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Petkowski JJ, Seager S, Bains W. Reasons why life on Earth rarely makes fluorine-containing compounds and their implications for the search for life beyond Earth. Sci Rep 2024; 14:15575. [PMID: 38971876 PMCID: PMC11227584 DOI: 10.1038/s41598-024-66265-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024] Open
Abstract
Life on Earth is known to rarely make fluorinated carbon compounds, as compared to other halocarbons. We quantify this rarity, based on our exhaustive natural products database curated from available literature. We build on explanations for the scarcity of fluorine chemistry in life on Earth, namely that the exclusion of the C-F bond stems from the unique physico-chemical properties of fluorine, predominantly its extreme electronegativity and strong hydration shell. We further show that the C-F bond is very hard to synthesize and when it is made by life its potential biological functions can be readily provided by alternative functional groups that are much less costly to incorporate into existing biochemistry. As a result, the overall evolutionary cost-to-benefit balance of incorporation of the C-F bond into the chemical repertoire of life is not favorable. We argue that the limitations of organofluorine chemistry are likely universal in that they do not exclusively apply to specifics of Earth's biochemistry. C-F bonds, therefore, will be rare in life beyond Earth no matter its chemical makeup.
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Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Faculty of Environmental Engineering, Wroclaw University of Science and Technology, 50-370, Wroclaw, Poland.
- JJ Scientific, Warsaw, Mazowieckie, Poland.
| | - Sara Seager
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - William Bains
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- School of Physics & Astronomy, Cardiff University, 4 The Parade, Cardiff, CF24 3AA, UK
- Rufus Scientific, Melbourn, Royston, Herts, UK
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2
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Gozari M, Alborz M, El-Seedi HR, Jassbi AR. Chemistry, biosynthesis and biological activity of terpenoids and meroterpenoids in bacteria and fungi isolated from different marine habitats. Eur J Med Chem 2020; 210:112957. [PMID: 33160760 DOI: 10.1016/j.ejmech.2020.112957] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/16/2020] [Accepted: 10/17/2020] [Indexed: 02/06/2023]
Abstract
The marine environment with its vast biological diversity encompasses many organisms that produce bioactive natural products. Marine microorganisms are rich sources of compounds from many structural classes with a multitude of biological activities. The biosynthesis of microbial natural products depends on a variety of biotic and abiotic factors in the marine environment, including temperature, nutrients, salinity and interaction with other microorganisms. Terpenoids, as one of the most important groups of natural products in terrestrial microorganisms are important metabolites for marine microorganisms. Here, we have reviewed the chemistry, biosynthesis and pharmacological activities of terpenoids, extracted from marine microbes, and then survey their potential applications in drug development. We also discussed the different habitats in which marine microorganisms are found including sediments, the flora, such as seaweeds, sea grasses, and mangroves as well as the fauna like sponges and corals. Amongst these habitats, marine sediments are the major source for terpenoids producing microorganisms. The marine bacteria produce mostly meroterpenoids, while the fungi are well known for production of isoprenoids. Interestingly, marine-derived microbial terpenoids have some structural characteristics such as halogenation, which are catalyzed by specific enzymes with distinct substrate specificity. These compounds have anticancer, antibacterial, antifungal, antimalarial and anti-inflammatory properties. The information collected here might provide useful clues for developing new medications.
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Affiliation(s)
- Mohsen Gozari
- Persian Gulf and Oman Sea Ecological Research Center, Iranian Fisheries Science Research Institute, Agricultural Research, Education and Extension Organization, Bandar Abbas, Iran
| | - Maryam Alborz
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hesham R El-Seedi
- Pharmacognosy Group, Department of Pharmaceutical Biosciences, BMC, Uppsala University, SE-751 23, Uppsala, Sweden; International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, PR China
| | - Amir Reza Jassbi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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3
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Gutleben J, Koehorst JJ, McPherson K, Pomponi S, Wijffels RH, Smidt H, Sipkema D. Diversity of tryptophan halogenases in sponges of the genus Aplysina. FEMS Microbiol Ecol 2019; 95:fiz108. [PMID: 31276591 PMCID: PMC6644159 DOI: 10.1093/femsec/fiz108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/04/2019] [Indexed: 12/21/2022] Open
Abstract
Marine sponges are a prolific source of novel enzymes with promising biotechnological potential. Especially halogenases, which are key enzymes in the biosynthesis of brominated and chlorinated secondary metabolites, possess interesting properties towards the production of pharmaceuticals that are often halogenated. In this study we used a polymerase chain reaction (PCR)-based screening to simultaneously examine and compare the richness and diversity of putative tryptophan halogenase protein sequences and bacterial community structures of six Aplysina species from the Mediterranean and Caribbean seas. At the phylum level, bacterial community composition was similar amongst all investigated species and predominated by Actinobacteria, Chloroflexi, Cyanobacteria, Gemmatimonadetes, and Proteobacteria. We detected four phylogenetically diverse clades of putative tryptophan halogenase protein sequences, which were only distantly related to previously reported halogenases. The Mediterranean species Aplysina aerophoba harbored unique halogenase sequences, of which the most predominant was related to a sponge-associated Psychrobacter-derived sequence. In contrast, the Caribbean species shared numerous novel halogenase sequence variants and exhibited a highly similar bacterial community composition at the operational taxonomic unit (OTU) level. Correlations of relative abundances of halogenases with those of bacterial taxa suggest that prominent sponge symbiotic bacteria, including Chloroflexi and Actinobacteria, are putative producers of the detected enzymes and may thus contribute to the chemical defense of their host.
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Affiliation(s)
- Johanna Gutleben
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Kyle McPherson
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Shirley Pomponi
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
- Florida Atlantic University – Harbor Branch, 5600 U.S. 1, Fort Pierce, FL 34946, the United States
| | - René H Wijffels
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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4
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Genome- and MS-based mining of antibacterial chlorinated chromones and xanthones from the phytopathogenic fungus Bipolaris sorokiniana strain 11134. Appl Microbiol Biotechnol 2019; 103:5167-5181. [PMID: 31001746 DOI: 10.1007/s00253-019-09821-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/18/2022]
Abstract
Halogen substituents are important for biological activity in many compounds. Genome-based mining of halogenase along with its biosynthetic gene cluster provided an efficient approach for the discovery of naturally occurring organohalogen compounds. Analysis of the genome sequence of a phytopathogenic fungus Bipolaris sorokiniana 11134 revealed a polyketide gene cluster adjacent to a flavin-dependent halogenase capable of encoding halogenated polyketides, which are rarely reported in phytopathogenic fungi. Furthermore, MS- and UV-guided isolation and purification led to the identification of five chlorine-containing natural products together with seven other chromones and xanthones. Two of the chlorinated compounds and four chromones are new compounds. Their structures were elucidated by NMR spectroscopic analysis and HRESIMS data. The biosynthetic gene clusters of isolated compounds and their putative biosynthetic pathway are also proposed. One new chlorinated compound showed activity against Staphylococcus aureus, methicillin-resistant S. aureus, and three clinical-resistant S. aureus strains with a shared minimum inhibitory concentration (MIC) of 12.5 μg/mL. Genome-based mining of halogenases combined with high-resolution MS- and UV-guided identification provides an efficient approach to discover new halogenated natural products from microorganisms.
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5
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Backenköhler J, Spindler S, Spiteller P. Total Synthesis of Damirone C, Makaluvamine O, Makaluvone, Batzelline C and Batzelline D. ChemistrySelect 2017. [DOI: 10.1002/slct.201700285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jana Backenköhler
- Universität BremenInstitut für Organische und Analytische Chemie Leobener Str. NW2C 28359 Bremen Germany
| | - Stefanie Spindler
- Universität BremenInstitut für Organische und Analytische Chemie Leobener Str. NW2C 28359 Bremen Germany
| | - Peter Spiteller
- Universität BremenInstitut für Organische und Analytische Chemie Leobener Str. NW2C 28359 Bremen Germany
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6
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Metal complexes of anthranilic acid derivatives: A new class of non-competitive α-glucosidase inhibitors. CHINESE CHEM LETT 2016. [DOI: 10.1016/j.cclet.2016.01.052] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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7
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Junk L, Kazmaier U. Synthesis of indoles and tryptophan derivatives via photoinduced nitrene C–H insertion. Org Biomol Chem 2016; 14:2916-23. [DOI: 10.1039/c5ob02563j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Functionalized indoles and tryptophans can be obtained from stannylated alkenes and o-iodoanilines via Stille coupling.
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Affiliation(s)
- Lukas Junk
- Institute of Organic Chemistry
- Saarland University
- 66041 Saarbrücken
- Germany
| | - Uli Kazmaier
- Institute of Organic Chemistry
- Saarland University
- 66041 Saarbrücken
- Germany
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8
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Ma L, Bartholome A, Tong MH, Qin Z, Yu Y, Shepherd T, Kyeremeh K, Deng H, O'Hagan D. Identification of a fluorometabolite from Streptomyces sp. MA37: (2 R3 S4 S)-5-fluoro-2,3,4-trihydroxypentanoic acid. Chem Sci 2015; 6:1414-1419. [PMID: 29861965 PMCID: PMC5947533 DOI: 10.1039/c4sc03540b] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 11/26/2014] [Indexed: 01/19/2023] Open
Abstract
(2R3S4S)-5-Fluoro-2,3,4-trihydroxypentanoic acid (5-FHPA) has been discovered as a new fluorometabolite in the soil bacterium Streptomyces sp. MA37. Exogenous addition of 5-fluoro-5-deoxy-d-ribose (5-FDR) into the cell free extract of MA37 demonstrated that 5-FDR was an intermediate to a range of unidentified fluorometabolites, distinct from fluoroacetate (FAc) and 4-fluorothreonine (4-FT). Bioinformatics analysis allowed identification of a gene cluster (fdr), encoding a pathway to the biosynthesis of 5-FHPA. Over-expression and in vitro assay of FdrC indicated that FdrC is a NAD+ dependent dehydrogenase responsible for oxidation of 5-FDR into 5-fluoro-5-deoxy-lactone, followed by hydrolysis to 5-FHPA. The identity of 5-FHPA in the fermentation broth was confirmed by synthesis of a reference compound and then co-correlation by 19F-NMR and GC-MS analysis. The occurrence of 5-FHPA proves the existence of a new fluorometabolite pathway.
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Affiliation(s)
- Long Ma
- EaStChem School of Chemistry , University of St Andrews , North Haugh , St Andrews KY169ST , UK .
| | - Axel Bartholome
- EaStChem School of Chemistry , University of St Andrews , North Haugh , St Andrews KY169ST , UK .
| | - Ming Him Tong
- Marine Biodiscovery Centre , Department of Chemistry , University of Aberdeen , Meston Walk , Aberdeen AB24 3UE , UK .
| | - Zhiwei Qin
- Marine Biodiscovery Centre , Department of Chemistry , University of Aberdeen , Meston Walk , Aberdeen AB24 3UE , UK .
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education) , School of Pharmaceutical Sciences , Wuhan University , 185 East Lake Road , Wuhan 430071 , P. R. China
| | - Thomas Shepherd
- The James Hutton Institute , Invergowrie , Dundee , DD2 5DA , UK
| | - Kwaku Kyeremeh
- Department of Chemistry , University of Ghana , FGO Torto Building , Legon , Ghana
| | - Hai Deng
- Marine Biodiscovery Centre , Department of Chemistry , University of Aberdeen , Meston Walk , Aberdeen AB24 3UE , UK .
| | - David O'Hagan
- EaStChem School of Chemistry , University of St Andrews , North Haugh , St Andrews KY169ST , UK .
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9
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Bhuma N, Vangala M, Nair RJ, Sabharwal SG, Dhavale DD. Halogenated d-xylono-δ-lactams: synthesis and enzyme inhibition study. Carbohydr Res 2015; 402:215-24. [DOI: 10.1016/j.carres.2014.10.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/18/2014] [Accepted: 10/23/2014] [Indexed: 10/24/2022]
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10
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O'Hagan D, Deng H. Enzymatic fluorination and biotechnological developments of the fluorinase. Chem Rev 2014; 115:634-49. [PMID: 25253234 DOI: 10.1021/cr500209t] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- David O'Hagan
- EaStChem School of Chemistry, University of St Andrews , North Haugh, St Andrews KY169ST, United Kingdom
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11
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Mahidol C, Kittakoop P, Prachyawarakorn V, Pailee P, Prawat H, Ruchirawat S. Recent investigations of bioactive natural products from endophytic, marine-derived, insect pathogenic fungi and Thai medicinal plants. PURE APPL CHEM 2014. [DOI: 10.1515/pac-2013-1206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractLiving organisms in Thailand are very diverse due to the unique geographical location of Thailand. The diversity of Thai bioresources has proven to be a rich source of biologically active compounds. The present review covers bioactive substances from Thai endophytic, marine-derived, insect pathogenic fungi and medicinal plants. Many new compounds isolated from Thai bioresources have diverse skeletons belonging to various classes of natural products. These compounds exhibited an array of biological activities, and some are of pharmaceutical interest. Bioactive compounds from Thai bioresources have not only attracted organic chemists to develop strategies for total synthesis, but also attracted (chemical) biologists to investigate the mechanisms of action. The chemistry and biology of some selected compounds are also discussed in this review.
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Affiliation(s)
- Chulabhorn Mahidol
- 1Chulabhorn Research Institute, Chulabhorn Graduate Institute, and Center of Excellence on Environmental Health and Toxicology (EHT), Kamphang Phet 6 Road, Laksi, Bangkok 10210, Thailand
| | - Prasat Kittakoop
- 1Chulabhorn Research Institute, Chulabhorn Graduate Institute, and Center of Excellence on Environmental Health and Toxicology (EHT), Kamphang Phet 6 Road, Laksi, Bangkok 10210, Thailand
| | - Vilailak Prachyawarakorn
- 1Chulabhorn Research Institute, Chulabhorn Graduate Institute, and Center of Excellence on Environmental Health and Toxicology (EHT), Kamphang Phet 6 Road, Laksi, Bangkok 10210, Thailand
| | - Phanruethai Pailee
- 1Chulabhorn Research Institute, Chulabhorn Graduate Institute, and Center of Excellence on Environmental Health and Toxicology (EHT), Kamphang Phet 6 Road, Laksi, Bangkok 10210, Thailand
| | - Hunsa Prawat
- 1Chulabhorn Research Institute, Chulabhorn Graduate Institute, and Center of Excellence on Environmental Health and Toxicology (EHT), Kamphang Phet 6 Road, Laksi, Bangkok 10210, Thailand
| | - Somsak Ruchirawat
- 1Chulabhorn Research Institute, Chulabhorn Graduate Institute, and Center of Excellence on Environmental Health and Toxicology (EHT), Kamphang Phet 6 Road, Laksi, Bangkok 10210, Thailand
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12
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Hutchinson RI, Grant RJ, Murphy CD. Biosynthetic Origin of [R-(Z)]-4-Amino-3-chloro-2-pentenedioic Acid inStreptomyces viridogenes. Biosci Biotechnol Biochem 2014; 70:3046-9. [PMID: 17151454 DOI: 10.1271/bbb.60372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The biosynthesis of the chlorinated amino acid [R-(Z)]-4-amino-3-chloro-2-pentenedioic acid (ACPA) was investigated. Feeding studies with Streptomyces viridogenes were conducted in resting cells. Substantial incorporation from [(15)N]- and [(13)C]-enriched glutamate and proline indicated that the biosynthetic origin of ACPA is one of these amino acids. Experiments with deuterated glutamate and proline imply that chlorination does not occur via a radical mechanism, but rather suggest that a FADH(2)-dependent halogenase is involved.
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Affiliation(s)
- Robin I Hutchinson
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, Ardmore House, University College Dublin
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13
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Harnessing the potential of halogenated natural product biosynthesis by mangrove-derived actinomycetes. Mar Drugs 2013; 11:3875-90. [PMID: 24129229 PMCID: PMC3826140 DOI: 10.3390/md11103875] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 09/26/2013] [Accepted: 09/27/2013] [Indexed: 12/30/2022] Open
Abstract
Mangrove-derived actinomycetes are promising sources of bioactive natural products. In this study, using homologous screening of the biosynthetic genes and anti-microorganism/tumor assaying, 163 strains of actinomycetes isolated from mangrove sediments were investigated for their potential to produce halogenated metabolites. The FADH2-dependent halogenase genes, identified in PCR-screening, were clustered in distinct clades in the phylogenetic analysis. The coexistence of either polyketide synthase (PKS) or nonribosomal peptide synthetase (NRPS) as the backbone synthetases in the strains harboring the halogenase indicated that these strains had the potential to produce structurally diversified antibiotics. As a validation, a new enduracidin producer, Streptomyces atrovirens MGR140, was identified and confirmed by gene disruption and HPLC analysis. Moreover, a putative ansamycin biosynthesis gene cluster was detected in Streptomyces albogriseolus MGR072. Our results highlight that combined genome mining is an efficient technique to tap promising sources of halogenated natural products synthesized by mangrove-derived actinomycetes.
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Bayer K, Scheuermayer M, Fieseler L, Hentschel U. Genomic mining for novel FADH₂-dependent halogenases in marine sponge-associated microbial consortia. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:63-72. [PMID: 22562484 DOI: 10.1007/s10126-012-9455-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 04/15/2012] [Indexed: 05/31/2023]
Abstract
Many marine sponges (Porifera) are known to contain large amounts of phylogenetically diverse microorganisms. Sponges are also known for their large arsenal of natural products, many of which are halogenated. In this study, 36 different FADH₂-dependent halogenase gene fragments were amplified from various Caribbean and Mediterranean sponges using newly designed degenerate PCR primers. Four unique halogenase-positive fosmid clones, all containing the highly conserved amino acid motif "GxGxxG", were identified in the microbial metagenome of Aplysina aerophoba. Sequence analysis of one halogenase-bearing fosmid revealed notably two open reading frames with high homologies to efflux and multidrug resistance proteins. Single cell genomic analysis allowed for a taxonomic assignment of the halogenase genes to specific symbiotic lineages. Specifically, the halogenase cluster S1 is predicted to be produced by a deltaproteobacterial symbiont and halogenase cluster S2 by a poribacterial sponge symbiont. An additional halogenase gene is possibly produced by an actinobacterial symbiont of marine sponges. The identification of three novel, phylogenetically, and possibly also functionally distinct halogenase gene clusters indicates that the microbial consortia of sponges are a valuable resource for novel enzymes involved in halogenation reactions.
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Affiliation(s)
- Kristina Bayer
- Julius-von-Sachs Institute for Biological Sciences, University of Wuerzburg, Julius-von-Sachs Platz 3, D-97082 Wuerzburg, Germany
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15
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Sureram S, Kesornpun C, Mahidol C, Ruchirawat S, Kittakoop P. Directed biosynthesis through biohalogenation of secondary metabolites of the marine-derived fungus Aspergillus unguis. RSC Adv 2013. [DOI: 10.1039/c2ra23021f] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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16
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Insights into fluorometabolite biosynthesis in Streptomyces cattleya DSM46488 through genome sequence and knockout mutants. Bioorg Chem 2012; 44:1-7. [PMID: 22858315 DOI: 10.1016/j.bioorg.2012.06.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 06/20/2012] [Indexed: 11/20/2022]
Abstract
Streptomyces cattleya DSM 46488 is unusual in its ability to biosynthesise fluorine containing natural products, where it can produce fluoroacetate and 4-fluorothreonine. The individual enzymes involved in fluorometabolite biosynthesis have already been demonstrated in in vitro investigations. Candidate genes for the individual biosynthetic steps were located from recent genome sequences. In vivo inactivation of individual genes including those encoding the S-adenosyl-l-methionine:fluoride adenosyltransferase (fluorinase, SCATT_41540), 5'-fluoro-5'-deoxyadenosine phosphorylase (SCATT_41550), fluoroacetyl-CoA thioesterase (SCATT_41470), 5-fluoro-5-deoxyribose-1-phosphate isomerase (SCATT_20080) and a 4-fluorothreonine acetaldehyde transaldolase (SCATT_p11780) confirm that they are essential for fluorometabolite production. Notably gene disruption of the transaldolase (SCATT_p11780) resulted in a mutant which could produce fluoroacetate but was blocked in its ability to biosynthesise 4-fluorothreonine, revealing a branchpoint role for the PLP-transaldolase.
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17
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Owusu-Ansah E, Durow AC, Harding JR, Jordan AC, O'Connell SJ, Willis CL. Synthesis of dysideaproline E using organocatalysis. Org Biomol Chem 2011; 9:265-72. [DOI: 10.1039/c0ob00617c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Schmidberger JW, James AB, Edwards R, Naismith JH, O’Hagan D. Halomethane biosynthesis: structure of a SAM-dependent halide methyltransferase from Arabidopsis thaliana. Angew Chem Int Ed Engl 2010; 49:3646-8. [PMID: 20376845 PMCID: PMC3386781 DOI: 10.1002/anie.201000119] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A product structure of the halomethane producing enzyme in plants (Arabidopsis thaliana ) is reported and a model for presentation of chloride/bromide ion to the methyl group of S-adenosyl-L-methionine (SAM) is presented to rationalise nucleophilic halide attack for halomethane production, gaseous natural products that are produced globally.
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Affiliation(s)
- Jason W. Schmidberger
- University of St Andrews, Department of Chemistry, Centre for Biomolecular Sciences, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | | | - Robert Edwards
- University of Durham, School of Biological & Medical Sciences, South Road, Durham, DH1 3LE, UK Fax: (+44) 191 3341201
| | - James H. Naismith
- University of St Andrews, Department of Chemistry, Centre for Biomolecular Sciences, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - David O’Hagan
- University of St Andrews, Department of Chemistry, Centre for Biomolecular Sciences, North Haugh, St Andrews, Fife, KY16 9ST, UK
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Iyer LM, Abhiman S, de Souza RF, Aravind L. Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase. Nucleic Acids Res 2010; 38:5261-79. [PMID: 20423905 PMCID: PMC2938197 DOI: 10.1093/nar/gkq265] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Unlike classical 2-oxoglutarate and iron-dependent dioxygenases, which include several nucleic acid modifiers, the structurally similar jumonji-related dioxygenase superfamily was only known to catalyze peptide modifications. Using comparative genomics methods, we predict that a family of jumonji-related enzymes catalyzes wybutosine hydroxylation/peroxidation at position 37 of eukaryotic tRNAPhe. Identification of this enzyme raised questions regarding the emergence of protein- and nucleic acid-modifying activities among jumonji-related domains. We addressed these with a natural classification of DSBH domains and reconstructed the precursor of the dioxygenases as a sugar-binding domain. This precursor gave rise to sugar epimerases and metal-binding sugar isomerases. The sugar isomerase active site was exapted for catalysis of oxygenation, with a radiation of these enzymes in bacteria, probably due to impetus from the primary oxygenation event in Earth’s history. 2-Oxoglutarate-dependent versions appear to have further expanded with rise of the tricarboxylic acid cycle. We identify previously under-appreciated aspects of their active site and multiple independent innovations of 2-oxoacid-binding basic residues among these superfamilies. We show that double-stranded β-helix dioxygenases diversified extensively in biosynthesis and modification of halogenated siderophores, antibiotics, peptide secondary metabolites and glycine-rich collagen-like proteins in bacteria. Jumonji-related domains diversified into three distinct lineages in bacterial secondary metabolism systems and these were precursors of the three major clades of eukaryotic enzymes. The specificity of wybutosine hydroxylase/peroxidase probably relates to the structural similarity of the modified moiety to the ancestral amino acid substrate of this superfamily.
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Affiliation(s)
- Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Schmidberger J, James A, Edwards R, Naismith J, O'Hagan D. Halomethane Biosynthesis: Structure of a SAM-Dependent Halide Methyltransferase from Arabidopsis thaliana. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000119] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Cristiano R, Ma K, Pottanat G, Weiss RG. Tetraalkylphosphonium Trihalides. Room Temperature Ionic Liquids As Halogenation Reagents. J Org Chem 2009; 74:9027-33. [DOI: 10.1021/jo901735h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rodrigo Cristiano
- Department of Chemistry, Georgetown University, Washington, D.C. 20057-1227
| | - Kefeng Ma
- Department of Chemistry, Georgetown University, Washington, D.C. 20057-1227
| | - George Pottanat
- Department of Chemistry, Georgetown University, Washington, D.C. 20057-1227
| | - Richard G. Weiss
- Department of Chemistry, Georgetown University, Washington, D.C. 20057-1227
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Wagner C, El Omari M, König GM. Biohalogenation: nature's way to synthesize halogenated metabolites. JOURNAL OF NATURAL PRODUCTS 2009; 72:540-553. [PMID: 19245259 DOI: 10.1021/np800651m] [Citation(s) in RCA: 156] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Halogenated natural products are widely distributed in nature, some of them showing potent biological activities. Incorporation of halogen atoms in drug leads is a common strategy to modify molecules in order to vary their bioactivities and specificities. Chemical halogenation, however, often requires harsh reaction conditions and results in unwanted byproduct formation. It is thus of great interest to investigate the biosynthesis of halogenated natural products and the biotechnological potential of halogenating enzymes. This review aims to give a comprehensive overview on the current knowledge concerning biological halogenations.
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Affiliation(s)
- Claudia Wagner
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115 Bonn, Germany
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23
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Buedenbender S, Rachid S, Müller R, Schulz GE. Structure and action of the myxobacterial chondrochloren halogenase CndH: a new variant of FAD-dependent halogenases. J Mol Biol 2008; 385:520-30. [PMID: 19000696 DOI: 10.1016/j.jmb.2008.10.057] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 10/11/2008] [Accepted: 10/21/2008] [Indexed: 10/21/2022]
Abstract
The crystal structure of the FAD-dependent chondrochloren halogenase CndH has been established at 2.1 A resolution. The enzyme contains the characteristic FAD-binding scaffold of the glutathione reductase superfamily. Except for its C-terminal domain, the chainfold of CndH is virtually identical with those of FAD-dependent aromatic hydroxylases. When compared to the structurally known FAD-dependent halogenases PrnA and RebH, CndH lacks a 45 residue segment near position 100 and deviates in the C-terminal domain. Both variations are near the active center and appear to reflect substrate differences. Whereas PrnA and RebH modify free tryptophan, CndH halogenates the tyrosyl group of a chondrochloren precursor that is most likely bound to a carrier protein. In contrast to PrnA and RebH, which enclose their small substrate completely, CndH has a large non-polar surface patch that may accommodate the putative carrier. Apart from the substrate binding site, the active center of CndH corresponds to those of PrnA and RebH. At the halogenation site, CndH has the characteristic lysine (Lys76) but lacks the required base Glu346 (PrnA). This base may be supplied by a residue of its C-terminal domain or by the carrier. These differences were corroborated by an overall sequence comparison between the known FAD-dependent halogenases, which revealed a split into a PrnA-RebH group and a CndH group. The two functionally established members of the CndH group use carrier-bound substrates, whereas three members of PrnA-RebH group are known to accept a free amino acid. Given the structural and functional distinction, we classify CndH as a new variant B of the FAD-dependent halogenases, adding a new feature to the structurally established variant A enzymes PrnA and RebH.
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Affiliation(s)
- Stefan Buedenbender
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstr. 21, D-79104 Freiburg im Breisgau, Germany
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CHEN XP, HUANG MF, WANG B. Flavin-dependent Tryptophan Halogenases and Their Use in Formation of Novel Tryptophan Derived Compounds. CHINESE J CHEM 2008. [DOI: 10.1002/cjoc.200890269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Kuetchou Ngnigha A, Muffler K, Ernyei A, van Pée KH, Ulber R. Biologische Halogenierung. CHEM-ING-TECH 2008. [DOI: 10.1002/cite.200800005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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26
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Ardá A, G. Soengas R, Nieto MI, Jiménez C, Rodríguez J. Total Synthesis of (−)-Dysithiazolamide. Org Lett 2008; 10:2175-8. [DOI: 10.1021/ol800551g] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ana Ardá
- Departamento de Química Fundamental, Facultade de Ciencias, Campus da Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - Raquel G. Soengas
- Departamento de Química Fundamental, Facultade de Ciencias, Campus da Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - M. Isabel Nieto
- Departamento de Química Fundamental, Facultade de Ciencias, Campus da Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - Carlos Jiménez
- Departamento de Química Fundamental, Facultade de Ciencias, Campus da Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
| | - Jaime Rodríguez
- Departamento de Química Fundamental, Facultade de Ciencias, Campus da Zapateira, Universidade da Coruña, 15071 A Coruña, Spain
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Wagner C, Molitor IM, König GM. Critical view on the monochlorodimedone assay utilized to detect haloperoxidase activity. PHYTOCHEMISTRY 2008; 69:323-32. [PMID: 17889043 DOI: 10.1016/j.phytochem.2007.07.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Revised: 07/16/2007] [Accepted: 07/29/2007] [Indexed: 05/17/2023]
Abstract
The current study aimed to identify the halogenating enzymes involved in the biosynthesis of the ambigols A, B, C and tjipanazole D, isolated from the cyanobacterium Fischerella ambigua. Haloperoxidase (HPO) activity within F. ambigua was therefore assayed spectrophotometrically by using monochlorodimedone (MCD) during protein purification. This strategy revealed the isolation of a protein positive in the MCD-assay, but an involvement in halogenating processes could not be verified. N-terminal sequencing rather demonstrated homology to cytochrome c(6) from other cyanobacteria and green algae. From our findings it thus has to be concluded that the spectrophotometrical MCD-assay routinely used to detect HPO activity may yield false positive results, mainly since the assay focuses on the decline of the educt and not on the formation of the product. Our data indicate that the reaction of MCD with proteins of the cytochrome c- family leads to unspecific products.
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Affiliation(s)
- Claudia Wagner
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, D-53115 Bonn, Germany
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Peters S, Spiteller P. Chloro- and bromophenols from cultures of Mycena alcalina. JOURNAL OF NATURAL PRODUCTS 2006; 69:1809-12. [PMID: 17190467 DOI: 10.1021/np0603368] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Three new chlorinated phenols have been isolated from mycelial cultures of the mushroom Mycena alcalina. Their structures were determined by mass spectrometry and 1D and 2D NMR experiments. Addition of bromide to the medium resulted in the production of the corresponding brominated phenols. In addition, small amounts of the nonhalogenated precursor were also isolated, indicating that the halogenated metabolites are generated by a regioselectively operating halogenase.
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Affiliation(s)
- Silke Peters
- Institut für Organische Chemie und Biochemie II der Technischen Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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Durow AC, Long GC, O'Connell SJ, Willis CL. Total Synthesis of the Chlorinated Marine Natural Product Dysamide B. Org Lett 2006; 8:5401-4. [PMID: 17078728 DOI: 10.1021/ol062279f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[Structure: see text] Two approaches to the synthesis of (2S,4S)-5,5-dichloroleucine are compared, and the parent amino acid was used in the first total synthesis of the polychlorinated marine natural product, dysamide B. A key step was the lead tetraacetate-mediated decarboxylation of an alpha,alpha-dichloro acid in the presence of 1,4-cyclohexadiene to generate the dichloromethyl group.
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Affiliation(s)
- Amanda C Durow
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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