1
|
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.
Collapse
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
| |
Collapse
|
2
|
Motter J, Benckendorff CMM, Westarp S, Sunde-Brown P, Neubauer P, Kurreck A, Miller GJ. Purine nucleoside antibiotics: recent synthetic advances harnessing chemistry and biology. Nat Prod Rep 2024; 41:873-884. [PMID: 38197414 PMCID: PMC11188666 DOI: 10.1039/d3np00051f] [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] [Received: 10/12/2023] [Indexed: 01/11/2024]
Abstract
Covering: 2019 to 2023Nucleoside analogues represent one of the most important classes of small molecule pharmaceuticals and their therapeutic development is successfully established within oncology and for the treatment of viral infections. However, there are currently no nucleoside analogues in clinical use for the management of bacterial infections. Despite this, a significant number of clinically recognised nucleoside analogues are known to possess some antibiotic activity, thereby establishing a potential source for new therapeutic discovery in this area. Furthermore, given the rise in antibiotic resistance, the discovery of new clinical candidates remains an urgent global priority and natural product-derived nucleoside analogues may also present a rich source of discovery space for new modalities. This Highlight, covering work published from 2019 to 2023, presents a current perspective surrounding the synthesis of natural purine nucleoside antibiotics. By amalgamating recent efforts from synthetic chemistry with advances in biosynthetic understanding and the use of recombinant enzymes, prospects towards different structural classes of purines are detailed.
Collapse
Affiliation(s)
- Jonas Motter
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
| | - Caecilie M M Benckendorff
- School of Chemical and Physical Sciences and Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
| | - Sarah Westarp
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany.
| | - Peter Sunde-Brown
- School of Chemical and Physical Sciences and Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Ackerstraße 76, D-13355, Berlin, Germany
- BioNukleo GmbH, Ackerstraße 76, 13355 Berlin, Germany.
| | - Gavin J Miller
- School of Chemical and Physical Sciences and Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|