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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Lemos Cruz P, Carqueijeiro I, Koudounas K, Bomzan DP, Stander EA, Abdallah C, Kulagina N, Oudin A, Lanoue A, Giglioli-Guivarc'h N, Nagegowda DA, Papon N, Besseau S, Clastre M, Courdavault V. Identification of a second 16-hydroxytabersonine-O-methyltransferase suggests an evolutionary relationship between alkaloid and flavonoid metabolisms in Catharanthus roseus. Protoplasma 2023; 260:607-624. [PMID: 35947213 DOI: 10.1007/s00709-022-01801-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The medicinal plant Catharanthus roseus biosynthesizes many important drugs for human health, including the anticancer monoterpene indole alkaloids (MIAs) vinblastine and vincristine. Over the past decades, the continuous increase in pharmaceutical demand has prompted several research groups to characterize MIA biosynthetic pathways for considering future metabolic engineering processes of supply. In line with previous work suggesting that diversification can potentially occur at various steps along the vindoline branch, we were here interested in investigating the involvement of distinct isoforms of tabersonine-16-O-methyltransferase (16OMT) which plays a pivotal role in the MIA biosynthetic pathway. By combining homology searches based on the previously characterized 16OMT1, phylogenetic analyses, functional assays in yeast, and biochemical and in planta characterizations, we identified a second isoform of 16OMT, referred to as 16OMT2. 16OMT2 appears to be a multifunctional enzyme working on both MIA and flavonoid substrates, suggesting that a constrained evolution of the enzyme for accommodating the MIA substrate has probably occurred to favor the apparition of 16OMT2 from an ancestral specific flavonoid-O-methyltransferase. Since 16OMT1 and 16OMT2 displays a high sequence identity and similar kinetic parameters for 16-hydroxytabersonine, we postulate that 16OMT1 may result from a later 16OMT2 gene duplication accompanied by a continuous neofunctionalization leading to an almost complete loss of flavonoid O-methyltransferase activity. Overall, these results participate in increasing our knowledge on the evolutionary processes that have likely led to enzyme co-optation for MIA synthesis.
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Affiliation(s)
- Pamela Lemos Cruz
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Ines Carqueijeiro
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | | | - Dikki Pedenla Bomzan
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru, 560065, India
| | - Emily Amor Stander
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Cécile Abdallah
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Natalja Kulagina
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Audrey Oudin
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Arnaud Lanoue
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | | | - Dinesh A Nagegowda
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru, 560065, India
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR, ICAT, F-49000, Angers, France
| | - Sébastien Besseau
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Marc Clastre
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Vincent Courdavault
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France.
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3
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Cuello C, Stander EA, Jansen HJ, Dugé De Bernonville T, Oudin A, Birer Williams C, Lanoue A, Giglioli Guivarc'h N, Papon N, Dirks RP, Jensen MK, O'Connor SE, Besseau S, Courdavault V. An updated version of the Madagascar periwinkle genome. F1000Res 2022; 11:1541. [PMID: 36761838 PMCID: PMC9902796 DOI: 10.12688/f1000research.129212.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
The Madagascar periwinkle, Catharanthus roseus, belongs to the Apocynaceae family. This medicinal plant, endemic to Madagascar, produces many important drugs including the monoterpene indole alkaloids (MIA) vincristine and vinblastine used to treat cancer worldwide. Here, we provide a new version of the C. roseus genome sequence obtained through the combination of Oxford Nanopore Technologies long-reads and Illumina short-reads. This more contiguous assembly consists of 173 scaffolds with a total length of 581.128 Mb and an N50 of 12.241 Mb. Using publicly available RNAseq data, 21,061 protein coding genes were predicted and functionally annotated. A total of 42.87% of the genome was annotated as transposable elements, most of them being long-terminal repeats. Together with the increasing access to MIA-producing plant genomes, this updated version should ease evolutionary studies leading to a better understanding of MIA biosynthetic pathway evolution.
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Affiliation(s)
- Clément Cuello
- 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
| | - Hans J. Jansen
- Future Genomics Technologies, Leiden, 2333BE, The Netherlands
| | - Thomas Dugé De Bernonville
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, 37200, France,Present address: Centre de Recherche, Limagrain, Chappes, 07745, France
| | - Audrey Oudin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, 37200, France
| | | | - Arnaud Lanoue
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, 37200, France
| | | | - Nicolas Papon
- IRF, SFR ICAT, Univ Angers, Univ Brest, Angers, 49000, France
| | - Ron P. Dirks
- Future Genomics Technologies, Leiden, 2333BE, The Netherlands
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Sarah Ellen O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Sébastien Besseau
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, 37200, France
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, 37200, France,
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Stander EA, Cuello C, Birer-Williams C, Kulagina N, Jansen HJ, Carqueijeiro I, Méteignier LV, Vergès V, Oudin A, Papon N, Dirks RP, Jensen MK, O’Connor SE, Dugé de Bernonville T, Besseau S, Courdavault V. The Vinca minor genome highlights conserved evolutionary traits in monoterpene indole alkaloid synthesis. G3 (Bethesda) 2022; 12:jkac268. [PMID: 36200869 PMCID: PMC9713385 DOI: 10.1093/g3journal/jkac268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 09/28/2022] [Indexed: 11/26/2023]
Abstract
Vinca minor, also known as the lesser periwinkle, is a well-known species from the Apocynaceae, native to central and southern Europe. This plant synthesizes monoterpene indole alkaloids, which are a class of specialized metabolites displaying a wide range of bioactive- and pharmacologically important properties. Within the almost 50 monoterpene indole alkaloids it produces, V. minor mainly accumulates vincamine, which is commercially used as a nootropic. Using a combination of Oxford Nanopore Technologies long read- and Illumina short-read sequencing, a 679,098 Mb V. minor genome was assembled into 296 scaffolds with an N50 scaffold length of 6 Mb, and encoding 29,624 genes. These genes were functionally annotated and used in a comparative genomic analysis to establish gene families and to investigate gene family expansion and contraction across the phylogenetic tree. Furthermore, homology-based monoterpene indole alkaloid gene predictions together with a metabolic analysis across 4 different V. minor tissue types guided the identification of candidate monoterpene indole alkaloid genes. These candidates were finally used to identify monoterpene indole alkaloid gene clusters, which combined with synteny analysis allowed for the discovery of a functionally validated vincadifformine-16-hydroxylase, reinforcing the potential of this dataset for monoterpene indole alkaloids gene discovery. It is expected that access to these resources will facilitate the elucidation of unknown monoterpene indole alkaloid biosynthetic routes with the potential of transferring these pathways to heterologous expression systems for large-scale monoterpene indole alkaloid production.
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Affiliation(s)
- Emily Amor Stander
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | | | - Natalja Kulagina
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Hans J Jansen
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands
| | - Ines Carqueijeiro
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | | | - Valentin Vergès
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Audrey Oudin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Ron P Dirks
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Sarah Ellen O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | | | - 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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5
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Cuello C, Stander EA, Jansen HJ, Dugé de Bernonville T, Lanoue A, Giglioli-Guivarc'h N, Papon N, Dirks RP, Jensen MK, O'Connor SE, Besseau S, Courdavault V. Genome Assembly of the Medicinal Plant Voacanga thouarsii. Genome Biol Evol 2022; 14:evac158. [PMID: 36300641 PMCID: PMC9673491 DOI: 10.1093/gbe/evac158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2022] [Indexed: 11/26/2023] Open
Abstract
The Apocynaceae tree Voacanga thouarsii, native to southern Africa and Madagascar, produces monoterpene indole alkaloids (MIA), which are specialized metabolites with a wide range of bioactive properties. Voacanga species mainly accumulates tabersonine in seeds making these species valuable medicinal plants currently used for industrial MIA production. Despite their importance, the MIA biosynthesis in Voacanga species remains poorly studied. Here, we report the first genome assembly and annotation of a Voacanga species. The combined assembly of Oxford Nanopore Technologies long-reads and Illumina short-reads resulted in 3,406 scaffolds with a total length of 1,354.26 Mb and an N50 of 3.04 Mb. A total of 33,300 protein-coding genes were predicted and functionally annotated. These genes were then used to establish gene families and to investigate gene family expansion and contraction across the phylogenetic tree. A transposable element (TE) analysis showed the highest proportion of TE in Voacanga thouarsii compared with all other MIA-producing plants. In a nutshell, this first reference genome of V. thouarsii will thus contribute to strengthen future comparative and evolutionary studies in MIA-producing plants leading to a better understanding of MIA pathway evolution. This will also allow the potential identification of new MIA biosynthetic genes for metabolic engineering purposes.
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Affiliation(s)
- Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Emily Amor Stander
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Hans J Jansen
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands
| | | | - Arnaud Lanoue
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | | | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Ron P Dirks
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Sarah Ellen O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - 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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Stander EA, Dugé de Bernonville T, Papon N, Courdavault V. Chromosome-scale genomes throw light on plant drug biosynthesis. Trends Pharmacol Sci 2022; 43:542-545. [DOI: 10.1016/j.tips.2022.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 01/18/2023]
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Dugé de Bernonville T, Amor Stander E, Dugé de Bernonville G, Besseau S, Courdavault V. Predicting Monoterpene Indole Alkaloid-Related Genes from Expression Data with Artificial Neural Networks. Methods Mol Biol 2022; 2505:131-140. [PMID: 35732942 DOI: 10.1007/978-1-0716-2349-7_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Elucidation of biological pathways leading to specialized metabolites remains a complex task. It is however a mandatory step to allow bioproduction into heterologous hosts. Many steps have already been identified using conventional approaches, enlarging the space of known possible chemical steps. In the recent past years, identification of missing steps has been fueled by the generation of genomic and transcriptomic data for nonmodel species. The analysis of gene expression profiles has revealed that in many cases, genes encoding enzymes involved in the same biosynthetic pathways are coexpressed across different tissue types and environmental conditions. Hence, coexpressed studies, either in the form of differential gene expression, gene coexpression network, or unsupervised clustering methods, have helped deciphering missing steps to complete knowledge on biosynthetic pathways. Already identified biosynthetic steps can be used as baits to capture the remaining unknown steps. The present protocol shows how supervised machine learning in the form of artificial neural networks (ANNs) can efficiently classify genes as specialized metabolism related or not according to their expression levels. Using Catharanthus roseus as an example, we show that ANN trained on a minimal set of bait genes results in many true positives (correctly predicted genes) while keeping false positives low (containing possible candidate genes).
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Affiliation(s)
| | - Emily Amor Stander
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | | | - Sébastien Besseau
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
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Amor Stander E, Dugé de Bernonville T, Courdavault V. RNA-seq Analysis of Monoterpene Indole Alkaloid Biosynthetic Pathway Elucidation in Catharanthus roseus. Methods Mol Biol 2022; 2505:113-130. [PMID: 35732941 DOI: 10.1007/978-1-0716-2349-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Increased affordability and availability of high-throughput next-generation sequencing (NGS) technologies have resulted in an explosion of available RNA-seq data, igniting a variety of data-mining methodologies, valuable for plant-specialized biosynthetic pathway discovery. When combined with traditional homology-based annotations, these methods can facilitate short-listing candidate genes for downstream functional validation screenings. Genes related to common pathways often display homogenous expression patterns across different tissue types and experimental conditions. Here, we describe bioinformatic protocols for exploiting such coexpression to shortlist candidate genes of the well-described monoterpene indole alkaloid (MIA) pathway of Catharanthus roseus. These methods aim to inspire researchers to utilize this publicly available RNA-seq treasure trove to guide their own endeavors in the characterization of missing steps in plant metabolic pathways.
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Affiliation(s)
- Emily Amor Stander
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France.
| | | | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France.
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9
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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 Physiol 2021; 187:846-857. [PMID: 34608956 PMCID: PMC8491018 DOI: 10.1093/plphys/kiab285] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Stander EA, Sepúlveda LJ, Dugé de Bernonville T, Carqueijeiro I, Koudounas K, Lemos Cruz P, Besseau S, Lanoue A, Papon N, Giglioli-Guivarc’h N, Dirks R, O’Connor SE, Atehortùa L, Oudin A, Courdavault V. Identifying Genes Involved in alkaloid Biosynthesis in Vinca minor Through Transcriptomics and Gene Co-Expression Analysis. Biomolecules 2020; 10:biom10121595. [PMID: 33255314 PMCID: PMC7761029 DOI: 10.3390/biom10121595] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 12/19/2022] Open
Abstract
The lesser periwinkle Vinca minor accumulates numerous monoterpene indole alkaloids (MIAs) including the vasodilator vincamine. While the biosynthetic pathway of MIAs has been largely elucidated in other Apocynaceae such as Catharanthus roseus, the counterpart in V. minor remains mostly unknown, especially for reactions leading to MIAs specific to this plant. As a consequence, we generated a comprehensive V. minor transcriptome elaborated from eight distinct samples including roots, old and young leaves exposed to low or high light exposure conditions. This optimized resource exhibits an improved completeness compared to already published ones. Through homology-based searches using C. roseus genes as bait, we predicted candidate genes for all common steps of the MIA pathway as illustrated by the cloning of a tabersonine/vincadifformine 16-O-methyltransferase (Vm16OMT) isoform. The functional validation of this enzyme revealed its capacity of methylating 16-hydroxylated derivatives of tabersonine, vincadifformine and lochnericine with a Km 0.94 ± 0.06 µM for 16-hydroxytabersonine. Furthermore, by combining expression of fusions with yellow fluorescent proteins and interaction assays, we established that Vm16OMT is located in the cytosol and forms homodimers. Finally, a gene co-expression network was performed to identify candidate genes of the missing V. minor biosynthetic steps to guide MIA pathway elucidation.
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Affiliation(s)
- Emily Amor Stander
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Liuda Johana Sepúlveda
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
- Laboratorio de Biotecnología, Sede de Investigación Universitaria, Universidad de Antioquia, Antioquia Medellin 050021, Colombia;
| | - Thomas Dugé de Bernonville
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Inês Carqueijeiro
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Konstantinos Koudounas
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Pamela Lemos Cruz
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Sébastien Besseau
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Arnaud Lanoue
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Nicolas Papon
- Host-Pathogen Interaction Study Group (GEIHP, EA 3142), UNIV Angers, UNIV Brest, 49933 Angers, France;
| | - Nathalie Giglioli-Guivarc’h
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Ron Dirks
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands;
| | - Sarah Ellen O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany;
| | - Lucia Atehortùa
- Laboratorio de Biotecnología, Sede de Investigación Universitaria, Universidad de Antioquia, Antioquia Medellin 050021, Colombia;
| | - Audrey Oudin
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
- Correspondence: (A.O.); (V.C.)
| | - Vincent Courdavault
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
- Correspondence: (A.O.); (V.C.)
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Stander EA, Williams W, Mgwatyu Y, van Heusden P, Rautenbach F, Marnewick J, Le Roes-Hill M, Hesse U. Transcriptomics of the Rooibos (Aspalathus linearis) Species Complex. BioTech 2020; 9:biotech9040019. [PMID: 35822822 PMCID: PMC9258316 DOI: 10.3390/biotech9040019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/28/2020] [Accepted: 08/04/2020] [Indexed: 12/18/2022] Open
Abstract
Rooibos (Aspalathus linearis), widely known as a herbal tea, is endemic to the Cape Floristic Region of South Africa (SA). It produces a wide range of phenolic compounds that have been associated with diverse health promoting properties of the plant. The species comprises several growth forms that differ in their morphology and biochemical composition, only one of which is cultivated and used commercially. Here, we established methodologies for non-invasive transcriptome research of wild-growing South African plant species, including (1) harvesting and transport of plant material suitable for RNA sequencing; (2) inexpensive, high-throughput biochemical sample screening; (3) extraction of high-quality RNA from recalcitrant, polysaccharide- and polyphenol rich plant material; and (4) biocomputational analysis of Illumina sequencing data, together with the evaluation of programs for transcriptome assembly (Trinity, IDBA-Trans, SOAPdenovo-Trans, CLC), protein prediction, as well as functional and taxonomic transcript annotation. In the process, we established a biochemically characterized sample pool from 44 distinct rooibos ecotypes (1–5 harvests) and generated four in-depth annotated transcriptomes (each comprising on average ≈86,000 transcripts) from rooibos plants that represent distinct growth forms and differ in their biochemical profiles. These resources will serve future rooibos research and plant breeding endeavours.
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Affiliation(s)
- Emily Amor Stander
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa; (E.A.S.); (W.W.); (Y.M.); (P.v.H.)
| | - Wesley Williams
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa; (E.A.S.); (W.W.); (Y.M.); (P.v.H.)
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville 7535, South Africa
| | - Yamkela Mgwatyu
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa; (E.A.S.); (W.W.); (Y.M.); (P.v.H.)
| | - Peter van Heusden
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa; (E.A.S.); (W.W.); (Y.M.); (P.v.H.)
| | - Fanie Rautenbach
- Applied Microbial and Health Biotechnology Institute, Cape Peninsula University of Technology, Bellville 7535, South Africa; (F.R.); (J.M.); (M.L.R.-H.)
| | - Jeanine Marnewick
- Applied Microbial and Health Biotechnology Institute, Cape Peninsula University of Technology, Bellville 7535, South Africa; (F.R.); (J.M.); (M.L.R.-H.)
| | - Marilize Le Roes-Hill
- Applied Microbial and Health Biotechnology Institute, Cape Peninsula University of Technology, Bellville 7535, South Africa; (F.R.); (J.M.); (M.L.R.-H.)
| | - Uljana Hesse
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa; (E.A.S.); (W.W.); (Y.M.); (P.v.H.)
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville 7535, South Africa
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa
- Correspondence:
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12
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van Zyl LJ, Abrahams Y, Stander EA, Kirby-McCollough B, Jourdain R, Clavaud C, Breton L, Trindade M. Novel phages of healthy skin metaviromes from South Africa. Sci Rep 2018; 8:12265. [PMID: 30115980 PMCID: PMC6095929 DOI: 10.1038/s41598-018-30705-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 07/27/2018] [Indexed: 12/15/2022] Open
Abstract
Recent skin metagenomic studies have investigated the harbored viral diversity and its possible influence on healthy skin microbial populations, and tried to establish global patterns of skin-phage evolution. However, the detail associated with the phages that potentially play a role in skin health has not been investigated. While skin metagenome and -metavirome studies have indicated that the skin virome is highly site specific and shows marked interpersonal variation, they have not assessed the presence/absence of individual phages. Here, we took a semi-culture independent approach (metaviromic) to better understand the composition of phage communities on skin from South African study participants. Our data set adds over 130 new phage species of the skin to existing databases. We demonstrated that identical phages were present on different individuals and in different body sites, and we conducted a detailed analysis of the structural organization of these phages. We further found that a bacteriophage related to the Staphylococcus capitis phage Stb20 may be a common skin commensal virus potentially regulating its host and its activities on the skin.
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Affiliation(s)
- Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa.
| | - Yoonus Abrahams
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa
| | - Emily Amor Stander
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa
| | - Bronwyn Kirby-McCollough
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa
| | - Roland Jourdain
- L'Oréal Research and Innovation, 1 Avenue Eugène Schueller, 93600, Aulnay sous Bois, France
| | - Cécile Clavaud
- L'Oréal Research and Innovation, 1 Avenue Eugène Schueller, 93600, Aulnay sous Bois, France
| | - Lionel Breton
- L'Oréal Research and Innovation, 1 Avenue Eugène Schueller, 93600, Aulnay sous Bois, France
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, South Africa
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