechevalieria rhizosphaerae NEAU-A2. Through a combination of isotopic labeling, genome mining, and enzymatic characterization studies, the programmed assembly of the fully substituted hydroxypyridine moiety in karnamicin is proposed to be due to sequential operation of a hybrid polyketide synthase-nonribosomal peptide synthetase, two regioselective pyridine ring flavoprotein hydroxylases, and a methyltransferase. Based on AlphaFold protein structures predictions, molecular docking, and site-directed mutagenesis, we find that two pyridine hydroxylases deploy active site residues distinct from other flavoprotein monooxygenases to direct the chemo- and regioselective hydroxylation of the pyridine nucleus. Pleasingly, karnamicins show significant angiotensin-converting enzyme inhibitory activity with IC50 values ranging from 0.24 to 5.81 μM, suggesting their potential use for the treatment of hypertension and related diseases.
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Li Y, Ma Q, Zhang J, Meng N, Su J, Wang J. Transcriptomic profiling reveals the molecular responses of Rhodococcus aetherivorans DMU1 to skatole stress. Ecotoxicol Environ Saf 2023; 249:114464. [PMID: 38321683 DOI: 10.1016/j.ecoenv.2022.114464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 02/08/2024]
Abstract
Skatole is a typical malodor compound in animal wastes. Several skatole-degrading bacterial strains have been obtained, whereas the molecular response of strains to skatole stress has not been well elucidated. Herein, the skatole degradation by a Gram-positive strain Rhodococcus aetherivorans DMU1 was investigated. Strain DMU1 showed high efficiency in skatole degradation under the conditions of 25-40 °C and pH 7.0-10.0. It could utilize various aromatics, including cresols, phenol, and methylindoles, as the sole carbon source for growth, implying its potential in the bioremediation application of animal wastes. Transcriptomic sequencing revealed that 328 genes were up-regulated and 640 genes were down-regulated in strain DMU1 when grown in the skatole-containing medium. Skatole increased the gene expression levels of antioxidant defense systems and heat shock proteins. The expression of ribosome-related genes was significantly inhibited which implied the growth inhibition of skatole. A rich set of oxidoreductases were changed, and a novel gene cluster containing the flavoprotein monooxygenase and ring-hydroxylating oxygenase genes was highly up-regulated, which was probably involved in skatole upstream degradation. The upregulation pattern of this gene cluster was further verified by qRT-PCR assay. Furthermore, skatole should be mainly degraded via the catechol ortho-cleavage pathway with cat25170 as the functional gene. The gene cat25170 was cloned and expressed in E. coli BL21(DE3). Pure enzyme assays showed that Cat25170 could catalyze catechol with Km 9.96 μmol/L and kcat 12.36 s-1.
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Affiliation(s)
- Yujie Li
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Qiao Ma
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China.
| | - Jiaxin Zhang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Nan Meng
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jiancheng Su
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China; College of Life Sciences, Sichuan University, Sichuan 610064, China
| | - Jingwei Wang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
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34
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Suzuki H, Mori R, Kato M, Shimizu M. Biochemical characterization of hydroquinone hydroxylase from Phanerochaete chrysosporium. J Biosci Bioeng 2023; 135:17-24. [PMID: 36344390 DOI: 10.1016/j.jbiosc.2022.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
The white-rot fungus Phanerochaete chrysosporium can degrade lignin polymers using extracellular, non-specific, one-electron oxidizing enzymes. This results in the formation of guaiacyl (G), syringyl (S), and hydroxyphenyl (H) units, such as vanillic acid, syringic acid, and p-hydroxybenzoic acid (p-HBA) and the corresponding aldehydes, which are further metabolized intracellularly. Therefore, the aim of this study was to identify proteins involved in the hydroxylation of H-unit fragments such as p-HBA and its decarboxylated product hydroquinone (HQ) in P. chrysosporium. A flavoprotein monooxygenase (FPMO), PcFPMO2, was identified and its activity was characterized. Recombinant PcFPMO2 with an N-terminal polyhistidine tag was produced in Escherichia coli and purified. In the presence of NADPH, PcFPMO2 used six phenolic compounds as substrates. PcFPMO2 catalyzed the hydroxylation of the H-unit fragments such as p-HBA and HQ, and the G-unit derivative methoxyhydroquinone (MHQ). The highest catalytic efficiency (kcat/Km) was observed with HQ, indicating that PcFPMO2 could be involved in HQ hydroxylation in vivo. Additionally, PcFPMO2 converted MHQ to 3-, 5-, and 6-methoxy-1,2,4-trihydroxybenzene (3-, 5-, and 6-MTHB), respectively, suggesting that PcFPMO2 might partially be involved in MHQ degradation, following aromatic ring fission, via three MTHBs. FPMOs are divided into eight groups (groups A to H). This is the first study to show MHQ hydroxylase activity of a FPMO-group A superfamily member. These findings highlight the unique substrate spectrum of PcFPMO2, making it an attractive candidate for biotechnological applications.
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Affiliation(s)
- Hiromitsu Suzuki
- Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
| | - Reini Mori
- Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
| | - Masashi Kato
- Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan
| | - Motoyuki Shimizu
- Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, Nagoya, Aichi 468-8502, Japan.
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35
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Orsi E, Claassens NJ, Nikel PI, Lindner SN. Optimizing microbial networks through metabolic bypasses. Biotechnol Adv 2022; 60:108035. [PMID: 36096403 DOI: 10.1016/j.biotechadv.2022.108035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 01/29/2023]
Abstract
Metabolism has long been considered as a relatively stiff set of biochemical reactions. This somewhat outdated and dogmatic view has been challenged over the last years, as multiple studies exposed unprecedented plasticity of metabolism by exploring rational and evolutionary modifications within the metabolic network of cell factories. Of particular importance is the emergence of metabolic bypasses, which consist of enzymatic reaction(s) that support unnatural connections between metabolic nodes. Such novel topologies can be generated through the introduction of heterologous enzymes or by upregulating native enzymes (sometimes relying on promiscuous activities thereof). Altogether, the adoption of bypasses resulted in an expansion in the capacity of the host's metabolic network, which can be harnessed for bioproduction. In this review, we discuss modifications to the canonical architecture of central carbon metabolism derived from such bypasses towards six optimization purposes: stoichiometric gain, overcoming kinetic limitations, solving thermodynamic barriers, circumventing toxic intermediates, uncoupling product synthesis from biomass formation, and altering redox cofactor specificity. The metabolic costs associated with bypass-implementation are likewise discussed, including tailoring their design towards improving bioproduction.
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Affiliation(s)
- Enrico Orsi
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Department of Biochemistry, Charité Universitätsmedizin, Virchowweg 6, 10117 Berlin, Germany.
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36
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Liu Y, Chen Q, Zhu B, Pei X, Liu Y, Wu Z. Sequence-guided stereo-enhancing and -inverting of (R)-styrene monooxygenases for highly enantioselective epoxidation. Molecular Catalysis 2022; 531:112680. [DOI: 10.1016/j.mcat.2022.112680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Chen Y, Zhang J, Yang Y, Xiang K, Li H, Sun D, Chen L. Kynurenine‐3‐monooxygenase (KMO): From its biological functions to therapeutic effect in diseases progression. J Cell Physiol 2022; 237:4339-4355. [DOI: 10.1002/jcp.30876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/21/2022] [Accepted: 09/01/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Yanmei Chen
- Key Laboratory of Structure‐Based Drug Design & Discovery, Wuya College of Innovation, School of Traditional Chinese Materia Medica, Ministry of Education Shenyang Pharmaceutical University Shenyang China
| | - Jiahui Zhang
- Key Laboratory of Structure‐Based Drug Design & Discovery, Wuya College of Innovation, School of Traditional Chinese Materia Medica, Ministry of Education Shenyang Pharmaceutical University Shenyang China
| | - Yueying Yang
- Key Laboratory of Structure‐Based Drug Design & Discovery, Wuya College of Innovation, School of Traditional Chinese Materia Medica, Ministry of Education Shenyang Pharmaceutical University Shenyang China
| | - Ke Xiang
- Key Laboratory of Structure‐Based Drug Design & Discovery, Wuya College of Innovation, School of Traditional Chinese Materia Medica, Ministry of Education Shenyang Pharmaceutical University Shenyang China
| | - Hua Li
- Key Laboratory of Structure‐Based Drug Design & Discovery, Wuya College of Innovation, School of Traditional Chinese Materia Medica, Ministry of Education Shenyang Pharmaceutical University Shenyang China
- College of Pharmacy Fujian University of Traditional Chinese Medicine Fuzhou China
| | - Dejuan Sun
- Key Laboratory of Structure‐Based Drug Design & Discovery, Wuya College of Innovation, School of Traditional Chinese Materia Medica, Ministry of Education Shenyang Pharmaceutical University Shenyang China
| | - Lixia Chen
- Key Laboratory of Structure‐Based Drug Design & Discovery, Wuya College of Innovation, School of Traditional Chinese Materia Medica, Ministry of Education Shenyang Pharmaceutical University Shenyang China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Lin H, Meng Y, Li N, Tang Y, Dong S, Wu Z, Xu C, Kazlauskas R, Chen H. Enzymatic Enantioselective anti‐Markovnikov Hydration of Aryl Alkenes. Angew Chem Int Ed Engl 2022; 61:e202206472. [DOI: 10.1002/anie.202206472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Hui Lin
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| | - Yinyin Meng
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| | - Na Li
- College of Biological Engineering Henan University of Technology 100 Lianhua Street Zhengzhou 450001 China
| | - Yanhong Tang
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| | - Shuang Dong
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| | - Zhongliu Wu
- CAS Key Laboratory of Environmental and Applied Microbiology & Environmental Microbiology Key Laboratory of Sichuan Province Chengdu Institute of Biology Chinese Academy of Sciences Chengdu 610041 China
| | - Cuilian Xu
- College of Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| | - Romas Kazlauskas
- Department of Biochemistry Molecular Biology and Biophysics and the BioTechnology Institute University of Minnesota St Paul MN 55108 USA
| | - Hongge Chen
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
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40
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Wei S, Xu G, Zhou J, Ni Y. A novel 4-hydroxyacetophenone monooxygenase featuring aromatic substrates preference for enantioselective access to sulfoxides. Molecular Catalysis 2022; 528:112496. [DOI: 10.1016/j.mcat.2022.112496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Xu X, Zhang Y, Wang S, Xu L, Su B, Wang L, Lin J. “Nonpolarity paving” in substrate tunnel of a Limnobacter sp. Phenylacetone monooxygenase for efficient single whole-cell synthesis of esomeprazole. Bioorg Chem 2022; 125:105867. [DOI: 10.1016/j.bioorg.2022.105867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 11/18/2022]
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42
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Gorbunova TI, Egorova DO, Pervova MG, Kir'yanova TD, Plotnikova EG. Degradability of commercial mixtures of polychlorobiphenyls by three Rhodococcus strains. Arch Microbiol 2022; 204:534. [PMID: 35907040 DOI: 10.1007/s00203-022-03131-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022]
Abstract
Biodegradative characteristics were investigated for the commercially available mixtures of polychlorinated biphenyls (PCBs) Trikhlorbifenil and Sovol degraded by the Rhodococcus wratislaviensis КT112-7, Rhodococcus wratislaviensis CH628 and Rhodococcus ruber P25 strains isolated from the natural habitats. For bioutilization of the Trikhlorbifenil, all three strains were found to have a high biodegrading potential: the complete destruction was achieved in 10-14 days. For the mixture Sovol, the bioutilization parameters were found to be of lower values: the degradation of the PCBs congeners was 96-98% after 14 days. For the tested polychlorobiphenyl mixtures, the structural specificities of congeners are discussed, the genes encoding monooxygenases are revealed, and explanation is given to the differences in biodegradative characteristics of the Rhodococcus strains towards di-, tri-, tetra-, penta-, hexa- and heptachlorobiphenyls. The presented data are highly relevant for environmental remediation of objects polluted with the extremely hazardous polychlorobiphenyls.
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Affiliation(s)
- Tatyana I Gorbunova
- I.Ya. Postovskii Institute of Organic Synthesis, Yekaterinburg, 620137, Russia.
| | - Darya O Egorova
- Institute of Ecology and Genetics of Microorganisms, Perm, 614081, Russia
| | - Marina G Pervova
- I.Ya. Postovskii Institute of Organic Synthesis, Yekaterinburg, 620137, Russia
| | | | - Elena G Plotnikova
- Institute of Ecology and Genetics of Microorganisms, Perm, 614081, Russia
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43
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Toplak M, Nagel A, Frensch B, Lechtenberg T, Teufel R. An acetyltransferase controls the metabolic flux in rubromycin polyketide biosynthesis by direct modulation of redox tailoring enzymes. Chem Sci 2022; 13:7157-7164. [PMID: 35799824 PMCID: PMC9215129 DOI: 10.1039/d2sc01952c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/16/2022] [Indexed: 01/14/2023] Open
Abstract
The often complex control of bacterial natural product biosynthesis typically involves global and pathway-specific transcriptional regulators of gene expression, which often limits the yield of bioactive compounds under laboratory conditions. However, little is known about regulation mechanisms on the enzymatic level. Here, we report a novel regulatory principle for natural products involving a dedicated acetyltransferase, which modifies a redox-tailoring enzyme and thereby enables pathway furcation and alternating pharmacophore assembly in rubromycin polyketide biosynthesis. The rubromycins such as griseorhodin (grh) A are complex bioactive aromatic polyketides from Actinobacteria with a hallmark bisbenzannulated [5,6]-spiroketal pharmacophore that is mainly installed by two flavoprotein monooxygenases. First, GrhO5 converts the advanced precursor collinone into the [6,6]-spiroketal containing dihydrolenticulone, before GrhO6 effectuates a ring contraction to afford the [5,6]-spiroketal. Our results show that pharmacophore assembly in addition involves the acetyl-CoA-dependent acetyltransferase GrhJ that activates GrhO6 to allow the rapid generation and release of its labile product, which is subsequently sequestered by ketoreductase GrhO10 and converted into a stable intermediate. Consequently, the biosynthesis is directed to the generation of canonical rubromycins, while the alternative spontaneous [5,6]-spiroketal hydrolysis to a ring-opened pathway product is thwarted. Presumably, this allows the bacteria to rapidly adjust the biosynthesis of functionally distinct secondary metabolites depending on nutrient and precursor (i.e. acetyl-CoA) availability. Our study thus illustrates how natural product biosynthesis can be enzymatically regulated and provides new perspectives for the improvement of in vitro enzyme activities and natural product titers via biotechnological approaches. Characterization of the acetyltransferase GrhJ reveals the surprising acetylation of flavoenzyme GrhO6 in rubromycin polyketide biosynthesis, showcasing a novel principle for the enzymatic regulation of secondary metabolic pathways.![]()
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Affiliation(s)
- Marina Toplak
- Faculty of Biology, University of Freiburg Schänzlestrasse 1 79104 Freiburg Germany
| | - Adelheid Nagel
- Faculty of Biology, University of Freiburg Schänzlestrasse 1 79104 Freiburg Germany
| | - Britta Frensch
- Faculty of Biology, University of Freiburg Schänzlestrasse 1 79104 Freiburg Germany
| | - Thorsten Lechtenberg
- Faculty of Biology, University of Freiburg Schänzlestrasse 1 79104 Freiburg Germany
| | - Robin Teufel
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland
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Abstract
C-H oxyfunctionalisation remains a distinct challenge for synthetic organic chemists. Oxygenases and peroxygenases (grouped here as "oxygenating biocatalysts") catalyse the oxidation of a substrate with molecular oxygen or hydrogen peroxide as oxidant. The application of oxygenating biocatalysts in organic synthesis has dramatically increased over the last decade, producing complex compounds with potential uses in the pharmaceutical industry. This review will focus on hydroxyl functionalisation using oxygenating biocatalysts as a tool for drug discovery and development. Established oxygenating biocatalysts, such as cytochrome P450s and flavin-dependent monooxygenases, have widely been adopted for this purpose, but can suffer from low activity, instability or limited substrate scope. Therefore, emerging oxygenating biocatalysts which offer an alternative will also be covered, as well as considering the ways in which these hydroxylation biotransformations can be applied in drug discovery and development, such as late-stage functionalisation (LSF) and in biocatalytic cascades.
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Affiliation(s)
- Sacha N. Charlton
- School of ChemistryUniversity of Bristol, Cantock's CloseBristolBS8 1TSUK
| | - Martin A. Hayes
- Compound Synthesis and ManagementDiscovery SciencesBiopharmaceuticals R&DAstraZenecaGothenburgSweden
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Röllig R, Paul CE, Katia D, Kara S, Alphand V. Exploring the temperature effect on enantioselectivity of a Baeyer-Villiger biooxidation by the 2,5-DKCMO module: The SLM approach. Chembiochem 2022; 23:e202200293. [PMID: 35648642 PMCID: PMC9400988 DOI: 10.1002/cbic.202200293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Indexed: 11/08/2022]
Abstract
Temperature is a crucial parameter for biological and chemical processes. Its effect on enzymatically catalysed reactions has been known for decades, and the stereo- and enantiopreference are often temperature-dependent. For the first time, we present the temperature effect on the Baeyer-Villiger oxidation of rac- bicyclo[3.2.0]hept-2-en-6-one by the type II Bayer-Villiger monooxygenase, 2,5-DKCMO. In the absence of a reductase and driven by the hydride-donation of a synthetic nicotinamide analogue, the clear trend for a decreasing enantioselectivity at higher temperatures was observed. "Traditional" approaches such as the determination of the enantiomeric ratio (E) appeared unsuitable due to the complexity of the system. To quantify the trend, we chose to use the 'Shape Language Modelling' (SLM), a tool that allows the reaction to be described at all points in a shape prescriptive manner. Thus, without knowing the equation of the reaction, the substrate ee can be estimated that at any conversion.
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Affiliation(s)
- Robert Röllig
- Aix-Marseille Université: Aix-Marseille Universite, Institut des Sciences moléculaires de Marseille, Avenue Escadrille Normandie Niemen, 13013, Marseille, FRANCE
| | - Caroline E Paul
- Delft University of Technology: Technische Universiteit Delft, Department of Biotechnology, NETHERLANDS
| | - Duquesne Katia
- Aix-Marseille Université: Aix-Marseille Universite, Aix Marseille Université, Ecole centrale, CNRS, iSm2, FRANCE
| | - Selin Kara
- Aarhus University: Aarhus Universitet, Biological and Chemical Engineering, Gustav Wieds Vej 10, 8000, Aarhus, DENMARK
| | - Véronique Alphand
- iSm2 UMR7313, Aix Marseille Université, Ecole Centrale,CNRS, avenue Escadrille Normandie Niemen, 13397, Marseille, FRANCE
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46
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Lin H, Meng Y, Li N, Tang Y, Dong S, Wu Z, Xu C, Kazlauskas R, Chen H. Enzymatic Enantioselective anti‐Markovnikov Hydration of Aryl Alkenes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hui Lin
- Henan Agricultural University College of Life Science 95 Wenhua Road 450002 Zhengzhou CHINA
| | - Yinyin Meng
- Henan Agricultural University College of Life Sciences CHINA
| | - Na Li
- Henan University of Technology College of Biological Engineering CHINA
| | - Yanhong Tang
- Henan Agricultural University College of Life Sciences CHINA
| | - Shuang Dong
- Henan Agricultural University College of Life Sciences CHINA
| | - Zhongliu Wu
- Chengdu Institute of Biology CAS Key Laboratory of Environmental and Applied Microbiology CHINA
| | - Cuilian Xu
- Henan Agricultural University College of Sciences CHINA
| | - Romas Kazlauskas
- University of Minnesota College of Biological Sciences Department of Biochemistry, Molecular Biology and Biophysics CHINA
| | - Hongge Chen
- Henan Agricultural University College of Life Sciences CHINA
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47
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Dong S, Fan D, Liu Q, Meng Y, Liu X, Yang S, Lin H, Li N, Chen H. Enantioselectivity and key residue of Herbaspirillum huttiense monooxygenase in asymmetric epoxidation of styrenes. Appl Microbiol Biotechnol 2022. [PMID: 35230494 DOI: 10.1007/s00253-022-11843-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 02/14/2022] [Accepted: 02/19/2022] [Indexed: 11/02/2022]
Abstract
Styrene monooxygenases (SMOs) are powerful enzymes for the synthesis of enantiopure epoxides, but these SMOs have narrow substrate spectra, and the residues in controlling enantioselectivity of SMOs remains unclear. A monooxygenase from Herbaspirillum huttiense (HhMO) was found to have excellent enantioselectivities and diastereoselectivities in the epoxidation of unconjugated terminal alkenes. Here we found that HhMO could also transfer styrene into styrene epoxide with 75% ee, and it could also catalyze the epoxidation of styrene derivatives into the corresponding epoxides with enantioselectivities up to 99% ee. Meanwhile, site 199 in the substrate access channel of HhMO was found to play an important role in the controlling enantioselectivity of the epoxidation. The E199L variant catalyzed the epoxidation of styrene with > 99% ee. The identification of critical residue that affects the enantioselectivity of SMOs would thus be valuable for creating efficient monooxygenases for the preparation of essential enantiopure epoxides. KEY POINTS: • Bioexpoxidation of both conjugated and unconjugated alkenes by HhMO with excellent enantioselectivities. • Gating residue 199 played an essential role in controlling the enantioselectivity of SMO. • HhMO E199L catalyzed the epoxidation of styrenes with up to > 99% ee.
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48
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Deng Y, Zhou Q, Wu Y, Chen X, Zhong F. Properties and Mechanisms of Flavin-Dependent Monooxygenases and Their Applications in Natural Product Synthesis. Int J Mol Sci 2022; 23:2622. [PMID: 35269764 PMCID: PMC8910399 DOI: 10.3390/ijms23052622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [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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49
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Abstract
Molybdenum- and tungsten-dependent proteins catalyze essential processes in living organisms and biogeochemical cycles. Among these enzymes, members of the dimethyl sulfoxide (DMSO) reductase superfamily are considered the most diverse, facilitating a wide range of chemical transformations that can be categorized as oxygen atom installation, removal, and transfer. Importantly, DMSO reductase enzymes provide high efficiency and excellent selectivity while operating under mild conditions without conventional oxidants such as oxygen or peroxides. Despite the potential utility of these enzymes as biocatalysts, such applications have not been fully explored. In addition, the vast majority of DMSO reductase enzymes still remain uncharacterized. In this review, we describe the reactivities, proposed mechanisms, and potential synthetic applications of selected enzymes in the DMSO reductase superfamily. We also highlight emerging opportunities to discover new chemical activity and current challenges in studying and engineering proteins in the DMSO reductase superfamily. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Chi Chip Le
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
| | - Minwoo Bae
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
| | - Sina Kiamehr
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA;
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50
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Trisrivirat D, Sutthaphirom C, Pimviriyakul P, Chaiyen P. Dual activities of oxidation and oxidative decarboxylation by flavoenzymes. Chembiochem 2022; 23:e202100666. [PMID: 35040514 DOI: 10.1002/cbic.202100666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/17/2022] [Indexed: 11/07/2022]
Abstract
Specific flavoenzyme oxidases catalyze oxidative decarboxylation in addition to their classical oxidation reactions in the same active sites. The mechanisms underlying oxidative decarboxylation by these enzymes and how they control their two activities are not clearly known. This article reviews the current state of knowledge of four enzymes from the l-amino acid oxidase and l-hydroxy acid oxidase families, including l-tryptophan 2-monooxygenase, l-phenylalanine 2-oxidase and l-lysine oxidase/monooxygenase and lactate monooxygenase which catalyze substrate oxidation and oxidative decarboxylation. Apart from specific interactions to allow substrate oxidation by the flavin cofactor, specific binding of oxidized product in the active sites appears to be important for enabling subsequent decarboxylation by these enzymes. Based on recent findings of l-lysine oxidase/monooxygenase, we propose that nucleophilic attack of H2O2 on the imino acid product is the mechanism enabling oxidative decarboxylation.
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Affiliation(s)
- Duangthip Trisrivirat
- VISTEC: Vidyasirimedhi Institute of Science and Technology, Biomolecular Science and Engineering, THAILAND
| | - Chalermroj Sutthaphirom
- VISTEC: Vidyasirimedhi Institute of Science and Technology, Biomolecular Science and Engineering, THAILAND
| | | | - Pimchai Chaiyen
- Vidyasirimedhi Institute of Science and Technology (VISTEC), School of Biomolecular Science and Engineering, 555 Moo 1 Payupnai, 21210, Wangchan District, THAILAND
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