1
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Shende VV, Bauman KD, Moore BS. The shikimate pathway: gateway to metabolic diversity. Nat Prod Rep 2024; 41:604-648. [PMID: 38170905 PMCID: PMC11043010 DOI: 10.1039/d3np00037k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Covering: 1997 to 2023The shikimate pathway is the metabolic process responsible for the biosynthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Seven metabolic steps convert phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) into shikimate and ultimately chorismate, which serves as the branch point for dedicated aromatic amino acid biosynthesis. Bacteria, fungi, algae, and plants (yet not animals) biosynthesize chorismate and exploit its intermediates in their specialized metabolism. This review highlights the metabolic diversity derived from intermediates of the shikimate pathway along the seven steps from PEP and E4P to chorismate, as well as additional sections on compounds derived from prephenate, anthranilate and the synonymous aminoshikimate pathway. We discuss the genomic basis and biochemical support leading to shikimate-derived antibiotics, lipids, pigments, cofactors, and other metabolites across the tree of life.
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Affiliation(s)
- Vikram V Shende
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Katherine D Bauman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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2
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Alexandrino DAM, Carvalho MF. Defluorination as the key trait to gauge the biodegradability of fluorinated pollutants in environmental microbial communities. Methods Enzymol 2024; 696:321-338. [PMID: 38658086 DOI: 10.1016/bs.mie.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Research on microbial defluorination is largely centred on controlled experiments using axenic or well defined microbial inocula. These approaches serve a relevant purpose in the field, offering fundamental biochemical and mechanistic insights on the intricacies of biological defluorination. However, they fail to account for the effective contribution of environmental microbial communities in the recycling of fluoroorganic pollutants, a highly relevant perspective from an environmental risk assessment standpoint, while also missing an important outlook on how community-wide dynamics can leverage the breakdown of C─F bonds in these recalcitrant compounds. With that in mind, this chapter provides experimental and methodological insights on the study of microbial defluorination in wild environmental communities, using this critical catabolic step as the de facto endpoint to evolve, select and cultivate microorganisms with improved defluorination performances.
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Affiliation(s)
- Diogo A M Alexandrino
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal; Department of Environmental Health, School of Health, P. Porto, Porto, Portugal
| | - Maria F Carvalho
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal; ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal.
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3
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Huang W, Huang S, Sun Z, Zhang W, Zeng Z, Yuan B. Chemoenzymatic Synthesis of Sterically Hindered Biaryls by Suzuki Coupling and Vanadium Chloroperoxidase Catalyzed Halogenations. Chembiochem 2023; 24:e202200610. [PMID: 36325954 DOI: 10.1002/cbic.202200610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/02/2022] [Indexed: 11/06/2022]
Abstract
Halogenated biaryls are vital structural skeletons in bioactive products. In this study, an effective chemoenzymatic halogenation by vanadium-dependent chloroperoxidase from Camponotus inaequalis (CiVCPO) enabled the transformation of freely rotating biaryl bonds to sterically hindered axis. The yields were up to 84 % for the tribrominated biaryl products and up to 65 % when isolated. Furthermore, a one-pot, two-step chemoenzymatic strategy by incorporating transition metal catalyzed Suzuki coupling and the chemoenzymatic halogenation in aqueous phase were described. This strategy demonstrates a simplified one-pot reaction sequence with organometallic and biocatalytic procedures under economical and environmentally beneficial conditions that may inspire further research on synthesis of sterically hindered biaryls.
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Affiliation(s)
- Wansheng Huang
- School of Pharmacy, Hubei University of Science and Technology, 88 Xianning Avenue, Xianning, Hubei, 437100, P. R. China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, P. R. China
| | - Shengtang Huang
- School of Pharmacy, Hubei University of Science and Technology, 88 Xianning Avenue, Xianning, Hubei, 437100, P. R. China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, P. R. China.,National Innovation Center for Synthetic Biotechnology, 32 West 7th Avenue, Tianjin, 300308, P. R. China
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, P. R. China.,National Innovation Center for Synthetic Biotechnology, 32 West 7th Avenue, Tianjin, 300308, P. R. China
| | - Zhigang Zeng
- School of Nuclear Technology and Chemistry & Biology, Hubei Key Laboratory of Radiation Chemistry and Functional Materials, Hubei University of Science and Technology, 88 Xianning Avenue, Xianning, Hubei, 437100, P. R. China.,Hubei Industry Technology Research Institute of Intelligent Health, 88 Xianning Avenue, Xianning, Hubei, 437100, P. R. China
| | - Bo Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, P. R. China.,National Innovation Center for Synthetic Biotechnology, 32 West 7th Avenue, Tianjin, 300308, P. R. China
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4
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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: 4] [Impact Index Per Article: 4.0] [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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5
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Ruan Z, Wang M, Yang C, Zhu L, Su Z, Hong R. Total Synthesis of (+)-Hinckdentine A: Harnessing Noncovalent Interactions for Organocatalytic Bromination. JACS AU 2022; 2:793-800. [PMID: 35557764 PMCID: PMC9088303 DOI: 10.1021/jacsau.2c00048] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 05/25/2023]
Abstract
Hinckdentine A, a marine-sponge-derived tribrominated indole alkaloid bearing a unique indolo[1,2-c]quinazoline skeleton, was completed in 12 steps featuring the construction of the Nα-quaternary carbon center by asymmetric azo-ene cyclization. A novel organocatalyst was developed to promote high-yielding tribromination, which represents a challenging process encountered in previous syntheses. Density functional theory calculations scrutinized viable substrates and deciphered the origin of the enhancement of C8 electrophilic bromination with a bifunctional organocatalyst. Moreover, the application of organocatalyst-enabled bromination on various substrates was demonstrated to highlight future late functionalizations of biologically intriguing targets.
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Affiliation(s)
- Zhuwei Ruan
- CAS
Key Laboratory of Synthetic Chemistry of Natural Substances, Center
for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing 101419, China
| | - Min Wang
- Key
Laboratory of Green Chemistry and Technology, Ministry of Education,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Chen Yang
- CAS
Key Laboratory of Synthetic Chemistry of Natural Substances, Center
for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing 101419, China
| | - Lili Zhu
- CAS
Key Laboratory of Synthetic Chemistry of Natural Substances, Center
for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing 101419, China
| | - Zhishan Su
- Key
Laboratory of Green Chemistry and Technology, Ministry of Education,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Ran Hong
- CAS
Key Laboratory of Synthetic Chemistry of Natural Substances, Center
for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing 101419, China
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6
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Zheng J, Antrobus S, Feng W, Purdy TN, Moore BS, Pessah IN. Marine and Anthropogenic Bromopyrroles Alter Cellular Ca 2+ Dynamics of Murine Cortical Neuronal Networks by Targeting the Ryanodine Receptor and Sarco/Endoplasmic Reticulum Ca 2+-ATPase. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:16023-16033. [PMID: 34788016 PMCID: PMC8813095 DOI: 10.1021/acs.est.1c05214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Bromopyrroles (BrPyr) are synthesized naturally by marine sponge symbionts and produced anthropogenically as byproducts of wastewater treatment. BrPyr interact with ryanodine receptors (RYRs) and sarco/endoplasmic reticulum (SR/ER) Ca2+-ATPase (SERCA). Influences of BrPyr on the neuronal network activity remain uncharted. BrPyr analogues with differing spectra of RYR/SERCA activities were tested using RYR-null or RYR1-expressing HEK293 and murine cortical neuronal/glial cocultures (NGCs) loaded with Fluo-4 to elucidate their mechanisms altering Ca2+ dynamics. The NGC electrical spike activity (ESA) was measured from NGCs plated on multielectrode arrays. Nanomolar tetrabromopyrrole (TBP, 1) potentiated caffeine-triggered Ca2+ release independent of extracellular [Ca2+] in RYR1-HEK293, whereas higher concentrations produce slow and sustained rise in cytoplasmic [Ca2+] independent of RYR1 expression. TBP, 2,3,5-tribromopyrrole (2), pyrrole (3), 2,3,4-tribromopyrrole (4), and ethyl 4-bromopyrrole-2-carboxylate (5) added acutely to NGC showed differential potency; rank order TBP (IC50 ≈ 220 nM) > 2 ≫ 5, whereas 3 and 4 were inactive at 10 μM. TBP >2 μM elicited sustained elevation of cytoplasmic [Ca2+] and loss of neuronal viability. TBP did not alter network ESA. BrPyr from marine and anthropogenic sources are ecological signaling molecules and emerging anthropogenic pollutants of concern to environmental and human health that potently alter ER Ca2+ dynamics and warrant further investigation in vivo.
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Affiliation(s)
- Jing Zheng
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California 95616, United States
| | - Shane Antrobus
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California 95616, United States
| | - Wei Feng
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California 95616, United States
| | - Trevor N Purdy
- Center for Marine Biotechnology and Biomedicine, University of California, San Diego, California 92037, United States
- Scripps Institution of Oceanography, University of California, San Diego, California 92037, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92037, United States
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, University of California, San Diego, California 92037, United States
- Scripps Institution of Oceanography, University of California, San Diego, California 92037, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92037, United States
| | - Isaac N Pessah
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California 95616, United States
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7
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Adak S, Moore BS. Cryptic halogenation reactions in natural product biosynthesis. Nat Prod Rep 2021; 38:1760-1774. [PMID: 34676862 DOI: 10.1039/d1np00010a] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: Up to December 2020Enzymatic halogenation reactions are essential for the production of thousands of halogenated natural products. However, in recent years, scientists discovered several halogenases that transiently incorporate halogen atoms in intermediate biosynthetic molecules to activate them for further chemical reactions such as cyclopropanation, terminal alkyne formation, C-/O-alkylation, biaryl coupling, and C-C rearrangements. In each case, the halogen atom is lost in the course of biosynthesis to the final product and is hence termed "cryptic". In this review, we provide an overview of our current knowledge of cryptic halogenation reactions in natural product biosynthesis.
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Affiliation(s)
- Sanjoy Adak
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093, USA.
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093, USA. .,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA
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8
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C4 Bacterial Volatiles Improve Plant Health. Pathogens 2021; 10:pathogens10060682. [PMID: 34072921 PMCID: PMC8227687 DOI: 10.3390/pathogens10060682] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/10/2021] [Accepted: 05/24/2021] [Indexed: 02/04/2023] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) associated with plant roots can trigger plant growth promotion and induced systemic resistance. Several bacterial determinants including cell-wall components and secreted compounds have been identified to date. Here, we review a group of low-molecular-weight volatile compounds released by PGPR, which improve plant health, mostly by protecting plants against pathogen attack under greenhouse and field conditions. We particularly focus on C4 bacterial volatile compounds (BVCs), such as 2,3-butanediol and acetoin, which have been shown to activate the plant immune response and to promote plant growth at the molecular level as well as in large-scale field applications. We also disc/ uss the potential applications, metabolic engineering, and large-scale fermentation of C4 BVCs. The C4 bacterial volatiles act as airborne signals and therefore represent a new type of biocontrol agent. Further advances in the encapsulation procedure, together with the development of standards and guidelines, will promote the application of C4 volatiles in the field.
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9
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Sobrado P. Role of reduced flavin in dehalogenation reactions. Arch Biochem Biophys 2020; 697:108696. [PMID: 33245912 DOI: 10.1016/j.abb.2020.108696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022]
Abstract
Halogenated organic compounds are extensively used in the cosmetic, pharmaceutical, and chemical industries. Several naturally occurring halogen-containing natural products are also produced, mainly by marine organisms. These compounds accumulate in the environment due to their chemical stability and lack of biological pathways for their degradation. However, a few enzymes have been identified that perform dehalogenation reactions in specific biological pathways and others have been identified to have secondary activities toward halogenated compounds. Various mechanisms for dehalogenation of I, Cl, Br, and F containing compounds have been elucidated. These have been grouped into reductive, oxidative, and hydrolytic mechanisms. Flavin-dependent enzymes have been shown to catalyze oxidative dehalogenation reactions utilizing the C4a-hydroperoxyflavin intermediate. In addition, flavoenzymes perform reductive dehalogenation, forming transient flavin semiquinones. Recently, flavin-dependent enzymes have also been shown to perform dehalogenation reactions where the reduced form of the flavin produces a covalent intermediate. Here, recent studies on the reactions of flavoenzymes in dehalogenation reactions, with a focus on covalent catalytic dehalogenation mechanisms, are described.
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Affiliation(s)
- Pablo Sobrado
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, VA, 24061, USA.
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10
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Hüttel W, Müller M. Regio- and stereoselective intermolecular phenol coupling enzymes in secondary metabolite biosynthesis. Nat Prod Rep 2020; 38:1011-1043. [PMID: 33196733 DOI: 10.1039/d0np00010h] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 2005 to 2020Phenol coupling is a key reaction in the biosynthesis of important biopolymers such as lignin and melanin and of a plethora of biarylic secondary metabolites. The reaction usually leads to several different regioisomeric products due to the delocalization of a radical in the reaction intermediates. If axial chirality is involved, stereoisomeric products are obtained provided no external factor influences the selectivity. Hence, in non-enzymatic organic synthesis it is notoriously difficult to control the selectivity of the reaction, in particular if the coupling is intermolecular. From biosynthesis, it is known that especially fungi, plants, and bacteria produce biarylic compounds regio- and stereoselectively. Nonetheless, the involved enzymes long evaded discovery. First progress was made in the late 1990s; however, the breakthrough came only with the genomic era and, in particular, in the last few years the number of relevant publications has dramatically increased. The discoveries reviewed in this article reveal a remarkable diversity of enzymes that catalyze oxidative intermolecular phenol coupling, including various classes of laccases, cytochrome P450 enzymes, and heme peroxidases. Particularly in the case of laccases, the catalytic systems are often complex and additional proteins, substrates, or reaction conditions have a strong influence on activity and regio- and atroposelectivity. Although the field of (selective) enzymatic phenol coupling is still in its infancy, the diversity of enzymes identified recently could make it easier to select suitable candidates for biotechnological development and to approach this challenging reaction through biocatalysis.
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Affiliation(s)
- Wolfgang Hüttel
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104 Freiburg, Germany.
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11
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Atashgahi S. Discovered by genomics: putative reductive dehalogenases with N-terminus transmembrane helixes. FEMS Microbiol Ecol 2020; 95:5426821. [PMID: 30942854 PMCID: PMC6797604 DOI: 10.1093/femsec/fiz048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/02/2019] [Indexed: 11/13/2022] Open
Abstract
Attempts for bioremediation of toxic organohalogens resulted in the identification of organohalide-respiring bacteria harbouring reductive dehalogenases (RDases) enzymes. RDases consist of the catalytic subunit (RdhA, encoded by rdhA) that does not have membrane-integral domains, and a small putative membrane anchor (RdhB, encoded by rdhB) that (presumably) locates the A subunit to the outside of the cytoplasmic membrane. Recent genomic studies identified a putative rdh gene in an uncultured deltaproteobacterial genome that was not accompanied by an rdhB gene, but contained transmembrane helixes in N-terminus. Therefore, rather than having a separate membrane anchor protein, this putative RDase is likely a hybrid of RdhA and RdhB, and directly connected to the membrane with transmembrane helixes. However, functionality of the hybrid putative RDase remains unknown. Further analysis showed that the hybrid putative rdh genes are present in the genomes of pure cultures and uncultured members of Bacteriodetes and Deltaproteobacteria, but also in the genomes of the candidate divisions. The encoded hybrid putative RDases have cytoplasmic or exoplasmic C-terminus localization, and cluster phylogenetically separately from the existing RDase groups. With increasing availability of (meta)genomes, more diverse and likely novel rdh genes are expected, but questions regarding their functionality and ecological roles remain open.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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12
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Duell ER, Milzarek TM, El Omari M, Linares-Otoya LJ, Schäberle TF, König GM, Gulder TAM. Identification, cloning, expression and functional interrogation of the biosynthetic pathway of the polychlorinated triphenyls ambigol A–C from Fischerella ambigua 108b. Org Chem Front 2020. [DOI: 10.1039/d0qo00707b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The biosynthetic pathway to the ambigols A–C from Fischerella ambigua 108b has been identified, cloned, heterologously expressed and functionally studied, including in-depth analysis of the biaryl coupling biochemistry in vivo and in vitro.
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Affiliation(s)
- Elke R. Duell
- Biosystems Chemistry
- Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM)
- Technical University of Munich
- 85748 Garching
- Germany
| | - Tobias M. Milzarek
- Biosystems Chemistry
- Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM)
- Technical University of Munich
- 85748 Garching
- Germany
| | - Mustafa El Omari
- Institute for Pharmaceutical Biology
- University of Bonn
- 53115 Bonn
- Germany
| | - Luis J. Linares-Otoya
- Institute for Insect Biotechnology
- Justus Liebig University of Giessen
- 35392 Giessen
- Germany
- Department of Bioresources
| | - Till F. Schäberle
- Institute for Insect Biotechnology
- Justus Liebig University of Giessen
- 35392 Giessen
- Germany
- Department of Bioresources
| | | | - Tobias A. M. Gulder
- Biosystems Chemistry
- Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM)
- Technical University of Munich
- 85748 Garching
- Germany
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13
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Karimi S, Ma S, Qu M, Chen B, Ramig K, Greer EM, Szalda DJ, Neary MC, Berkowitz WF, Subramaniam G. A new synthesis of biologically active pyrroles: Formal synthesis of pentabromopseudilin, bimetopyrol, and several antitubercular agents. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.3780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Sasan Karimi
- Department of ChemistryQueensborough Community College of the City University of New York Bayside New York
| | - Shuai Ma
- Department of Chemistry and BiochemistryQueens College of the City University of New York Flushing New York
| | - Michelle Qu
- Department of ChemistryQueensborough Community College of the City University of New York Bayside New York
| | - Biling Chen
- Department of ChemistryQueensborough Community College of the City University of New York Bayside New York
| | - Keith Ramig
- Department of Natural SciencesBaruch College of the City University of New York New York New York
| | - Edyta M. Greer
- Department of Natural SciencesBaruch College of the City University of New York New York New York
| | - David J. Szalda
- Department of Natural SciencesBaruch College of the City University of New York New York New York
| | - Michelle C. Neary
- Department of ChemistryHunter College of the City University of New York New York New York
| | - William F. Berkowitz
- Department of Chemistry and BiochemistryQueens College of the City University of New York Flushing New York
| | - Gopal Subramaniam
- Department of Chemistry and BiochemistryQueens College of the City University of New York Flushing New York
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14
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Chekan JR, Lee GY, El Gamal A, Purdy TN, Houk KN, Moore BS. Bacterial Tetrabromopyrrole Debrominase Shares a Reductive Dehalogenation Strategy with Human Thyroid Deiodinase. Biochemistry 2019; 58:5329-5338. [PMID: 31117392 DOI: 10.1021/acs.biochem.9b00318] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzymatic dehalogenation is an important and well-studied biological process in both the detoxification and catabolism of small molecules, many of which are anthropogenic in origin. However, dedicated dehalogenation reactions that replace a halogen atom with a hydrogen are rare in the biosynthesis of natural products. In fact, the debrominase Bmp8 is the only known example. It catalyzes the reductive debromination of the coral settlement cue and the potential human toxin 2,3,4,5-tetrabromopyrrole as part of the biosynthesis of the antibiotic pentabromopseudilin. Using a combination of protein crystallography, mutagenesis, and computational modeling, we propose a catalytic mechanism for Bmp8 that is reminiscent of that catalyzed by human deiodinases in the maintenance of thyroid hormones. The identification of the key catalytic residues enabled us to recognize divergent functional homologues of Bmp8. Characterization of one of these homologues demonstrated its debromination activity even though it is found in a completely distinct genomic context. This observation suggests that additional enzymes outside those associated with the tetrabromopyrrole biosynthetic pathway may be able to alter the lifetime of this compound in the environment.
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Affiliation(s)
- Jonathan R Chekan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093 , United States
| | - Ga Young Lee
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Abrahim El Gamal
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093 , United States
| | - Trevor N Purdy
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093 , United States
| | - K N Houk
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093 , United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California San Diego , La Jolla , California 92093 , United States
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15
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Busch J, Agarwal V, Schorn M, Machado H, Moore BS, Rouse GW, Gram L, Jensen PR. Diversity and distribution of the bmp gene cluster and its Polybrominated products in the genus Pseudoalteromonas. Environ Microbiol 2019; 21:1575-1585. [PMID: 30652406 DOI: 10.1111/1462-2920.14532] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 01/10/2019] [Accepted: 01/12/2019] [Indexed: 12/18/2022]
Abstract
The production of pentabromopseudilin and related brominated compounds by Pseudoalteromonas spp. has recently been linked to the bmp biosynthetic gene cluster. This study explored the distribution and evolutionary history of this gene cluster in the genus Pseudoalteromonas. A phylogeny of the genus revealed numerous clades that do not contain type strains, suggesting considerable species level diversity has yet to be described. Comparative genomics revealed four distinct versions of the gene cluster distributed among 19 of the 101 Pseudoalteromonas genomes examined. These were largely localized to the least inclusive clades containing the Pseudoalteromonas luteoviolacea and Pseudoalteromonas phenolica type strains and show clear evidence of gene and gene cluster loss in certain lineages. Bmp gene phylogeny is largely congruent with the Pseudoalteromonas species phylogeny, suggesting vertical inheritance within the genus. However, the gene cluster is found in three different genomic environments suggesting either chromosomal rearrangement or multiple acquisition events. Bmp conservation within certain lineages suggests the encoded products are highly relevant to the ecology of these bacteria.
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Affiliation(s)
- Julia Busch
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Scripps Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Vinayak Agarwal
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Scripps Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Michelle Schorn
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Scripps Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Henrique Machado
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800, Kgs. Lyngby, Denmark
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Scripps Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800, Kgs. Lyngby, Denmark
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Scripps Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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16
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Thapa HR, Robbins JM, Moore BS, Agarwal V. Insights into Thiotemplated Pyrrole Biosynthesis Gained from the Crystal Structure of Flavin-Dependent Oxidase in Complex with Carrier Protein. Biochemistry 2019; 58:918-929. [PMID: 30620182 DOI: 10.1021/acs.biochem.8b01177] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sequential enzymatic reactions on substrates tethered to carrier proteins (CPs) generate thiotemplated building blocks that are then delivered to nonribosomal peptide synthetases (NRPSs) to generate peptidic natural products. The underlying diversity of these thiotemplated building blocks is the principal driver of the chemical diversity of NRPS-derived natural products. Structural insights into recognition of CPs by tailoring enzymes that generate these building blocks are sparse. Here we present the crystal structure of a flavin-dependent prolyl oxidase that furnishes thiotemplated pyrrole as the product, in complex with its cognate CP in the holo and product-bound states. The thiotemplated pyrrole is an intermediate that is well-represented in natural product biosynthetic pathways. Our results delineate the interactions between the CP and the oxidase while also providing insights into the stereospecificity of the enzymatic oxidation of the prolyl heterocycle to the aromatic pyrrole. Biochemical validation of the interaction between the CP and the oxidase demonstrates that NRPSs recognize and bind to their CPs using interactions quite different from those of fatty acid and polyketide biosynthetic enzymes. Our results posit that structural diversity in natural product biosynthesis can be, and is, derived from subtle modifications of primary metabolic enzymes.
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Affiliation(s)
- Hem R Thapa
- School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - John M Robbins
- School of Chemical and Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.,Krone Engineered Biosystems Building , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Bradley S Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093 , United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.,School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
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17
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Atashgahi S, Liebensteiner MG, Janssen DB, Smidt H, Stams AJM, Sipkema D. Microbial Synthesis and Transformation of Inorganic and Organic Chlorine Compounds. Front Microbiol 2018; 9:3079. [PMID: 30619161 PMCID: PMC6299022 DOI: 10.3389/fmicb.2018.03079] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/29/2018] [Indexed: 12/26/2022] Open
Abstract
Organic and inorganic chlorine compounds are formed by a broad range of natural geochemical, photochemical and biological processes. In addition, chlorine compounds are produced in large quantities for industrial, agricultural and pharmaceutical purposes, which has led to widespread environmental pollution. Abiotic transformations and microbial metabolism of inorganic and organic chlorine compounds combined with human activities constitute the chlorine cycle on Earth. Naturally occurring organochlorines compounds are synthesized and transformed by diverse groups of (micro)organisms in the presence or absence of oxygen. In turn, anthropogenic chlorine contaminants may be degraded under natural or stimulated conditions. Here, we review phylogeny, biochemistry and ecology of microorganisms mediating chlorination and dechlorination processes. In addition, the co-occurrence and potential interdependency of catabolic and anabolic transformations of natural and synthetic chlorine compounds are discussed for selected microorganisms and particular ecosystems.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | | | - Dick B. Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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18
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Zheng J, McKinnie SMK, El Gamal A, Feng W, Dong Y, Agarwal V, Fenical W, Kumar A, Cao Z, Moore BS, Pessah IN. Organohalogens Naturally Biosynthesized in Marine Environments and Produced as Disinfection Byproducts Alter Sarco/Endoplasmic Reticulum Ca 2+ Dynamics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5469-5478. [PMID: 29617551 PMCID: PMC6195434 DOI: 10.1021/acs.est.8b00512] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Contemporary sources of organohalogens produced as disinfection byproducts (DBPs) are receiving considerable attention as emerging pollutants because of their abundance, persistence, and potential to structurally mimic natural organohalogens produced by bacteria that serve signaling or toxicological functions in marine environments. Here, we tested 34 organohalogens from anthropogenic and marine sources to identify compounds active toward ryanodine receptor (RyR1), known toxicological targets of non-dioxin-like polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs). [3H]Ryanodine ([3H]Ry) binding screening (≤2 μM) identified 10 highly active organohalogens. Further analysis indicated that 2,3-dibromoindole (14), tetrabromopyrrole (31), and 2,3,5-tribromopyrrole (34) at 10 μM were the most efficacious at enhancing [3H]Ry binding. Interestingly, these congeners also inhibited microsomal sarcoplasmic/endoplasmic reticulum (SR/ER) Ca2+ ATPase (SERCA1a). Dual SERCA1a inhibition and RyR1 activation triggered Ca2+ efflux from microsomal vesicles with initial rates rank ordered 31 > 34 > 14. Hexabromobipyrroles (25) enhanced [3H]Ry binding moderately with strong SERCA1a inhibition, whereas pyrrole (24), 2,3,4-tribromopyrrole (26), and ethyl-4-bromopyrrole-2-carboxylate (27) were inactive. Of three PBDE derivatives of marine origin active in the [3H]Ry assay, 4'-hydroxy-2,3',4,5',6-pentabromodiphenyl ether (18) was also a highly potent SERCA1a inhibitor. Molecular targets of marine organohalogens that are also DBPs of emerging environmental concern are likely to contribute to their toxicity.
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Affiliation(s)
- Jing Zheng
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California 95616, United States
- Department of TCM Pharmacology, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Shaun M. K. McKinnie
- Center for Oceans and Human Health, Scripps Institution of Oceanography & Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0021, United States
| | - Abrahim El Gamal
- Center for Oceans and Human Health, Scripps Institution of Oceanography & Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0021, United States
| | - Wei Feng
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California 95616, United States
| | - Yao Dong
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California 95616, United States
| | | | | | - Abdhesh Kumar
- Center for Oceans and Human Health, Scripps Institution of Oceanography & Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0021, United States
| | - Zhengyu Cao
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California 95616, United States
- Department of TCM Pharmacology, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Bradley S. Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography & Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0021, United States
| | - Isaac N. Pessah
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, California 95616, United States
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19
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Skiba MA, Maloney FP, Dan Q, Fraley AE, Aldrich CC, Smith JL, Brown WC. PKS-NRPS Enzymology and Structural Biology: Considerations in Protein Production. Methods Enzymol 2018; 604:45-88. [PMID: 29779664 PMCID: PMC5992914 DOI: 10.1016/bs.mie.2018.01.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The structural diversity and complexity of marine natural products have made them a rich and productive source of new bioactive molecules for drug development. The identification of these new compounds has led to extensive study of the protein constituents of the biosynthetic pathways from the producing microbes. Essential processes in the dissection of biosynthesis have been the elucidation of catalytic functions and the determination of 3D structures for enzymes of the polyketide synthases and nonribosomal peptide synthetases that carry out individual reactions. The size and complexity of these proteins present numerous difficulties in the process of going from gene to structure. Here, we review the problems that may be encountered at the various steps of this process and discuss some of the solutions devised in our and other labs for the cloning, production, purification, and structure solution of complex proteins using Escherichia coli as a heterologous host.
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Affiliation(s)
| | | | - Qingyun Dan
- University of Michigan, Ann Arbor, MI, United States
| | - Amy E Fraley
- University of Michigan, Ann Arbor, MI, United States
| | | | - Janet L Smith
- University of Michigan, Ann Arbor, MI, United States.
| | - W Clay Brown
- University of Michigan, Ann Arbor, MI, United States.
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20
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Chekan JR, Moore BS. Preparation and Characterization of Tetrabromopyrrole Debrominase From Marine Proteobacteria. Methods Enzymol 2018; 605:253-265. [PMID: 29909826 PMCID: PMC6211843 DOI: 10.1016/bs.mie.2018.01.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
While halogenases have been studied for decades, the first natural product dehalogenase was only recently described. This bacterial enzyme, Bmp8, catalyzes the reductive debromination of 2,3,4,5-tetrabromopyrrole to form 2,3,4-tribromopyrrole as part of the biosynthesis of pentabromopseudilin, a marine natural product. Bmp8 is hypothesized to utilize a catalytic mechanism analogous to the important human thyroid hormone deiodinase enzyme family, potentially enabling Bmp8 to serve as model system to study this conserved mechanism. Herein, we describe a method for the soluble expression and purification of Bmp8. Furthermore, we detail activity assay protocols to quantify both consumption of the tetrabromopyrrole substrate and formation of the tribromopyrrole product. These methods will enable further study of this unusual enzyme and its catalytic mechanism.
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Affiliation(s)
- Jonathan R Chekan
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, United States
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, United States.
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21
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Taheri Kal Koshvandi A, Heravi MM, Momeni T. Current Applications of Suzuki–Miyaura Coupling Reaction in The Total Synthesis of Natural Products: An update. Appl Organomet Chem 2018. [DOI: 10.10.1002/aoc.4210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Tayebeh Momeni
- Department of ChemistryAlzahra University Vanak Tehran Iran
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22
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Taheri Kal Koshvandi A, Heravi MM, Momeni T. Current Applications of Suzuki–Miyaura Coupling Reaction in The Total Synthesis of Natural Products: An update. Appl Organomet Chem 2018. [DOI: 10.1002/aoc.4210] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | | | - Tayebeh Momeni
- Department of ChemistryAlzahra University Vanak Tehran Iran
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23
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24
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Lu Q, Yu L, Liang Z, Yan Q, He Z, Luan T, Liang D, Wang S. Dehalococcoides as a Potential Biomarker Evidence for Uncharacterized Organohalides in Environmental Samples. Front Microbiol 2017; 8:1677. [PMID: 28919889 PMCID: PMC5585146 DOI: 10.3389/fmicb.2017.01677] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 08/18/2017] [Indexed: 12/24/2022] Open
Abstract
The massive production and improper disposal of organohalides resulted in worldwide contamination in soil and water. However, their environmental survey based on chromatographic methods was hindered by challenges in testing the extremely wide variety of organohalides. Dehalococcoides as obligate organohalide-respiring bacteria exclusively use organohalides as electron acceptors to support their growth, of which the presence could be coupled with organohalides and, therefore, could be employed as a biomarker of the organohalide pollution. In this study, Dehalococcoides was screened in various samples of bioreactors and subsurface environments, showing the wide distribution of Dehalococcoides in sludge and sediment. Further laboratory cultivation confirmed the dechlorination activities of those Dehalococcoides. Among those samples, Dehalococcoides accounting for 1.8% of the total microbial community was found in an anaerobic granular sludge sample collected from a full-scale bioreactor treating petroleum wastewater. Experimental evidence suggested that the influent wastewater in the bioreactor contained bromomethane which support the growth of Dehalococcoides. This study demonstrated that Dehalococcoides could be employed as a promising biomarker to test the present of organohalides in wastestreams or other environmental samples.
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Affiliation(s)
- Qihong Lu
- Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen UniversityGuangzhou, China
| | - Ling Yu
- Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen UniversityGuangzhou, China
| | - Zhiwei Liang
- Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen UniversityGuangzhou, China
| | - Qingyun Yan
- Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen UniversityGuangzhou, China
| | - Zhili He
- Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen UniversityGuangzhou, China
| | - Tiangang Luan
- State Key Laboratory of Pest Control and Resource Utilization, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Dawei Liang
- Beijing Key Laboratory of Bio-inspired Energy Materials and Devices, School of Chemistry and Environment, Beihang UniversityBeijing, China
| | - Shanquan Wang
- Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen UniversityGuangzhou, China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation TechnologyGuangzhou, China
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25
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Kum DY, Nazari M, McPhail KL, Cooper CS, Suyama TL. Two-step total synthesis of an anti-MRSA and myosin-inhibiting marine natural product pentabromopseudilin via Suzuki-Miyaura coupling of a MIDA boronate ester. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.07.057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Timmermans ML, Paudel YP, Ross AC. Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies. Mar Drugs 2017; 15:E235. [PMID: 28762997 PMCID: PMC5577590 DOI: 10.3390/md15080235] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 02/07/2023] Open
Abstract
The phylum proteobacteria contains a wide array of Gram-negative marine bacteria. With recent advances in genomic sequencing, genome analysis, and analytical chemistry techniques, a whole host of information is being revealed about the primary and secondary metabolism of marine proteobacteria. This has led to the discovery of a growing number of medically relevant natural products, including novel leads for the treatment of multidrug-resistant Staphylococcus aureus (MRSA) and cancer. Of equal interest, marine proteobacteria produce natural products whose structure and biosynthetic mechanisms differ from those of their terrestrial and actinobacterial counterparts. Notable features of secondary metabolites produced by marine proteobacteria include halogenation, sulfur-containing heterocycles, non-ribosomal peptides, and polyketides with unusual biosynthetic logic. As advances are made in the technology associated with functional genomics, such as computational sequence analysis, targeted DNA manipulation, and heterologous expression, it has become easier to probe the mechanisms for natural product biosynthesis. This review will focus on genomics driven approaches to understanding the biosynthetic mechanisms for natural products produced by marine proteobacteria.
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Affiliation(s)
| | - Yagya P Paudel
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
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27
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Sun Z, Su Q, Rokita SE. The distribution and mechanism of iodotyrosine deiodinase defied expectations. Arch Biochem Biophys 2017; 632:77-87. [PMID: 28774660 DOI: 10.1016/j.abb.2017.07.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/24/2017] [Accepted: 07/30/2017] [Indexed: 12/19/2022]
Abstract
Iodotyrosine deiodinase (IYD) is unusual for its reliance on flavin to promote reductive dehalogenation under aerobic conditions. As implied by the name, this enzyme was first discovered to catalyze iodide elimination from iodotyrosine for recycling iodide during synthesis of tetra- and triiodothyronine collectively known as thyroid hormone. However, IYD likely supports many more functions and has been shown to debrominate and dechlorinate bromo- and chlorotyrosines. A specificity for halotyrosines versus halophenols is well preserved from humans to bacteria. In all examples to date, the substrate zwitterion establishes polar contacts with both the protein and the isoalloxazine ring of flavin. Mechanistic data suggest dehalogenation is catalyzed by sequential one electron transfer steps from reduced flavin to substrate despite the initial expectations for a single two electron transfer mechanism. A purported flavin semiquinone intermediate is stabilized by hydrogen bonding between its N5 position and the side chain of a Thr. Mutation of this residue to Ala suppresses dehalogenation and enhances a nitroreductase activity that is reminiscent of other enzymes within the same structural superfamily.
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Affiliation(s)
- Zuodong Sun
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Qi Su
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Steven E Rokita
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
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28
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Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
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Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
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29
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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: 248] [Impact Index Per Article: 35.4] [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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30
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Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges. Nat Chem Biol 2017; 13:537-543. [PMID: 28319100 PMCID: PMC5391271 DOI: 10.1038/nchembio.2330] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 12/20/2016] [Indexed: 12/17/2022]
Abstract
Naturally produced polybrominated diphenyl ethers (PBDEs) pervade the marine environment and structurally resemble toxic man-made brominated flame retardants. PBDEs bioaccumulate in marine animals and are likely transferred to the human food chain. However, the biogenic basis for PBDE production in one of their most prolific sources, marine sponges of the order Dysideidae, remains unidentified. Here, we report the discovery of PBDE biosynthetic gene clusters within sponge-microbiome-associated cyanobacterial endosymbionts through the use of an unbiased metagenome-mining approach. Using expression of PBDE biosynthetic genes in heterologous cyanobacterial hosts, we correlate the structural diversity of naturally produced PBDEs to modifications within PBDE biosynthetic gene clusters in multiple sponge holobionts. Our results establish the genetic and molecular foundation for the production of PBDEs in one of the most abundant natural sources of these molecules, further setting the stage for a metagenomic-based inventory of other PBDE sources in the marine environment.
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Ingavat N, Kavran JM, Sun Z, Rokita SE. Active Site Binding Is Not Sufficient for Reductive Deiodination by Iodotyrosine Deiodinase. Biochemistry 2017; 56:1130-1139. [PMID: 28157283 PMCID: PMC5330855 DOI: 10.1021/acs.biochem.6b01308] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The minimal requirements for substrate recognition and turnover by iodotyrosine deiodinase were examined to learn the basis for its catalytic specificity. This enzyme is crucial for iodide homeostasis and the generation of thyroid hormone in chordates. 2-Iodophenol binds only very weakly to the human enzyme and is dehalogenated with a kcat/Km that is more than 4 orders of magnitude lower than that for iodotyrosine. This discrimination likely protects against a futile cycle of iodinating and deiodinating precursors of thyroid hormone biosynthesis. Surprisingly, a very similar catalytic selectivity was expressed by a bacterial homologue from Haliscomenobacter hydrossis. In this example, discrimination was not based on affinity since 4-cyano-2-iodophenol bound to the bacterial deiodinase with a Kd lower than that of iodotyrosine and yet was not detectably deiodinated. Other phenols including 2-iodophenol were deiodinated but only very inefficiently. Crystal structures of the bacterial enzyme with and without bound iodotyrosine are nearly superimposable and quite similar to the corresponding structures of the human enzyme. Likewise, the bacterial enzyme is activated for single electron transfer after binding to the substrate analogue fluorotyrosine as previously observed with the human enzyme. A cocrystal structure of bacterial deiodinase and 2-iodophenol indicates that this ligand stacks on the active site flavin mononucleotide (FMN) in a orientation analogous to that of bound iodotyrosine. However, 2-iodophenol association is not sufficient to activate the FMN chemistry required for catalysis, and thus the bacterial enzyme appears to share a similar specificity for halotyrosines even though their physiological roles are likely very different from those in humans.
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Affiliation(s)
- Nattha Ingavat
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218 United States
| | - Jennifer M. Kavran
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street Baltimore, Maryland 21205 United States,Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, 925 North Wolfe Street Baltimore, Maryland, 21205 United States
| | - Zuodong Sun
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218 United States
| | - Steven E. Rokita
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218 United States,Corresponding Author:
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