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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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Díaz-Díaz M, Antón-Domínguez BI, Raya MC, Bernal-Cabrera A, Medina-Marrero R, Trapero A, Agustí-Brisach C. Streptomyces spp. Strains as Potential Biological Control Agents against Verticillium Wilt of Olive. J Fungi (Basel) 2024; 10:138. [PMID: 38392810 PMCID: PMC10890128 DOI: 10.3390/jof10020138] [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: 01/02/2024] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Verticillium wilt of olive (VWO) caused by Verticillium dahliae is considered a major olive (Olea europaea) disease in Mediterranean-type climate regions. The lack of effective chemical products against VWO makes it necessary to search for alternatives such as biological control. The main goal of this study was to evaluate the effect of six Streptomyces spp. strains as biological control agents (BCAs) against VWO. All of them were molecularly characterized by sequencing 16S or 23S rRNA genes and via phylogenetic analysis. Their effect was evaluated in vitro on the mycelial growth of V. dahliae (isolates V004 and V323) and on microsclerotia (MS) viability using naturally infested soils. Bioassays in olive plants inoculated with V. dahliae were also conducted to evaluate their effect against disease progress. In all the experiments, the reference BCAs Fusarium oxysporum FO12 and Aureobasidium pullulans AP08 were included for comparative purposes. The six strains were identified as Streptomyces spp., and they were considered as potential new species. All the BCAs, including Streptomyces strains, showed a significant effect on mycelial growth inhibition for both V. dahliae isolates compared to the positive control, with FO12 being the most effective, followed by AP08, while the Streptomyces spp. strains showed an intermediate effect. All the BCAs tested also showed a significant effect on the inhibition of germination of V. dahliae MS compared to the untreated control, with FO12 being the most effective treatment. Irrigation treatments with Streptomyces strain CBQ-EBa-21 or FO12 were significantly more effective in reducing disease severity and disease progress in olive plants inoculated with V. dahliae compared to the remaining treatments. This study represents the first approach to elucidating the potential effect of Streptomyces strains against VWO.
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Affiliation(s)
- Miriam Díaz-Díaz
- Centro de Bioactivos Químicos (CBQ), Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
| | - Begoña I Antón-Domínguez
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
| | - María Carmen Raya
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
| | - Alexander Bernal-Cabrera
- Centro de Investigaciones Agropecuarias (CIAP), Facultad de Ciencias Agropecuarias, Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
- Departamento de Agronomía, Facultad de Ciencias Agropecuarias, Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
| | - Ricardo Medina-Marrero
- Centro de Bioactivos Químicos (CBQ), Universidad Central "Marta Abreu" de Las Villas (UCLV), Carretera Camajuaní km 5 1/2, Santa Clara 54830, Villa Clara, Cuba
| | - Antonio Trapero
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
| | - Carlos Agustí-Brisach
- Departamento de Agronomía, (Unit of Excellence 'María de Maeztu' 2020-2024), Universidad de Córdoba, Campus de Rabanales, Edif. C4, 14071 Córdoba, Spain
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Feng X, Zhang Q, Clarke DJ, Deng H, O’Hagan D. 3'- O-β-Glucosyl-4',5'-didehydro-5'-deoxyadenosine Is a Natural Product of the Nucleocidin Producers Streptomyces virens and Streptomyces calvus. JOURNAL OF NATURAL PRODUCTS 2023; 86:2326-2332. [PMID: 37748016 PMCID: PMC10616807 DOI: 10.1021/acs.jnatprod.3c00521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Indexed: 09/27/2023]
Abstract
3'-O-β-Glucosyl-4',5'-didehydro-5'-deoxyadenosine 13 is identified as a natural product of Streptomyces calvus and Streptomyces virens. It is also generated in vitro by direct β-glucosylation of 4',5'-didehydro-5'-deoxyadenosine 12 with the enzyme NucGT. The intact incorporation of oxygen-18 and deuterium isotopes from (±)[1-18O,1-2H2]-glycerol 14 into C-5' of nucleocidin 1 and its related metabolites precludes 3'-O-β-glucosyl-4',5'-didehydro-5'-deoxyadenosine 13 as a biosynthetic precursor to nucleocidin 1.
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Affiliation(s)
- Xuan Feng
- School
of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, U.K.
| | - Qingzhi Zhang
- School
of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, U.K.
| | - David J. Clarke
- EaStChem
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh, EH9 3FJ, U.K.
| | - Hai Deng
- Department
of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, U.K.
| | - David O’Hagan
- School
of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, U.K.
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Wojnowska M, Feng X, Chen Y, Deng H, O'Hagan D. Identification of Genes Essential for Fluorination and Sulfamylation within the Nucleocidin Gene Clusters of Streptomyces calvus and Streptomyces virens. Chembiochem 2023; 24:e202200684. [PMID: 36548247 PMCID: PMC10946740 DOI: 10.1002/cbic.202200684] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 12/24/2022]
Abstract
The gene cluster in Streptomyces calvus associated with the biosynthesis of the fluoro- and sulfamyl-metabolite nucleocidin was interrogated by systematic gene knockouts. Out of the 26 gene deletions, most did not affect fluorometabolite production, nine abolished sulfamylation but not fluorination, and three precluded fluorination, but had no effect on sulfamylation. In addition to nucI, nucG, nucJ, nucK, nucL, nucN, nucO, nucQ and nucP, we identified two genes (nucW, nucA), belonging to a phosphoadenosine phosphosulfate (PAPS) gene cluster, as required for sulfamyl assembly. Three genes (orf(-3), orf2 and orf3) were found to be essential for fluorination, although the activities of their protein products are unknown. These genes as well as nucK, nucN, nucO and nucPNP, whose knockouts produced results differing from those described in a recent report, were also deleted in Streptomyces virens - with confirmatory outcomes. This genetic profile should inform biochemistry aimed at uncovering the enzymology behind nucleocidin biosynthesis.
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Affiliation(s)
- Marta Wojnowska
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| | - Xuan Feng
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| | - Yawen Chen
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| | - Hai Deng
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| | - David O'Hagan
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
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Lowe PT, O'Hagan D. 4'-Fluoro-nucleosides and nucleotides: from nucleocidin to an emerging class of therapeutics. Chem Soc Rev 2023; 52:248-276. [PMID: 36472161 DOI: 10.1039/d2cs00762b] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The history and development of 4'-fluoro-nucleosides is discussed in this review. This is a class of nucleosides which have their origin in the discovery of the rare fluorine containing natural product nucleocidin. Nucleocidin contains a fluorine atom located at the 4'-position of its ribose ring. From its early isolation as an unexpected natural product, to its total synthesis and bioactivity assessment, nucleocidin has played a role in inspiring the exploration of 4'-fluoro-nucleosides as a privileged motif for nucleoside-based therapeutics.
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Affiliation(s)
- Phillip T Lowe
- School of Chemistry and Biomedical Sciences Research Centre, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK.
| | - David O'Hagan
- School of Chemistry and Biomedical Sciences Research Centre, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK.
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Pasternak ARO, Balunas MJ, Zechel DL. Discovery of 3'- O-β-Glucosyltubercidin and the Nucleoside Specific Glycosyltransferase AvpGT through Genome Mining. ACS Chem Biol 2022; 17:3507-3514. [PMID: 36356213 DOI: 10.1021/acschembio.2c00707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A genome mining approach was used to identify a hybrid tubercidin-nucleocidin biosynthetic gene cluster (BGC) in Streptomyces sp. AVP053U2. Analysis of culture extracts by liquid chromatography-mass spectrometry revealed the presence of a glucosylated tubercidin derivative. A gene, avpGT, was identified within the hybrid cluster that has homology to the glucosyltransferase that is responsible for 3'-O-β-glucosylation of the fluorinated natural product nucleocidin. AvpGT was heterologously expressed and purified from Escherichia coli for in vitro characterization. AvpGT is active toward UDP-glucose and UDP-galactose as glycosyl donors and several nucleosides as acceptors. Kinetic analysis revealed that AvpGT is most specific for UDP-glucose [kcat/KMapp = (1.1 ± 0.3) × 105 M-1·s-1] as the glycosyl donor and tubercidin [kcat/KMapp = (5.3 ± 1.8) × 104 M-1·s-1] as the glycosyl acceptor. NMR spectroscopic analysis revealed the product of this reaction to be 3'-O-β-glucopyranosyl tubercidin. A sequence analysis of AvpGT reveals a family of nucleoside-specific GTs, which may be used as markers of BGCs that produce glycosylated nucleosides.
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Affiliation(s)
- A R Ola Pasternak
- Department of Chemistry, Queen's University, Kingston, K7L 3N6 Ontario, Canada
| | - Marcy J Balunas
- Departments of Microbiology and Immunology and Medicinal Chemistry, University of Michigan, Ann Arbor, 48109 Michigan, United States
| | - David L Zechel
- Department of Chemistry, Queen's University, Kingston, K7L 3N6 Ontario, Canada
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Pasternak A, Bechthold A, Zechel DL. Identification of genes essential for sulfamate and fluorine incorporation during nucleocidin biosynthesis. Chembiochem 2022; 23:e202200140. [PMID: 35544615 DOI: 10.1002/cbic.202200140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/05/2022] [Indexed: 11/07/2022]
Abstract
Nucleocidin is an adenosine derivative containing 4'-fluoro and 5'-O-sulfamoyl substituents. In this study, nucleocidin biosynthesis is examined in two newly discovered producers, Streptomyces virens B-24331 and Streptomyces aureorectus B-24301, which produce nucleocidin and related derivatives at titres 30-fold greater than S. calvus . This enabled the identification of two new O -acetylated nucleocidin derivatives, and a potential glycosyl- O-acetyltransferase. Disruption of nucJ , nucG , and nucI , within S. virens B-24331, specifying a radical SAM / Fe-S dependent enzyme, sulfatase, and arylsulfatase, respectively, led to loss of 5'-O-sulfamoyl biosynthesis, but not fluoronucleoside production. Disruption of nucN , nucK , and nucO specifying an amidinotransferase, and two sulfotransferases respectively, led to loss of fluoronucleoside production. Identification of S. virens B-24331 as a genetically tractable and high producing strain sets the stage for understanding nucleocidin biosynthesis and highlights the utility of using 16S-RNA sequences to identify alternative producers of valuable compounds in the absence of genome sequence data.
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Affiliation(s)
- Aleksandra Pasternak
- Queen's University Faculty of Arts and Science, Chemistry, 90 Bader Lane, Chernoff Hall, K7L 3N6, Kingston, CANADA
| | - Andreas Bechthold
- Albert-Ludwigs-Universität Freiburg Fakultät für Chemie Pharmazie und Geowissenschaften: Albert-Ludwigs-Universitat Freiburg Fakultat fur Chemie und Pharmazie, Pharmaceutical Biology and Biotechnology, Stefan-Meier-Str. 19, 79104, Freiburg i. Br., GERMANY
| | - David L Zechel
- Queen's University, Department of Chemsitry, Chernoff Hall, K7L 3N6, Kingston, CANADA
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