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Wu S, Morotti ALM, Yang J, Wang E, Tatsis EC. Single-cell RNA sequencing facilitates the elucidation of the complete biosynthesis of the antidepressant hyperforin in St. John's wort. MOLECULAR PLANT 2024:S1674-2052(24)00258-2. [PMID: 39135343 DOI: 10.1016/j.molp.2024.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 08/27/2024]
Abstract
Hyperforin is the compound responsible for the effectiveness of St. John's wort (Hypericum perforatum) as an antidepressant, but its complete biosynthetic pathway remains unknown. Gene discovery based on co-expression analysis of bulk RNA-sequencing data or genome mining failed to discover the missing steps in hyperforin biosynthesis. In this study, we sequenced the 1.54-Gb tetraploid H. perforatum genome assembled into 32 chromosomes with the scaffold N50 value of 42.44 Mb. By single-cell RNA sequencing, we identified a type of cell, "Hyper cells", wherein hyperforin biosynthesis de novo takes place in both the leaves and flowers. Through pathway reconstitution in yeast and tobacco, we identified and characterized four transmembrane prenyltransferases (HpPT1-4) that are localized at the plastid envelope and complete the hyperforin biosynthetic pathway. The hyperforin polycyclic scaffold is created by a reaction cascade involving an irregular isoprenoid coupling and a tandem cyclization. Our findings reveal how and where hyperforin is biosynthesized, enabling synthetic-biology reconstitution of the complete pathway. Thus, this study not only deepens our comprehension of specialized metabolism at the cellular level but also provides strategic guidance for elucidation of the biosynthetic pathways of other specializied metabolites in plants.
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Affiliation(s)
- Song Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Ana Luisa Malaco Morotti
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Evangelos C Tatsis
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; CEPAMS - CAS-JIC Centre of Excellence for Plant and Microbial Science, Shanghai 200032, China.
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2
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Seligmann B, Liu S, Franke J. Chemical tools for unpicking plant specialised metabolic pathways. CURRENT OPINION IN PLANT BIOLOGY 2024; 80:102554. [PMID: 38820646 DOI: 10.1016/j.pbi.2024.102554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 06/02/2024]
Abstract
Elucidating the biochemical pathways of specialised metabolites in plants is key to enable or improve their sustainable biotechnological production. Chemical tools can greatly facilitate the discovery of biosynthetic genes and enzymes. Here, we summarise transdisciplinary approaches where methods from chemistry and chemical biology helped to overcome key challenges of pathway elucidation. Based on recent examples, we describe how state-of-the-art isotope labelling experiments can guide the selection of biosynthetic gene candidates, how affinity-based probes enable the identification of novel enzymes, how semisynthesis can improve the availability of elusive pathway intermediates, and how biomimetic reactions provide a better understanding of inherent chemical reactivity. We anticipate that a wider application of such chemical methods will accelerate the pace of pathway elucidation in plants.
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Affiliation(s)
- Benedikt Seligmann
- Leibniz University Hannover, Institute of Botany, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Shenyu Liu
- Leibniz University Hannover, Centre of Biomolecular Drug Research (BMWZ), Schneiderberg 38, 30167 Hannover, Germany
| | - Jakob Franke
- Leibniz University Hannover, Institute of Botany, Herrenhäuser Str. 2, 30419 Hannover, Germany; Leibniz University Hannover, Centre of Biomolecular Drug Research (BMWZ), Schneiderberg 38, 30167 Hannover, Germany.
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3
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Durand M, Besseau S, Papon N, Courdavault V. Unlocking plant bioactive pathways: omics data harnessing and machine learning assisting. Curr Opin Biotechnol 2024; 87:103135. [PMID: 38728826 DOI: 10.1016/j.copbio.2024.103135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/02/2024] [Accepted: 04/12/2024] [Indexed: 05/12/2024]
Abstract
Plant bioactives hold immense potential in the medicine and food industry. The recent advancements in omics applied in deciphering specialized metabolic pathways underscore the importance of high-quality genome releases and the wealth of data in metabolomics and transcriptomics. While harnessing data, whether integrated or standalone, has proven successful in unveiling plant natural product (PNP) biosynthetic pathways, the democratization of machine learning in biology opens exciting new opportunities for enhancing the exploration of these pathways. This review highlights the recent breakthroughs in disrupting plant-specialized biosynthetic pathways through the utilization of omics data harnessing and machine learning techniques.
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Affiliation(s)
- Mickael Durand
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France.
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4
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Guo J, Gao D, Lian J, Qu Y. De novo biosynthesis of antiarrhythmic alkaloid ajmaline. Nat Commun 2024; 15:457. [PMID: 38212296 PMCID: PMC10784492 DOI: 10.1038/s41467-024-44797-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024] Open
Abstract
The antiarrhythmic drug ajmaline is a monoterpenoid indole alkaloid (MIA) isolated from the Ayurvedic plant Rauvolfia serpentina (Indian Snakeroot). Research into the biosynthesis of ajmaline and another renowned MIA chemotherapeutic drug vinblastine has yielded pivotal advancements in the fields of plant specialized metabolism and engineering over recent decades. While the majority of vinblastine biosynthesis has been recently elucidated, the quest for comprehending ajmaline biosynthesis remains incomplete, marked by the absence of two critical enzymes. Here, we show the discovery and characterization of these two elusive reductases, alongside the identification of two physiologically relevant esterases that complete the biosynthesis of ajmaline. We show that ajmaline biosynthesis proceeds with vomilenine 1,2(R)-reduction followed by its 19,20(S)-reduction. This process is further modulated by two root-expressing esterases that deacetylate 17-O-acetylnorajmaline. Expanding upon the successful completion of the ajmaline biosynthetic pathway, we engineer the de novo biosynthesis of ajmaline in Baker's yeast.
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Affiliation(s)
- Jun Guo
- Department of Chemistry, University of New Brunswick, Fredericton, NB, Canada
| | - Di Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China.
- Zhejiang Key Laboratory of Smart Biomaterials, Zhejiang University, Hangzhou, China.
| | - Yang Qu
- Department of Chemistry, University of New Brunswick, Fredericton, NB, Canada.
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5
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Dror MJ, Misa J, Yee DA, Chu AM, Yu RK, Chan BB, Aoyama LS, Chaparala AP, O'Connor SE, Tang Y. Engineered biosynthesis of plant heteroyohimbine and corynantheine alkaloids in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2024; 51:kuad047. [PMID: 38140980 PMCID: PMC10995622 DOI: 10.1093/jimb/kuad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/21/2023] [Indexed: 12/24/2023]
Abstract
Monoterpene indole alkaloids (MIAs) are a class of natural products comprised of thousands of structurally unique bioactive compounds with significant therapeutic values. Due to difficulties associated with isolation from native plant species and organic synthesis of these structurally complex molecules, microbial production of MIAs using engineered hosts are highly desired. In this work, we report the engineering of fully integrated Saccharomyces cerevisiae strains that allow de novo access to strictosidine, the universal precursor to thousands of MIAs at 30-40 mg/L. The optimization efforts were based on a previously reported yeast strain that is engineered to produce high titers of the monoterpene precursor geraniol through compartmentalization of mevalonate pathway in the mitochondria. Our approaches here included the use of CRISPR-dCas9 interference to identify mitochondria diphosphate transporters that negatively impact the titer of the monoterpene, followed by genetic inactivation; the overexpression of transcriptional regulators that increase cellular respiration and mitochondria biogenesis. Strain construction included the strategic integration of genes encoding both MIA biosynthetic and accessory enzymes into the genome under a variety of constitutive and inducible promoters. Following successful de novo production of strictosidine, complex alkaloids belonging to heteroyohimbine and corynantheine families were reconstituted in the host with introduction of additional downstream enzymes. We demonstrate that the serpentine/alstonine pair can be produced at ∼5 mg/L titer, while corynantheidine, the precursor to mitragynine can be produced at ∼1 mg/L titer. Feeding of halogenated tryptamine led to the biosynthesis of analogs of alkaloids in both families. Collectively, our yeast strain represents an excellent starting point to further engineer biosynthetic bottlenecks in this pathway and to access additional MIAs and analogs through microbial fermentation. ONE SENTENCE SUMMARY An Saccharomyces cerevisiae-based microbial platform was developed for the biosynthesis of monoterpene indole alkaloids, including the universal precursor strictosidine and further modified heteroyohimbine and corynantheidine alkaloids.
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Affiliation(s)
- Moriel J Dror
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joshua Misa
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Danielle A Yee
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Angela M Chu
- Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
| | - Rachel K Yu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bradley B Chan
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lauren S Aoyama
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anjali P Chaparala
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
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6
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Bradley SA, Lehka BJ, Hansson FG, Adhikari KB, Rago D, Rubaszka P, Haidar AK, Chen L, Hansen LG, Gudich O, Giannakou K, Lengger B, Gill RT, Nakamura Y, de Bernonville TD, Koudounas K, Romero-Suarez D, Ding L, Qiao Y, Frimurer TM, Petersen AA, Besseau S, Kumar S, Gautron N, Melin C, Marc J, Jeanneau R, O'Connor SE, Courdavault V, Keasling JD, Zhang J, Jensen MK. Biosynthesis of natural and halogenated plant monoterpene indole alkaloids in yeast. Nat Chem Biol 2023; 19:1551-1560. [PMID: 37932529 PMCID: PMC10667104 DOI: 10.1038/s41589-023-01430-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/25/2023] [Indexed: 11/08/2023]
Abstract
Monoterpenoid indole alkaloids (MIAs) represent a large class of plant natural products with marketed pharmaceutical activities against a wide range of indications, including cancer, malaria and hypertension. Halogenated MIAs have shown improved pharmaceutical properties; however, synthesis of new-to-nature halogenated MIAs remains a challenge. Here we demonstrate a platform for de novo biosynthesis of two MIAs, serpentine and alstonine, in baker's yeast Saccharomyces cerevisiae and deploy it to systematically explore the biocatalytic potential of refactored MIA pathways for the production of halogenated MIAs. From this, we demonstrate conversion of individual haloindole derivatives to a total of 19 different new-to-nature haloserpentine and haloalstonine analogs. Furthermore, by process optimization and heterologous expression of a modified halogenase in the microbial MIA platform, we document de novo halogenation and biosynthesis of chloroalstonine. Together, this study highlights a microbial platform for enzymatic exploration and production of complex natural and new-to-nature MIAs with therapeutic potential.
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Affiliation(s)
- Samuel A Bradley
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Beata J Lehka
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Frederik G Hansson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Khem B Adhikari
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Daniela Rago
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Paulina Rubaszka
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ahmad K Haidar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ling Chen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lea G Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Olga Gudich
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Konstantina Giannakou
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Bettina Lengger
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ryan T Gill
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Yoko Nakamura
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | | | - David Romero-Suarez
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ling Ding
- Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Yijun Qiao
- Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Thomas M Frimurer
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Anja A Petersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Sébastien Besseau
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Sandeep Kumar
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Nicolas Gautron
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Celine Melin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Jillian Marc
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | | | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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7
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Stander EA, Lehka B, Carqueijeiro I, Cuello C, Hansson FG, Jansen HJ, Dugé De Bernonville T, Birer Williams C, Vergès V, Lezin E, Lorensen MDBB, Dang TT, Oudin A, Lanoue A, Durand M, Giglioli-Guivarc'h N, Janfelt C, Papon N, Dirks RP, O'connor SE, Jensen MK, Besseau S, Courdavault V. The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids. Commun Biol 2023; 6:1197. [PMID: 38001233 PMCID: PMC10673892 DOI: 10.1038/s42003-023-05574-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Monoterpene indole alkaloids (MIAs) are a structurally diverse family of specialized metabolites mainly produced in Gentianales to cope with environmental challenges. Due to their pharmacological properties, the biosynthetic modalities of several MIA types have been elucidated but not that of the yohimbanes. Here, we combine metabolomics, proteomics, transcriptomics and genome sequencing of Rauvolfia tetraphylla with machine learning to discover the unexpected multiple actors of this natural product synthesis. We identify a medium chain dehydrogenase/reductase (MDR) that produces a mixture of four diastereomers of yohimbanes including the well-known yohimbine and rauwolscine. In addition to this multifunctional yohimbane synthase (YOS), an MDR synthesizing mainly heteroyohimbanes and the short chain dehydrogenase vitrosamine synthase also display a yohimbane synthase side activity. Lastly, we establish that the combination of geissoschizine synthase with at least three other MDRs also produces a yohimbane mixture thus shedding light on the complex mechanisms evolved for the synthesis of these plant bioactives.
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Affiliation(s)
- Emily Amor Stander
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Beata Lehka
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Inês Carqueijeiro
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Frederik G Hansson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Hans J Jansen
- Future Genomics Technologies, 2333 BE, Leiden, The Netherlands
| | - Thomas Dugé De Bernonville
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
- Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Caroline Birer Williams
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Valentin Vergès
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Enzo Lezin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | | | - Thu-Thuy Dang
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
| | - Audrey Oudin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Arnaud Lanoue
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Mickael Durand
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | | | - Christian Janfelt
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000, Angers, France
| | - Ron P Dirks
- Future Genomics Technologies, 2333 BE, Leiden, The Netherlands
| | - Sarah Ellen O'connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany.
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark.
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France.
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France.
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8
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Lorensen MDBB, Bjarnholt N, St-Pierre B, Heinicke S, Courdavault V, O'Connor S, Janfelt C. Spatial localization of monoterpenoid indole alkaloids in Rauvolfia tetraphylla by high resolution mass spectrometry imaging. PHYTOCHEMISTRY 2023; 209:113620. [PMID: 36863602 DOI: 10.1016/j.phytochem.2023.113620] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Monoterpenoid indole alkaloids (MIAs) are a large group of biosynthetic compounds, which have pharmacological properties. One of these MIAs, reserpine, was discovered in the 1950s and has shown properties as an anti-hypertension and anti-microbial agent. Reserpine was found to be produced in various plant species within the genus of Rauvolfia. However, even though its presence is well known, it is still unknown in which tissues Rauvolfia produce reserpine and where the individual steps in the biosynthetic pathway take place. In this study, we explore how matrix assisted laser desorption ionization (MALDI) and desorption electrospray ionization (DESI) mass spectrometry imaging (MSI) can be used in the investigation of a proposed biosynthetic pathway by localizing reserpine and the theoretical intermediates of it. The results show that ions corresponding to intermediates of reserpine were localized in several of the major parts of Rauvolfia tetraphylla when analyzed by MALDI- and DESI-MSI. In stem tissue, reserpine and many of the intermediates were found compartmentalized in the xylem. For most samples, reserpine itself was mainly found in the outer layers of the sample, suggesting it may function as a defense compound. To further confirm the place of the different metabolites in the reserpine biosynthetic pathway, roots and leaves of R. tetraphylla were fed a stable-isotope labelled version of the precursor tryptamine. Subsequently, several of the proposed intermediates were detected in the normal version as well as in the isotope labelled versions, confirming that they were synthesized in planta from tryptamine. In this experiment, a potential novel dimeric MIA was discovered in leaf tissue of R. tetraphylla. The study constitutes to date the most comprehensive spatial mapping of metabolites in the R. tetraphylla plant. In addition, the article also contains new illustrations of the anatomy of R. tetraphylla.
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Affiliation(s)
| | - Nanna Bjarnholt
- Plant Biochemistry Laboratory and Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark
| | - Benoit St-Pierre
- Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, 37200, Tours, France
| | - Sarah Heinicke
- Max Planck Institute for Chemical Ecology, Department of Natural Product Biosynthesis, Hans-Knöll-Straße 8, 07745, Jena, Germany
| | - Vincent Courdavault
- Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, 37200, Tours, France
| | - Sarah O'Connor
- Max Planck Institute for Chemical Ecology, Department of Natural Product Biosynthesis, Hans-Knöll-Straße 8, 07745, Jena, Germany
| | - Christian Janfelt
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark.
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9
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Chuang L, Liu S, Franke J. Post-Cyclization Skeletal Rearrangements in Plant Triterpenoid Biosynthesis by a Pair of Branchpoint Isomerases. J Am Chem Soc 2023; 145:5083-5091. [PMID: 36821810 PMCID: PMC9999417 DOI: 10.1021/jacs.2c10838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Triterpenoids possess potent biological activities, but their polycyclic skeletons are challenging to synthesize. The skeletal diversity of triterpenoids in plants is generated by oxidosqualene cyclases based on epoxide-triggered cationic rearrangement cascades. Normally, triterpenoid skeletons then remain unaltered during subsequent tailoring steps. In contrast, the highly modified triterpenoids found in Sapindales plants imply the existence of post-cyclization skeletal rearrangement enzymes that have not yet been found. We report here a biosynthetic pathway in Sapindales plants for the modification of already cyclized tirucallane triterpenoids, controlling the pathway bifurcation between different plant triterpenoid classes. Using a combination of bioinformatics, heterologous expression in plants and chemical analyses, we identified a cytochrome P450 monooxygenase and two isomerases which harness the epoxidation-rearrangement biosynthetic logic of triterpene cyclizations for modifying the tirucallane scaffold. The two isomerases share the same epoxide substrate made by the cytochrome P450 monooxygenase CYP88A154, but generate two different rearrangement products, one containing a cyclopropane ring. Our findings reveal a process for skeletal rearrangements of triterpenoids in nature that expands their scaffold diversity after the initial cyclization. In addition, the enzymes described here are crucial for the biotechnological production of limonoid, quassinoid, apoprotolimonoid, and glabretane triterpenoids.
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Affiliation(s)
- Ling Chuang
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Shenyu Liu
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Jakob Franke
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany.,Institute of Botany, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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10
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Nguyen TAM, Grzech D, Chung K, Xia Z, Nguyen TD, Dang TTT. Discovery of a cytochrome P450 enzyme catalyzing the formation of spirooxindole alkaloid scaffold. FRONTIERS IN PLANT SCIENCE 2023; 14:1125158. [PMID: 36818833 PMCID: PMC9936145 DOI: 10.3389/fpls.2023.1125158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Spirooxindole alkaloids feature a unique scaffold of an oxindole ring sharing an atom with a heterocyclic moiety. These compounds display an extensive range of biological activities such as anticancer, antibiotics, and anti-hypertension. Despite their structural and functional significance, the establishment and rationale of the spirooxindole scaffold biosynthesis are yet to be elucidated. Herein, we report the discovery and characterization of a cytochrome P450 enzyme from kratom (Mitragyna speciosa) responsible for the formation of the spirooxindole alkaloids 3-epi-corynoxeine (3R, 7R) and isocorynoxeine (3S, 7S) from the corynanthe-type (3R)-secoyohimbane precursors. Expression of the newly discovered enzyme in Saccharomyces cerevisiae yeast allows for the efficient in vivo and in vitro production of spirooxindoles. This discovery highlights the versatility of plant cytochrome P450 enzymes in building unusual alkaloid scaffolds and opens a gateway to access the prestigious spirooxindole pharmacophore and its derivatives.
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Affiliation(s)
- Tuan-Anh M. Nguyen
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
| | - Dagny Grzech
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Khoa Chung
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Zhicheng Xia
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, BC, Canada
| | - Trinh-Don Nguyen
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
| | - Thu-Thuy T. Dang
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
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11
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Kwan BD, Seligmann B, Nguyen TD, Franke J, Dang TTT. Leveraging synthetic biology and metabolic engineering to overcome obstacles in plant pathway elucidation. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102330. [PMID: 36599248 DOI: 10.1016/j.pbi.2022.102330] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/22/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Major hurdles in plant biosynthetic pathway elucidation and engineering include the need for rapid testing of enzyme candidates and the lack of complex substrates that are often not accumulated in the plant, amenable to synthesis, or commercially available. Linking metabolic engineering with gene discovery in both yeast and plant holds great promise to expedite the elucidation process and, at the same time, provide a platform for the sustainable production of plant metabolites. In this review, we highlight how synthetic biology and metabolic engineering alleviated longstanding obstacles in plant pathway elucidation. Recent advances in developing these chassis that showcase established and emerging strategies in accelerating biosynthetic gene discovery will also be discussed.
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Affiliation(s)
- Brooke D Kwan
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, 3427 University Way, Kelowna, BC, Canada
| | - Benedikt Seligmann
- Leibniz University Hannover, Institute of Botany, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Trinh-Don Nguyen
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, 3427 University Way, Kelowna, BC, Canada
| | - Jakob Franke
- Leibniz University Hannover, Institute of Botany, Herrenhäuser Str. 2, 30419 Hannover, Germany.
| | - Thu-Thuy T Dang
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, 3427 University Way, Kelowna, BC, Canada.
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12
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Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses. BIOTECHNOLOGIA 2022; 103:355-384. [PMID: 36685700 PMCID: PMC9837557 DOI: 10.5114/bta.2022.120706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 07/25/2022] [Accepted: 09/16/2022] [Indexed: 01/06/2023] Open
Abstract
Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharmaceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of assembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated transcriptome for P. harmala including 42 656 coding sequences was created by merging de novo assembled transcriptomes. Around 35 000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress-responsive transcripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. harmala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their potential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.
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13
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Wang X, Kong D, Huang T, Xu F, Tang MC, Deng Z, Lin S. Flavoprotein StnP2 Catalyzes the β-Carboline Formation during the Streptonigrin Biosynthesis. ACS Chem Biol 2022; 17:3499-3506. [PMID: 36409520 DOI: 10.1021/acschembio.2c00704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
β-Carboline (βC) alkaloids constitute a large family of indole alkaloids that exhibit diverse pharmacological properties, such as antitumor, antiviral, antiparasitic, and antimicrobial activities. Here, we report that a flavoprotein StnP2 catalyzes the dehydrogenation at C1-N2 of a tetrahydro-β-carboline (THβC) generating a 3,4-dihydro-β-carboline (DHβC), and the DHβC subsequently undergoes a spontaneous dehydrogenation to βC formation involved in the biosynthesis of the antitumor agent streptonigrin. Biochemical characterization showed that StnP2 catalyzed the highly regio- and stereo-selective dehydrogenation, and StnP2 exhibits promiscuity toward different THβCs. This study provides an alternative kind of enzyme catalyzing the biosynthesis of βC alkaloids and enhances the importance of flavoproteins.
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Affiliation(s)
- Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Dekun Kong
- Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Chongqing 400715, China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Fei Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Man-Cheng Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.,Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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14
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Wang Y, Malaco Morotti AL, Xiao Y, Wang Z, Wu S, Chen J, Tatsis EC. Decoding the Cytochrome P450 Catalytic Activity in Divergence of Benzophenone and Xanthone Biosynthetic Pathways. ACS Catal 2022. [DOI: 10.1021/acscatal.2c03405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ya Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy
of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ana Luisa Malaco Morotti
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy
of Sciences, Shanghai 200032, China
| | - Yiren Xiao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy
of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy
of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy
of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China
| | - Evangelos C. Tatsis
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy
of Sciences, Shanghai 200032, China
- CEPAMS - CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Shanghai 20032, China
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15
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Malhotra K, Franke J. Cytochrome P450 monooxygenase-mediated tailoring of triterpenoids and steroids in plants. Beilstein J Org Chem 2022; 18:1289-1310. [PMID: 36225725 PMCID: PMC9520826 DOI: 10.3762/bjoc.18.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/02/2022] [Indexed: 11/25/2022] Open
Abstract
The cytochrome P450 monooxygenase (CYP) superfamily comprises hemethiolate enzymes that perform remarkable regio- and stereospecific oxidative chemistry. As such, CYPs are key agents for the structural and functional tailoring of triterpenoids, one of the largest classes of plant natural products with widespread applications in pharmaceuticals, food, cosmetics, and agricultural industries. In this review, we provide a full overview of 149 functionally characterised CYPs involved in the biosynthesis of triterpenoids and steroids in primary as well as in specialised metabolism. We describe the phylogenetic distribution of triterpenoid- and steroid-modifying CYPs across the plant CYPome, present a structure-based summary of their reactions, and highlight recent examples of particular interest to the field. Our review therefore provides a comprehensive up-to-date picture of CYPs involved in the biosynthesis of triterpenoids and steroids in plants as a starting point for future research.
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Affiliation(s)
- Karan Malhotra
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Jakob Franke
- Institute of Botany, Leibniz University Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
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16
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Williams D, Brzezinski W, Gordon H, De Luca V. Site directed mutagenesis of Catharanthus roseus (+)-vincadifformine 19-hydroxylase (CYP71BY3) results in two distinct enzymatic functions. PHYTOCHEMISTRY 2022; 201:113265. [PMID: 35660549 DOI: 10.1016/j.phytochem.2022.113265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/27/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
The most abundant monoterpenoid indole alkaloids (MIAs) in Catharanthus roseus roots include lochnericine and (+)-echitovenine. The formation of (+)-echitovenine involves a 3-step pathway including (+)-vincadifformine-19-hydroxylase (V19H) that differentiates it from a parallel pathway involved in the formation of lochnericine, hörhammericine and its O-acetylated derivative. Homology based modeling and docking experiments in the present study show that (+) and (-) vincadifformine can occupy the V19H active site and is proven experimentally by showing that (-)-vincadifformine is a competitive inhibitor of V19H. Comparative modeling of V19H with tabersonine 3-oxidase (T3O) and tabersonine 19-hydroxylase (T19H) that accept (-)-aspidosperma MIAs identified four conserved amino acid residues in T3O and T19H that were different in the V19H binding site and were used to generate a series of single-, double-, or four-point mutations in V19H. While all mutants retained their ability to convert (+)-vincadifformine to (+)-minovincinine only the four-point mutant gained T3O activity enabling it to convert (-)-tabersonine to tabersonine 2,3-epoxide. The gain of T3O-like activity following mutagenesis without the loss of V19H activity supports the hypothesis that V19H shares a common ancestor to T3O which is involved in vindoline biosynthesis in C. roseus leaves.
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Affiliation(s)
- Danielle Williams
- Department of Biological Sciences Brock University, 1812 Sir Isaac Brock Way, St Catharines, ON, L2S 3A1, Canada.
| | - Weronika Brzezinski
- Department of Biological Sciences Brock University, 1812 Sir Isaac Brock Way, St Catharines, ON, L2S 3A1, Canada.
| | - Heather Gordon
- Department of Chemistry, Brock University, 1812 Sir Isaac Brock Way, St Catharines, ON, L2S 3A1, Canada.
| | - Vincenzo De Luca
- Department of Biological Sciences Brock University, 1812 Sir Isaac Brock Way, St Catharines, ON, L2S 3A1, Canada.
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17
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Chuang L, Liu S, Biedermann D, Franke J. Identification of early quassinoid biosynthesis in the invasive tree of heaven ( Ailanthus altissima) confirms evolutionary origin from protolimonoids. FRONTIERS IN PLANT SCIENCE 2022; 13:958138. [PMID: 36082289 PMCID: PMC9445810 DOI: 10.3389/fpls.2022.958138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The tree of heaven, Ailanthus altissima (MILL.) SWINGLE, is a globally invasive plant known to secrete allelopathic metabolites called quassinoids. Quassinoids are highly modified triterpenoids. So far, nothing has been known about the biochemical basis of quassinoid biosynthesis. Here, based on transcriptome and metabolome data of Ailanthus altissima, we present the first three steps of quassinoid biosynthesis, which are catalysed by an oxidosqualene cyclase and two cytochrome P450 monooxygenases, resulting in the formation of the protolimonoid melianol. Strikingly, these steps are identical to the first steps of the biosynthesis of limonoids, structurally different triterpenoids from sister plant families within the same order Sapindales. Our results are therefore not only important to fully understand the biosynthesis of complex triterpenoids in plants, but also confirm the long-standing hypothesis that quassinoids and limonoids share an evolutionary origin. In addition, our transcriptome data for Ailanthus altissima will be beneficial to other researchers investigating the physiology and ecology of this invasive tree.
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Affiliation(s)
- Ling Chuang
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Hanover, Germany
| | - Shenyu Liu
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Hanover, Germany
| | - Dave Biedermann
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Hanover, Germany
| | - Jakob Franke
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Hanover, Germany
- Institute of Botany, Leibniz University Hannover, Hanover, Germany
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18
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Chuang L, Enders A, Offermann S, Bahnemann J, Franke J. 3D-printed autoclavable plant holders to facilitate large-scale protein production in plants. Eng Life Sci 2022; 22:803-810. [PMID: 36514535 PMCID: PMC9731595 DOI: 10.1002/elsc.202200001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 12/16/2022] Open
Abstract
The Australian tobacco plant Nicotiana benthamiana is becoming increasingly popular as a platform for protein production and metabolic engineering. In this system, gene expression is achieved transiently by infiltrating N. benthamiana plants with suspensions of Agrobacterium tumefaciens carrying vectors with the target genes. To infiltrate larger numbers of plants, vacuum infiltration is the most efficient approach known, which is already used on industrial scale. Current laboratory-scale solutions for vacuum infiltration, however, either require expensive custom-tailored equipment or produce large amounts of biologically contaminated waste. To overcome these problems and lower the burden to establish vacuum infiltration in new laboratories, we present here 3D-printed plant holders for vacuum infiltration. We demonstrate that our plant holders are simple to use and enable a throughput of around 40 plants per hour. In addition, our 3D-printed plant holders are made from autoclavable material, which tolerate at least 12 autoclave cycles, helping to limit the production of contaminated waste and thus contributing to increased sustainability in research. In conclusion, our plant holders provide a simple, robust, safe and transparent platform for laboratory-scale vacuum infiltration that can be readily adopted by new laboratories interested in protein and metabolite production in Nicotiana benthamiana. Practical application Transient expression in Nicotiana benthamiana provides a popular and rapid system for producing proteins in a plant host. To infiltrate larger numbers of plants (typically >20), vacuum infiltration is the method of choice. However, no system has been described so far which is robust to use and can be used without expensive and complex equipment. Our autoclavable 3D-printed plant holders presented here will greatly reduce the efforts required to adopt the vacuum infiltration technique in new laboratories. They are easy to use and can be autoclaved at least 12 times, which contributes to waste reduction and sustainability in research laboratories. We anticipate that the 3D printing design provided here will drastically lower the bar for new groups to employ vacuum infiltration for producing proteins and metabolites in Nicotiana benthamiana.
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Affiliation(s)
- Ling Chuang
- Centre of Biomolecular Drug ResearchLeibniz University HannoverHannoverGermany
| | - Anton Enders
- Institute of Technical ChemistryLeibniz University HannoverHannoverGermany
| | | | - Janina Bahnemann
- Institute of Technical ChemistryLeibniz University HannoverHannoverGermany,Institute of PhysicsUniversity of AugsburgAugsburgGermany
| | - Jakob Franke
- Centre of Biomolecular Drug ResearchLeibniz University HannoverHannoverGermany,Institute of BotanyLeibniz University HannoverHannoverGermany
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19
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Morey KJ, Peebles CAM. Hairy roots: An untapped potential for production of plant products. FRONTIERS IN PLANT SCIENCE 2022; 13:937095. [PMID: 35991443 PMCID: PMC9389236 DOI: 10.3389/fpls.2022.937095] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
While plants are an abundant source of valuable natural products, it is often challenging to produce those products for commercial application. Often organic synthesis is too expensive for a viable commercial product and the biosynthetic pathways are often so complex that transferring them to a microorganism is not trivial or feasible. For plants not suited to agricultural production of natural products, hairy root cultures offer an attractive option for a production platform which offers genetic and biochemical stability, fast growth, and a hormone free culture media. Advances in metabolic engineering and synthetic biology tools to engineer hairy roots along with bioreactor technology is to a point where commercial application of the technology will soon be realized. We discuss different applications of hairy roots. We also use a case study of the advancements in understanding of the terpenoid indole alkaloid pathway in Catharanthus roseus hairy roots to illustrate the advancements and challenges in pathway discovery and in pathway engineering.
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20
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Boccia M, Grzech D, Lopes AA, O’Connor SE, Caputi L. Directed Biosynthesis of New to Nature Alkaloids in a Heterologous Nicotiana benthamiana Expression Host. FRONTIERS IN PLANT SCIENCE 2022; 13:919443. [PMID: 35812900 PMCID: PMC9257203 DOI: 10.3389/fpls.2022.919443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/24/2022] [Indexed: 05/17/2023]
Abstract
Plants produce a wide variety of pharmacologically active molecules classified as natural products. Derivatization of these natural products can modulate or improve the bioactivity of the parent compound. Unfortunately, chemical derivatization of natural products is often difficult or impractical. Here we use the newly discovered biosynthetic genes for two monoterpene indole alkaloids, alstonine and stemmadenine acetate, to generate analogs of these compounds. We reconstitute these biosynthetic genes in the heterologous host Nicotiana benthamiana along with an unnatural starting substrate to produce the corresponding new-to-nature alkaloid product.
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Affiliation(s)
- Marianna Boccia
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Dagny Grzech
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Adriana A. Lopes
- Biotechnology Unit, Universidade de Ribeirão Preto (UNAERP), Ribeirão Preto, Brazil
| | - Sarah E. O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
- *Correspondence: Sarah E. O’Connor,
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
- Lorenzo Caputi,
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21
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Nguyen TAM, McConnachie M, Nguyen TD, Dang TTT. Discovery and Characterization of Oxidative Enzymes Involved in Monoterpenoid Indole Alkaloid Biosynthesis. Methods Mol Biol 2022; 2505:141-164. [PMID: 35732943 DOI: 10.1007/978-1-0716-2349-7_11] [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: 06/15/2023]
Abstract
Monoterpene indole alkaloid (MIA) constitutes a structurally diverse plant natural product group with remarkable pharmacological activities. Many MIAs have been routinely used as potent drugs for several diseases, including leukemia (vinblastine), lung cancer (camptothecin), and malaria (quinine). Nevertheless, MIAs are biosynthesized at extremely low abundance in plants and, in many cases, require additional chemical functionalizations before their therapeutic uses. As oxygenations and oxidative rearrangements are critical throughout MIAs' structural scaffolding and modifications, the discovery and engineering of oxidative enzymes play essential roles in understanding and boosting the supplies of MIAs. Recent advances in omics technologies and synthetic biology have provided unprecedented amount of biochemical data and tools, paving a wide pathway for discovering, characterizing, and engineering enzymes involved in MIA biosynthesis. Here, we discuss the latest progress in understanding the roles of oxidative enzymes in MIA metabolism and describe a bioinformatic and biochemical pipeline to identify, characterize, and make use of these plant biocatalysts.
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Affiliation(s)
- Tuan-Anh Minh Nguyen
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
| | - Matthew McConnachie
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
| | - Trinh-Don Nguyen
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
| | - Thu-Thuy T Dang
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada.
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22
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Discovering and harnessing oxidative enzymes for chemoenzymatic synthesis and diversification of anticancer camptothecin analogues. Commun Chem 2021; 4:177. [PMID: 36697859 PMCID: PMC9814082 DOI: 10.1038/s42004-021-00602-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/05/2021] [Indexed: 01/28/2023] Open
Abstract
Semi-synthetic derivatives of camptothecin, a quinoline alkaloid found in the Camptotheca acuminata tree, are potent anticancer agents. Here we discovered two C. acuminata cytochrome P450 monooxygenases that catalyze regio-specific 10- and 11-oxidations of camptothecin, and demonstrated combinatorial chemoenzymatic C-H functionalizations of the camptothecin scaffold using the new enzymes to produce a suite of anticancer drugs, including topotecan (Hycamtin®) and irinotecan (Camptosar®). This work sheds new light into camptothecin metabolism, and represents greener approaches for accessing clinically relevant camptothecin derivatives.
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23
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Wang H, Guo H, Wang N, Huo YX. Toward the Heterologous Biosynthesis of Plant Natural Products: Gene Discovery and Characterization. ACS Synth Biol 2021; 10:2784-2795. [PMID: 34757715 DOI: 10.1021/acssynbio.1c00315] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Plant natural products (PNPs) represent a vast and diverse group of natural products, which have wide applications such as emulsifiers in cosmetics, sweeteners in foods, and active ingredients in medicines. Large-scale production of certain PNPs (e.g., artemisinin, taxol) has been implemented by reconstruction of biosynthetic pathways in heterologous hosts. However, unknown biosynthetic pathways greatly restrict wide applications of heterologous production of PNPs of interest. With the rapid development of sequencing and multiomics analysis technologies, huge amounts of omics data, i.e., genomics, transcriptomics, and proteomics, have been deposited in public databases, which is a precious resource for identification of the unknown biosynthetic pathway of PNPs. Herein, we have enumerated the approaches which have been widely used to screen candidate genes involved in the biosynthesis of PNPs of interest. We also discuss recent developments in the characterization of putative genes and elucidation of the complete biosynthetic pathway in heterologous hosts.
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Affiliation(s)
- Huiyan Wang
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081 Beijing, China
| | - Hao Guo
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081 Beijing, China
| | - Ning Wang
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081 Beijing, China
| | - Yi-Xin Huo
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081 Beijing, China
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
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24
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Franke J, Zhang Y, Dang TTT. Editorial: Exploring and Engineering Plant Specialized Metabolism: Latest Advances and New Horizons. FRONTIERS IN PLANT SCIENCE 2021; 12:783465. [PMID: 34777454 PMCID: PMC8581220 DOI: 10.3389/fpls.2021.783465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Jakob Franke
- Institute of Botany, Leibniz University Hannover, Hanover, Germany
- Centre of Biomolecular Drug Research, Leibniz University Hannover, Hanover, Germany
| | - Yang Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Thu-Thuy T. Dang
- Department of Chemistry, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC, Canada
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25
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Nguyen TD. Gene discovery in plant metabolism: Listening to the sound of silence, but where? PLANT PHYSIOLOGY 2021; 187:670-672. [PMID: 34608980 PMCID: PMC8491014 DOI: 10.1093/plphys/kiab357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Trinh-Don Nguyen
- 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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26
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Yamamoto K, Grzech D, Koudounas K, Stander EA, Caputi L, Mimura T, Courdavault V, O’Connor SE. Improved virus-induced gene silencing allows discovery of a serpentine synthase gene in Catharanthus roseus. PLANT PHYSIOLOGY 2021; 187:846-857. [PMID: 34608956 PMCID: PMC8491018 DOI: 10.1093/plphys/kiab285] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/31/2021] [Indexed: 05/28/2023]
Abstract
Specialized metabolites are chemically complex small molecules with a myriad of biological functions. To investigate plant-specialized metabolite biosynthesis more effectively, we developed an improved method for virus-induced gene silencing (VIGS). We designed a plasmid that incorporates fragments of both the target gene and knockdown marker gene (phytoene desaturase, PDS), which identifies tissues that have been successfully silenced in planta. To demonstrate the utility of this method, we used the terpenoid indole alkaloid (TIA) pathway in Madagascar periwinkle (Catharanthus roseus) as a model system. Catharanthus roseus is a medicinal plant well known for producing many bioactive compounds, such as vinblastine and vincristine. Our VIGS method enabled the discovery of a previously unknown biosynthetic enzyme, serpentine synthase (SS). This enzyme is a cytochrome P450 (CYP) that produces the β-carboline alkaloids serpentine and alstonine, compounds with strong blue autofluorescence and potential pharmacological activity. The discovery of this enzyme highlights the complexity of TIA biosynthesis and demonstrates the utility of this improved VIGS method for discovering unidentified metabolic enzymes in plants.
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Affiliation(s)
- Kotaro Yamamoto
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan
| | - Dagny Grzech
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Konstantinos Koudounas
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, Tours 37200, France
| | - Emily Amor Stander
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, Tours 37200, France
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Tetsuro Mimura
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Vincent Courdavault
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, Tours 37200, France
| | - Sarah E. O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
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27
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Nguyen TD, Dang TTT. Cytochrome P450 Enzymes as Key Drivers of Alkaloid Chemical Diversification in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:682181. [PMID: 34367208 PMCID: PMC8336426 DOI: 10.3389/fpls.2021.682181] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/01/2021] [Indexed: 05/30/2023]
Abstract
Plants produce more than 20,000 nitrogen-containing heterocyclic metabolites called alkaloids. These chemicals serve numerous eco-physiological functions in the plants as well as medicines and psychedelic drugs for human for thousands of years, with the anti-cancer agent vinblastine and the painkiller morphine as the best-known examples. Cytochrome P450 monooxygenases (P450s) play a key role in generating the structural variety that underlies this functional diversity of alkaloids. Most alkaloid molecules are heavily oxygenated thanks to P450 enzymes' activities. Moreover, the formation and re-arrangement of alkaloid scaffolds such as ring formation, expansion, and breakage that contribute to their structural diversity and bioactivity are mainly catalyzed by P450s. The fast-expanding genomics and transcriptomics databases of plants have accelerated the investigation of alkaloid metabolism and many players behind the complexity and uniqueness of alkaloid biosynthetic pathways. Here we discuss recent discoveries of P450s involved in the chemical diversification of alkaloids and how these inform our approaches in understanding plant evolution and producing plant-derived drugs.
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28
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Colinas M, Pollier J, Vaneechoutte D, Malat DG, Schweizer F, De Milde L, De Clercq R, Guedes JG, Martínez-Cortés T, Molina-Hidalgo FJ, Sottomayor M, Vandepoele K, Goossens A. Subfunctionalization of Paralog Transcription Factors Contributes to Regulation of Alkaloid Pathway Branch Choice in Catharanthus roseus. FRONTIERS IN PLANT SCIENCE 2021; 12:687406. [PMID: 34113373 PMCID: PMC8186833 DOI: 10.3389/fpls.2021.687406] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Catharanthus roseus produces a diverse range of specialized metabolites of the monoterpenoid indole alkaloid (MIA) class in a heavily branched pathway. Recent great progress in identification of MIA biosynthesis genes revealed that the different pathway branch genes are expressed in a highly cell type- and organ-specific and stress-dependent manner. This implies a complex control by specific transcription factors (TFs), only partly revealed today. We generated and mined a comprehensive compendium of publicly available C. roseus transcriptome data for MIA pathway branch-specific TFs. Functional analysis was performed through extensive comparative gene expression analysis and profiling of over 40 MIA metabolites in the C. roseus flower petal expression system. We identified additional members of the known BIS and ORCA regulators. Further detailed study of the ORCA TFs suggests subfunctionalization of ORCA paralogs in terms of target gene-specific regulation and synergistic activity with the central jasmonate response regulator MYC2. Moreover, we identified specific amino acid residues within the ORCA DNA-binding domains that contribute to the differential regulation of some MIA pathway branches. Our results advance our understanding of TF paralog specificity for which, despite the common occurrence of closely related paralogs in many species, comparative studies are scarce.
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Affiliation(s)
- Maite Colinas
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jacob Pollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Dries Vaneechoutte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Deniz G. Malat
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Fabian Schweizer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Liesbeth De Milde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Rebecca De Clercq
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Joana G. Guedes
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairaão, Portugal
- I3S-Instituto de Investigação e Inovação em Saúde, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Teresa Martínez-Cortés
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairaão, Portugal
| | - Francisco J. Molina-Hidalgo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Mariana Sottomayor
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairaão, Portugal
- Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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29
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Mauger A, Jarret M, Kouklovsky C, Poupon E, Evanno L, Vincent G. The chemistry of mavacurane alkaloids: a rich source of bis-indole alkaloids. Nat Prod Rep 2021; 38:1852-1886. [PMID: 33666614 DOI: 10.1039/d0np00088d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: since early reports up to the end of 2020This review presents a complete coverage of the mavacuranes alkaloids since early reports till date. Mavacuranes alkaloids are a restrictive sub-group of monoterpene indole alkaloids (MIAs), which are represented by their two emblematic congeners, namely, C-mavacurine and pleiocarpamine. Their skeleton is defined by a bond between the indolic N1 nitrogen and the C16 carbon of the tetracyclic scaffold of the corynanthe group in MIA. A limited number of congeners is known as this skeleton can be considered as a cul-de-sac in main MIA biosynthetic routes. Thanks to the enhanced enamine-type reactivity, mavacuranes are frequently involved in the formation of multimeric MIA scaffolds. This review covers isolation aspects and synthetic approaches towards the mavacurane core and bisindole assemblies. To access the mavacurane core, only a few strategies are reported and the main synthetic difficulties usually originate from the important rigidity of the pentacyclic system. For the bisindole assemblies, biomimetic routes are privileged and deliver complex structures using smooth conditions.
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Affiliation(s)
- Audrey Mauger
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405 Orsay, France.
| | - Maxime Jarret
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405 Orsay, France.
| | - Cyrille Kouklovsky
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405 Orsay, France.
| | - Erwan Poupon
- Biomolécules: Conception, Isolement et Synthèse (BioCIS), Université Paris-Saclay, CNRS, 92290 Châtenay-Malabry, France.
| | - Laurent Evanno
- Biomolécules: Conception, Isolement et Synthèse (BioCIS), Université Paris-Saclay, CNRS, 92290 Châtenay-Malabry, France.
| | - Guillaume Vincent
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405 Orsay, France.
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30
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Trenti F, Yamamoto K, Hong B, Paetz C, Nakamura Y, O'Connor SE. Early and Late Steps of Quinine Biosynthesis. Org Lett 2021; 23:1793-1797. [PMID: 33625237 PMCID: PMC7944568 DOI: 10.1021/acs.orglett.1c00206] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
The enzymatic basis
for quinine 1 biosynthesis was
investigated. Transcriptomic data from the producing plant led to
the discovery of three enzymes involved in the early and late steps
of the pathway. A medium-chain alcohol dehydrogenase (CpDCS) and an
esterase (CpDCE) yielded the biosynthetic intermediate dihydrocorynantheal 2 from strictosidine aglycone 3. Additionally,
the discovery of an O-methyltransferase specific
for 6′-hydroxycinchoninone 4 suggested the final
step order to be cinchoninone 16/17 hydroxylation, methylation,
and keto-reduction.
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Affiliation(s)
- Francesco Trenti
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Kotaro Yamamoto
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Benke Hong
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Christian Paetz
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Yoko Nakamura
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
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31
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Ramzi AB, Baharum SN, Bunawan H, Scrutton NS. Streamlining Natural Products Biomanufacturing With Omics and Machine Learning Driven Microbial Engineering. Front Bioeng Biotechnol 2020; 8:608918. [PMID: 33409270 PMCID: PMC7779585 DOI: 10.3389/fbioe.2020.608918] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/18/2020] [Indexed: 01/25/2023] Open
Abstract
Increasing demands for the supply of biopharmaceuticals have propelled the advancement of metabolic engineering and synthetic biology strategies for biomanufacturing of bioactive natural products. Using metabolically engineered microbes as the bioproduction hosts, a variety of natural products including terpenes, flavonoids, alkaloids, and cannabinoids have been synthesized through the construction and expression of known and newly found biosynthetic genes primarily from model and non-model plants. The employment of omics technology and machine learning (ML) platforms as high throughput analytical tools has been increasingly leveraged in promoting data-guided optimization of targeted biosynthetic pathways and enhancement of the microbial production capacity, thereby representing a critical debottlenecking approach in improving and streamlining natural products biomanufacturing. To this end, this mini review summarizes recent efforts that utilize omics platforms and ML tools in strain optimization and prototyping and discusses the beneficial uses of omics-enabled discovery of plant biosynthetic genes in the production of complex plant-based natural products by bioengineered microbes.
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Affiliation(s)
- Ahmad Bazli Ramzi
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | | | - Hamidun Bunawan
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Nigel S Scrutton
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre, Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
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32
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Turpin V, Poupon E, Jullian J, Evanno L. Biosynthetically Relevant Reactivity of Polyneuridine Aldehyde. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Victor Turpin
- CNRS, BioCIS Université Paris‐Saclay 92290 Châtenay‐Malabry France
| | - Erwan Poupon
- CNRS, BioCIS Université Paris‐Saclay 92290 Châtenay‐Malabry France
| | | | - Laurent Evanno
- CNRS, BioCIS Université Paris‐Saclay 92290 Châtenay‐Malabry France
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33
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Godbole RC, Pable AA, Barvkar VT. Transcriptome-wide identification, characterization, and phylogenomic analysis of cytochrome P450s from Nothapodytes nimmoniana reveal candidate genes involved in the camptothecin biosynthetic pathway. Genome 2020; 64:1-14. [PMID: 32976723 DOI: 10.1139/gen-2020-0067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The plant Nothapodytes nimmoniana is an important source of camptothecin (CPT), an anticancer compound widely used in the treatment of colorectal, lung, and ovarian cancers. CPT is biosynthesized by the combination of the seco-iridoid and indole pathways in plants. The majority of the biosynthetic steps and associated genes still remain unknown. Certain reactions in the seco-iridoid pathway are catalyzed by cytochrome P450 enzymes. Hence, identifying transcriptionally active cytochrome P450 genes becomes essential in the elucidation of the CPT biosynthetic pathway. Here, we report the identification of 94 cytochrome P450s from the assembled transcriptomic data from leaf and root tissues of N. nimmoniana. The identified cytochrome P450 genes were full length and possessed all four conserved characteristic signature motifs of cytochrome P450 genes. Phylogenetic analysis of the protein sequences revealed their evolution and diversification and further categorized them into A-type (52.12%) and non-A-type (47.87%) cytochrome P450s. These 94 sequences represent 38 families and 63 subfamilies of cytochrome P450s. We also compared the transcriptional activity of identified cytochrome P450s with the expression of their homologs in the CPT-producing plant Ophiorrhiza pumila. Based on expression profiles and quantitative PCR validation, we propose NnCYP81CB1 and NnCYP89R1 as candidate cytochrome P450 genes involved in camptothecin biosynthesis in N. nimmoniana.
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Affiliation(s)
- Rucha C Godbole
- Department of Botany, Savitribai Phule Pune University, Pune-411007, India
| | - Anupama A Pable
- Department of Microbiology, Savitribai Phule Pune University, Pune-411007, India
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune-411007, India
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34
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Jarret M, Tap A, Turpin V, Denizot N, Kouklovsky C, Poupon E, Evanno L, Vincent G. Bioinspired Divergent Oxidative Cyclizations of Geissoschizine: Total Synthesis of (–)‐17‐nor‐Excelsinidine, (+)‐16‐
epi
‐Pleiocarpamine, (+)‐16‐Hydroxymethyl‐Pleiocarpamine and (+)‐Taberdivarine H. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000962] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Maxime Jarret
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) Université Paris‐Saclay, CNRS 91405 Orsay France
| | - Aurélien Tap
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) Université Paris‐Saclay, CNRS 91405 Orsay France
| | - Victor Turpin
- Biomolécules: Conception, Isolement et Synthèse (BioCIS) Université Paris‐Saclay, CNRS, BioCIS 92290 Châtenay‐Malabry France
| | - Natacha Denizot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) Université Paris‐Saclay, CNRS 91405 Orsay France
| | - Cyrille Kouklovsky
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) Université Paris‐Saclay, CNRS 91405 Orsay France
| | - Erwan Poupon
- Biomolécules: Conception, Isolement et Synthèse (BioCIS) Université Paris‐Saclay, CNRS, BioCIS 92290 Châtenay‐Malabry France
| | - Laurent Evanno
- Biomolécules: Conception, Isolement et Synthèse (BioCIS) Université Paris‐Saclay, CNRS, BioCIS 92290 Châtenay‐Malabry France
| | - Guillaume Vincent
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) Université Paris‐Saclay, CNRS 91405 Orsay France
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35
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Espinoza RV, Sherman DH. Exploring the molecular basis for selective C-H functionalization in plant P450s. Synth Syst Biotechnol 2020; 5:97-98. [PMID: 32551372 PMCID: PMC7292896 DOI: 10.1016/j.synbio.2020.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Rosa V. Espinoza
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, 48109, United States
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36
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Dugé de Bernonville T, Papon N, Clastre M, O’Connor SE, Courdavault V. Identifying Missing Biosynthesis Enzymes of Plant Natural Products. Trends Pharmacol Sci 2020; 41:142-146. [DOI: 10.1016/j.tips.2019.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 11/07/2019] [Accepted: 12/29/2019] [Indexed: 11/16/2022]
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37
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Norwood VM, Huigens RW. Harnessing the Chemistry of the Indole Heterocycle to Drive Discoveries in Biology and Medicine. Chembiochem 2019; 20:2273-2297. [DOI: 10.1002/cbic.201800768] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Verrill M. Norwood
- Department of Medicinal ChemistryCenter for Natural Products Drug Discovery and Development (CNPD3)University of Florida 1345 Center Drive Gainesville FL 32610 USA
| | - Robert W. Huigens
- Department of Medicinal ChemistryCenter for Natural Products Drug Discovery and Development (CNPD3)University of Florida 1345 Center Drive Gainesville FL 32610 USA
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38
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Collected mass spectrometry data on monoterpene indole alkaloids from natural product chemistry research. Sci Data 2019; 6:15. [PMID: 30944327 PMCID: PMC6480975 DOI: 10.1038/s41597-019-0028-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/25/2019] [Indexed: 11/21/2022] Open
Abstract
This Data Descriptor announces the submission to public repositories of the monoterpene indole alkaloid database (MIADB), a cumulative collection of 172 tandem mass spectrometry (MS/MS) spectra from multiple research projects conducted in eight natural product chemistry laboratories since the 1960s. All data have been annotated and organized to promote reuse by the community. Being a unique collection of these complex natural products, these data can be used to guide the dereplication and targeting of new related monoterpene indole alkaloids within complex mixtures when applying computer-based approaches, such as molecular networking. Each spectrum has its own accession number from CCMSLIB00004679916 to CCMSLIB00004680087 on the GNPS. The MIADB is available for download from MetaboLights under the identifier: MTBLS142 (https://www.ebi.ac.uk/metabolights/MTBLS142). Design Type(s) | mass spectrometry data transformation objective • mass spectrometry data analysis objective • data integration objective | Measurement Type(s) | mass spectrum | Technology Type(s) | liquid chromatography-tandem mass spectrometry | Factor Type(s) | | Sample Characteristic(s) | Strychnos usambarensis • Picralima nitida • Geissospermum laeve • Pleiocarpa mutica • Alstonia • Callichilia inaequalis • Chimarris cymosa • Mostuea brunonis • Gonioma < moth > • Cinchona • Catharanthus roseus • Voacanga grandifolia |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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39
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Hill RA, Sutherland A. Hot off the Press. Nat Prod Rep 2018; 35:1024-1028. [PMID: 30209473 DOI: 10.1039/c8np90032a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as huperphlegmine A from Huperzia phlegmaria.
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Affiliation(s)
- Robert A Hill
- School of Chemistry, Glasgow University, Glasgow, G12 8QQ, UK.
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40
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Otogo N’Nang E, Bernadat G, Mouray E, Kumulungui B, Grellier P, Poupon E, Champy P, Beniddir MA. Theionbrunonines A and B: Dimeric Vobasine Alkaloids Tethered by a Thioether Bridge from Mostuea brunonis. Org Lett 2018; 20:6596-6600. [DOI: 10.1021/acs.orglett.8b02961] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elvis Otogo N’Nang
- Équipe “Pharmacognosie-Chimie des Substances Naturelles” BioCIS, Université Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
- Laboratoire de Microbiologie, Université des Sciences et Techniques de Masuku, BP769 Franceville, Gabon
| | - Guillaume Bernadat
- Équipe “Pharmacognosie-Chimie des Substances Naturelles” BioCIS, Université Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Elisabeth Mouray
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Universités, CP52, 57, rue Cuvier, 75005 Paris, France
| | - Brice Kumulungui
- Laboratoire de Microbiologie, Université des Sciences et Techniques de Masuku, BP769 Franceville, Gabon
| | - Philippe Grellier
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Universités, CP52, 57, rue Cuvier, 75005 Paris, France
| | - Erwan Poupon
- Équipe “Pharmacognosie-Chimie des Substances Naturelles” BioCIS, Université Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Pierre Champy
- Équipe “Pharmacognosie-Chimie des Substances Naturelles” BioCIS, Université Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Mehdi A. Beniddir
- Équipe “Pharmacognosie-Chimie des Substances Naturelles” BioCIS, Université Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
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