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Cochereau B, Le Strat Y, Ji Q, Pawtowski A, Delage L, Weill A, Mazéas L, Hervé C, Burgaud G, Gunde-Cimerman N, Pouchus YF, Demont-Caulet N, Roullier C, Meslet-Cladiere L. Heterologous Expression and Biochemical Characterization of a New Chloroperoxidase Isolated from the Deep-Sea Hydrothermal Vent Black Yeast Hortaea werneckii UBOCC-A-208029. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:519-536. [PMID: 37354383 PMCID: PMC10427571 DOI: 10.1007/s10126-023-10222-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/04/2023] [Indexed: 06/26/2023]
Abstract
The initiation of this study relies on a targeted genome-mining approach to highlight the presence of a putative vanadium-dependent haloperoxidase-encoding gene in the deep-sea hydrothermal vent fungus Hortaea werneckii UBOCC-A-208029. To date, only three fungal vanadium-dependent haloperoxidases have been described, one from the terrestrial species Curvularia inaequalis, one from the fungal plant pathogen Botrytis cinerea, and one from a marine derived isolate identified as Alternaria didymospora. In this study, we describe a new vanadium chloroperoxidase from the black yeast H. werneckii, successfully cloned and overexpressed in a bacterial host, which possesses higher affinity for bromide (Km = 26 µM) than chloride (Km = 237 mM). The enzyme was biochemically characterized, and we have evaluated its potential for biocatalysis by determining its stability and tolerance in organic solvents. We also describe its potential three-dimensional structure by building a model using the AlphaFold 2 artificial intelligence tool. This model shows some conservation of the 3D structure of the active site compared to the vanadium chloroperoxidase from C. inaequalis but it also highlights some differences in the active site entrance and the volume of the active site pocket, underlining its originality.
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Affiliation(s)
- Bastien Cochereau
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Yoran Le Strat
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Qiaolin Ji
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Audrey Pawtowski
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
| | - Ludovic Delage
- Integrative Biology of Marine Models (LBI2M), UMR8227, Station Biologique de Roscoff (SBR), CNRS, Université, 29680, Roscoff, Sorbonne, France
| | - Amélie Weill
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Univ Brest, UBO Culture Collection (UBOCC), F-29280, Plouzané, France
| | - Lisa Mazéas
- Integrative Biology of Marine Models (LBI2M), UMR8227, Station Biologique de Roscoff (SBR), CNRS, Université, 29680, Roscoff, Sorbonne, France
| | - Cécile Hervé
- Integrative Biology of Marine Models (LBI2M), UMR8227, Station Biologique de Roscoff (SBR), CNRS, Université, 29680, Roscoff, Sorbonne, France
| | - Gaëtan Burgaud
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
| | - Nina Gunde-Cimerman
- Molecular Genetics and Biology of Microorganisms, Dept. Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Yves François Pouchus
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Nathalie Demont-Caulet
- INRAE, University of Paris, UMR ECOSYS, INRAE, Université Paris-Saclay, 78026, Versailles, AgroParisTech, France
| | - Catherine Roullier
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France.
| | - Laurence Meslet-Cladiere
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
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2
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Gribble GW. Naturally Occurring Organohalogen Compounds-A Comprehensive Review. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 121:1-546. [PMID: 37488466 DOI: 10.1007/978-3-031-26629-4_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.
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Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA.
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3
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Sam Chan HS, Nguyen QNN, Paton RS, Burton JW. Synthesis, Characterization, and Reactivity of Complex Tricyclic Oxonium Ions, Proposed Intermediates in Natural Product Biosynthesis. J Am Chem Soc 2019; 141:15951-15962. [PMID: 31560524 DOI: 10.1021/jacs.9b07438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Reactive intermediates frequently play significant roles in the biosynthesis of numerous classes of natural products although the direct observation of these biosynthetically relevant species is rare. We present here direct evidence for the existence of complex, thermally unstable, tricyclic oxonium ions that have been postulated as key reactive intermediates in the biosynthesis of numerous halogenated natural products from Laurencia species. Evidence for their existence comes from full characterization of these oxonium ions by low-temperature NMR spectroscopy supported by density functional theory (DFT) calculations, coupled with the direct generation of 10 natural products on exposure of the oxonium ions to various nucleophiles.
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Affiliation(s)
- Hau Sun Sam Chan
- Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford OX1 3TA , U.K
| | - Q Nhu N Nguyen
- Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford OX1 3TA , U.K
| | - Robert S Paton
- Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford OX1 3TA , U.K.,Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Jonathan W Burton
- Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford OX1 3TA , U.K
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4
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Zhang YA, Yaw N, Snyder SA. General Synthetic Approach for the Laurencia Family of Natural Products Empowered by a Potentially Biomimetic Ring Expansion. J Am Chem Soc 2019; 141:7776-7788. [DOI: 10.1021/jacs.9b01088] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Yu-An Zhang
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Natalie Yaw
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Scott A. Snyder
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
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5
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Höfler GT, But A, Hollmann F. Haloperoxidases as catalysts in organic synthesis. Org Biomol Chem 2019; 17:9267-9274. [DOI: 10.1039/c9ob01884k] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The current state-of-the-art of haloperoxidase catalysis in organic synthesis for halogenation reactions is presented in this review.
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Affiliation(s)
- Georg T. Höfler
- Department of Biotechnology
- Delft University of Technology
- 2629 HZ Delft
- The Netherlands
| | - Andrada But
- Department of Biotechnology
- Delft University of Technology
- 2629 HZ Delft
- The Netherlands
| | - Frank Hollmann
- Department of Biotechnology
- Delft University of Technology
- 2629 HZ Delft
- The Netherlands
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6
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Wever R, Krenn BE, Renirie R. Marine Vanadium-Dependent Haloperoxidases, Their Isolation, Characterization, and Application. Methods Enzymol 2018; 605:141-201. [PMID: 29909824 DOI: 10.1016/bs.mie.2018.02.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Vanadium-dependent haloperoxidases in seaweeds, cyanobacteria, fungi, and possibly phytoplankton play an important role in the release of halogenated volatile compounds in the environment. These halocarbons have effects on atmospheric chemistry since they cause ozone depletion. In this chapter, a survey is given of the different sources of these enzymes, some of their properties, the various methods to isolate them, and the bottlenecks in purification. The assays to detect and quantify haloperoxidase activity are described as well as their kinetic properties. Several practical tips and pitfalls are given which have not yet been published explicitly. Recent developments in research on structure and function of these enzymes are reviewed. Finally, the application of vanadium-dependent haloperoxidases in the biosynthesis of brominated and other compounds is discussed.
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Affiliation(s)
- Ron Wever
- University of Amsterdam, Van't Hoff Institute for Molecular Sciences, Amsterdam, The Netherlands.
| | - Bea E Krenn
- University of Amsterdam, Innovation Exchange Amsterdam, Amsterdam, The Netherlands
| | - Rokus Renirie
- University of Amsterdam, Van't Hoff Institute for Molecular Sciences, Amsterdam, The Netherlands
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7
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New Marine Antifouling Compounds from the Red Alga Laurencia sp. Mar Drugs 2017; 15:md15090267. [PMID: 28846653 PMCID: PMC5618406 DOI: 10.3390/md15090267] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/20/2017] [Accepted: 08/23/2017] [Indexed: 02/06/2023] Open
Abstract
Six new compounds, omaezol, intricatriol, hachijojimallenes A and B, debromoaplysinal, and 11,12-dihydro-3-hydroxyretinol have been isolated from four collections of Laurencia sp. These structures were determined by MS and NMR analyses. Their antifouling activities were evaluated together with eight previously known compounds isolated from the same samples. In particular, omaezol and hachijojimallene A showed potent activities (EC50 = 0.15–0.23 µg/mL) against larvae of the barnacle Amphibalanus amphitrite.
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8
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Latham J, Brandenburger E, Shepherd SA, Menon BRK, Micklefield J. Development of Halogenase Enzymes for Use in Synthesis. Chem Rev 2017; 118:232-269. [PMID: 28466644 DOI: 10.1021/acs.chemrev.7b00032] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature has evolved halogenase enzymes to regioselectively halogenate a diverse range of biosynthetic precursors, with the halogens introduced often having a profound effect on the biological activity of the resulting natural products. Synthetic endeavors to create non-natural bioactive small molecules for pharmaceutical and agrochemical applications have also arrived at a similar conclusion: halogens can dramatically improve the properties of organic molecules for selective modulation of biological targets in vivo. Consequently, a high proportion of pharmaceuticals and agrochemicals on the market today possess halogens. Halogenated organic compounds are also common intermediates in synthesis and are particularly valuable in metal-catalyzed cross-coupling reactions. Despite the potential utility of organohalogens, traditional nonenzymatic halogenation chemistry utilizes deleterious reagents and often lacks regiocontrol. Reliable, facile, and cleaner methods for the regioselective halogenation of organic compounds are therefore essential in the development of economical and environmentally friendly industrial processes. A potential avenue toward such methods is the use of halogenase enzymes, responsible for the biosynthesis of halogenated natural products, as biocatalysts. This Review will discuss advances in developing halogenases for biocatalysis, potential untapped sources of such biocatalysts and how further optimization of these enzymes is required to achieve the goal of industrial scale biohalogenation.
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Affiliation(s)
- Jonathan Latham
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Eileen Brandenburger
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sarah A Shepherd
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Binuraj R K Menon
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jason Micklefield
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
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9
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Agarwal V, Miles ZD, Winter JM, Eustáquio AS, El Gamal AA, Moore BS. Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse. Chem Rev 2017; 117:5619-5674. [PMID: 28106994 PMCID: PMC5575885 DOI: 10.1021/acs.chemrev.6b00571] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.
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Affiliation(s)
- Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
| | | | - Alessandra S. Eustáquio
- College of Pharmacy, Department of Medicinal Chemistry & Pharmacognosy and Center for Biomolecular Sciences, University of Illinois at Chicago
| | - Abrahim A. El Gamal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Bradley S. Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
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10
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Hoshino A, Nakai H, Morino M, Nishikawa K, Kodama T, Nishikibe K, Morimoto Y. Total Synthesis of the Cytotoxic Marine Triterpenoid Isodehydrothyrsiferol Reveals Partial Enantiodivergency in the Thyrsiferol Family of Natural Products. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Akihiro Hoshino
- Department of Chemistry, Graduate School of Science; Osaka City University; Sumiyoshi-ku Osaka 558-8585 Japan
| | - Haruka Nakai
- Department of Chemistry, Graduate School of Science; Osaka City University; Sumiyoshi-ku Osaka 558-8585 Japan
| | - Miyako Morino
- Department of Chemistry, Graduate School of Science; Osaka City University; Sumiyoshi-ku Osaka 558-8585 Japan
| | - Keisuke Nishikawa
- Department of Chemistry, Graduate School of Science; Osaka City University; Sumiyoshi-ku Osaka 558-8585 Japan
| | - Takeshi Kodama
- Department of Chemistry, Graduate School of Science; Osaka City University; Sumiyoshi-ku Osaka 558-8585 Japan
| | - Kento Nishikibe
- Department of Chemistry, Graduate School of Science; Osaka City University; Sumiyoshi-ku Osaka 558-8585 Japan
| | - Yoshiki Morimoto
- Department of Chemistry, Graduate School of Science; Osaka City University; Sumiyoshi-ku Osaka 558-8585 Japan
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11
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Hoshino A, Nakai H, Morino M, Nishikawa K, Kodama T, Nishikibe K, Morimoto Y. Total Synthesis of the Cytotoxic Marine Triterpenoid Isodehydrothyrsiferol Reveals Partial Enantiodivergency in the Thyrsiferol Family of Natural Products. Angew Chem Int Ed Engl 2017; 56:3064-3068. [DOI: 10.1002/anie.201611829] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/12/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Akihiro Hoshino
- Department of Chemistry, Graduate School of Science; Osaka City University; Sumiyoshi-ku Osaka 558-8585 Japan
| | - Haruka Nakai
- Department of Chemistry, Graduate School of Science; Osaka City University; Sumiyoshi-ku Osaka 558-8585 Japan
| | - Miyako Morino
- Department of Chemistry, Graduate School of Science; Osaka City University; Sumiyoshi-ku Osaka 558-8585 Japan
| | - Keisuke Nishikawa
- Department of Chemistry, Graduate School of Science; Osaka City University; Sumiyoshi-ku Osaka 558-8585 Japan
| | - Takeshi Kodama
- Department of Chemistry, Graduate School of Science; Osaka City University; Sumiyoshi-ku Osaka 558-8585 Japan
| | - Kento Nishikibe
- Department of Chemistry, Graduate School of Science; Osaka City University; Sumiyoshi-ku Osaka 558-8585 Japan
| | - Yoshiki Morimoto
- Department of Chemistry, Graduate School of Science; Osaka City University; Sumiyoshi-ku Osaka 558-8585 Japan
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