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Frey M, Bathe U, Meink L, Balcke GU, Schmidt J, Frolov A, Soboleva A, Hassanin A, Davari MD, Frank O, Schlagbauer V, Dawid C, Tissier A. Combinatorial biosynthesis in yeast leads to over 200 diterpenoids. Metab Eng 2024; 82:193-200. [PMID: 38387676 DOI: 10.1016/j.ymben.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/24/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024]
Abstract
Diterpenoids form a diverse group of natural products, many of which are or could become pharmaceuticals or industrial chemicals. The modular character of diterpene biosynthesis and the promiscuity of the enzymes involved make combinatorial biosynthesis a promising approach to generate libraries of diverse diterpenoids. Here, we report on the combinatorial assembly in yeast of ten diterpene synthases producing (+)-copalyl diphosphate-derived backbones and four cytochrome P450 oxygenases (CYPs) in diverse combinations. This resulted in the production of over 200 diterpenoids. Based on literature and chemical database searches, 162 of these compounds can be considered new-to-Nature. The CYPs accepted most substrates they were given but remained regioselective with few exceptions. Our results provide the basis for the systematic exploration of the diterpenoid chemical space in yeast using sequence databases.
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Affiliation(s)
- Maximilian Frey
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Ulschan Bathe
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany; Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Gainesville, FL 32611, USA
| | - Luca Meink
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Gerd U Balcke
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Jürgen Schmidt
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Andrej Frolov
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Alena Soboleva
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Ahmed Hassanin
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany; Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Mehdi D Davari
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Oliver Frank
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Verena Schlagbauer
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Corinna Dawid
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany; Martin-Luther University Halle-Wittenberg, Institute of Pharmacy, Kurt-Mothes-Strasse 3, 06120 Halle, Germany.
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Bui VH, Rodríguez-López CE, Dang TTT. Integration of discovery and engineering in plant alkaloid research: Recent developments in elucidation, reconstruction, and repurposing biosynthetic pathways. Curr Opin Plant Biol 2023; 74:102379. [PMID: 37182414 DOI: 10.1016/j.pbi.2023.102379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 05/16/2023]
Abstract
Plants synthesize tens of thousands of bioactive nitrogen-containing compounds called alkaloids, including some clinically important drugs in modern medicine. The discovery of new alkaloid structures and their metabolism in plants have provided ways to access these rich sources of bioactivities including new-to-nature compounds relevant to therapeutic and industrial applications. This review discusses recent advances in alkaloid biosynthesis discovery, including complete pathway elucidations. Additionally, the latest developments in the production of new and established plant alkaloids based on either biosynthesis or semisynthesis are discussed.
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Affiliation(s)
- Van-Hung Bui
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Carlos Eduardo Rodríguez-López
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L. 64849, Mexico.
| | - Thu-Thuy T Dang
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, 3247 University Way, Kelowna, BC V1V 1V7, Canada.
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Schmidt M, Pei L, Budisa N. Xenobiology: State-of-the-Art, Ethics, and Philosophy of New-to-Nature Organisms. Adv Biochem Eng Biotechnol 2018; 162:301-315. [PMID: 28567486 DOI: 10.1007/10_2016_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The basic chemical constitution of all living organisms in the context of carbon-based chemistry consists of a limited number of small molecules and polymers. Until the twenty-first century, biology was mainly an analytical science and has now reached a point where it merges with engineering science, paving the way for synthetic biology. One of the objectives of synthetic biology is to try to change the chemical compositions of living cells, that is, to create an artificial biological diversity, which in turn fosters a new sub-field of synthetic biology, xenobiology. In particular, the genetic code in living systems is based on highly standardized chemistry composed of the same "letters" or nucleotides as informational polymers (DNA, RNA) and the 20 amino acids which serve as basic building blocks for proteins. The universality of the genetic code enables not only vertical gene transfer within the same species but also horizontal gene transfer across biological taxa, which require a high degree of standardization and interconnectivity. Although some minor alterations of the standard genetic code are found in nature (e.g., proteins containing non-conical amino acids exist in nature, and some organisms use alternated coding systems), all structurally deep chemistry changes within living systems are generally lethal, making the creation of artificial biological system an extremely difficult challenge.In this context, one of the great challenges for bioscience is the development of a strategy for expanding the standard basic chemical repertoire of living cells. Attempts to alter the meaning of the genetic information stored in DNA as an informational polymer by changing the chemistry of the polymer (i.e., xeno-nucleic acids) or by changes in the genetic code have already yielded successful results. In the future this should enable the partial or full redirection of the biological information flow to generate "new" version(s) of the genetic code derived from the "old" biological world.In addition to the scientific challenges, the attempt to increase biochemical diversity also raises important ethical and philosophical issues. Although promotors of this branch of synthetic biology highlight the many potential applications to come (e.g., novel tools for diagnostics and fighting infection diseases), such developments could also bring risks affecting social, political, and other structures of nearly all societies.
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Affiliation(s)
- Markus Schmidt
- Biofaction KG, Kundmanngasse 39/12, Vienna, 1030, Austria.
| | - Lei Pei
- Biofaction KG, Kundmanngasse 39/12, Vienna, 1030, Austria
| | - Nediljko Budisa
- AK Biokatalyse, Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623, Berlin, Germany
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