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Chen H, Sahu SK, Wang S, Liu J, Yang J, Cheng L, Chiu TY, Liu H. Chromosome-level Alstonia scholaris genome unveils evolutionary insights into biosynthesis of monoterpenoid indole alkaloids. iScience 2024; 27:109599. [PMID: 38646178 PMCID: PMC11033161 DOI: 10.1016/j.isci.2024.109599] [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: 11/17/2023] [Revised: 01/25/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Alstonia scholaris of the Apocynaceae family is a medicinal plant with a rich source of bioactive monoterpenoid indole alkaloids (MIAs), which possess anti-cancer activity like vinca alkaloids. To gain genomic insights into MIA biosynthesis, we assembled a high-quality chromosome-level genome for A. scholaris using nanopore and Hi-C data. The 444.95 Mb genome contained 35,488 protein-coding genes. A total of 20 chromosomes were assembled with a scaffold N50 of 21.75 Mb. The genome contained a cluster of strictosidine synthases and tryptophan decarboxylases with synteny to other species and a saccharide-terpene cluster involved in the monoterpenoid biosynthesis pathway of the MIA upstream pathway. The multi-omics data of A. scholaris provide a valuable resource for understanding the evolutionary origins of MIAs and for discovering biosynthetic pathways and synthetic biology efforts for producing pharmaceutically useful alkaloids.
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Affiliation(s)
- Haixia Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Shujie Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Jia Liu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Jinlong Yang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Le Cheng
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Tsan-Yu Chiu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
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2
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Cole-Osborn LF, McCallan SA, Prifti O, Abu R, Sjoelund V, Lee-Parsons CWT. The role of the Golden2-like (GLK) transcription factor in regulating terpenoid indole alkaloid biosynthesis in Catharanthus roseus. PLANT CELL REPORTS 2024; 43:141. [PMID: 38743349 PMCID: PMC11093837 DOI: 10.1007/s00299-024-03208-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/27/2024] [Indexed: 05/16/2024]
Abstract
KEY MESSAGE A GLK homologue was identified and functionally characterized in Catharanthus roseus. Silencing CrGLK with VIGS or the chloroplast retrograde signaling inducer lincomycin increased terpenoid indole alkaloid biosynthesis. Catharanthus roseus is the sole source of the chemotherapeutic terpenoid indole alkaloids (TIAs) vinblastine and vincristine. TIA pathway genes, particularly genes in the vindoline pathway, are expressed at higher levels in immature versus mature leaves, but the molecular mechanisms responsible for this developmental regulation are unknown. We investigated the role of GOLDEN2-LIKE (GLK) transcription factors in contributing to this ontogenetic regulation since GLKs are active in seedlings upon light exposure and in the leaf's early development, but their activity is repressed as leaves age and senesce. We identified a GLK homologue in C. roseus and functionally characterized its role in regulating TIA biosynthesis, with a focus on the vindoline pathway, by transiently reducing its expression through two separate methods: virus-induced gene silencing (VIGS) and application of chloroplast retrograde signaling inducers, norflurazon and lincomycin. Reducing CrGLK levels with each method reduced chlorophyll accumulation and the expression of the light harvesting complex subunit (LHCB2.2), confirming its functional homology with GLKs in other plant species. In contrast, reducing CrGLK via VIGS or lincomycin increased TIA accumulation and TIA pathway gene expression, suggesting that CrGLK may repress TIA biosynthesis. However, norflurazon had no effect on TIA gene expression, indicating that reducing CrGLK alone is not sufficient to induce TIA biosynthesis. Future work is needed to clarify the specific molecular mechanisms leading to increased TIA biosynthesis with CrGLK silencing. This is the first identification and characterization of GLK in C. roseus and the first investigation of how chloroplast retrograde signaling might regulate TIA biosynthesis.
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Affiliation(s)
- Lauren F Cole-Osborn
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA
- Department of Bioengineering, Northeastern University, Boston, USA
| | - Shannon A McCallan
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, USA
| | - Olga Prifti
- Department of Bioengineering, Northeastern University, Boston, USA
| | - Rafay Abu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, USA
| | - Virginie Sjoelund
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, USA
| | - Carolyn W T Lee-Parsons
- Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA.
- Department of Bioengineering, Northeastern University, Boston, USA.
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, USA.
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3
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Cuello C, Jansen HJ, Abdallah C, Zamar Mbadinga DL, Birer Williams C, Durand M, Oudin A, Papon N, Giglioli-Guivarc'h N, Dirks RP, Jensen MK, O'Connor SE, Besseau S, Courdavault V. The Madagascar palm genome provides new insights on the evolution of Apocynaceae specialized metabolism. Heliyon 2024; 10:e28078. [PMID: 38533072 PMCID: PMC10963385 DOI: 10.1016/j.heliyon.2024.e28078] [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: 12/01/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Specialized metabolites possess diverse interesting biological activities and some cardenolides- and monoterpene indole alkaloids- (MIAs) derived pharmaceuticals are currently used to treat human diseases such as cancers or hypertension. While these two families of biocompounds are produced by specific subfamilies of Apocynaceae, one member of this medicinal plant family, the succulent tree Pachypodium lamerei Drake (also known as Madagascar palm), does not produce such specialized metabolites. To explore the evolutionary paths that have led to the emergence and loss of cardenolide and MIA biosynthesis in Apocynaceae, we sequenced and assembled the P. lamerei genome by combining Oxford Nanopore Technologies long-reads and Illumina short-reads. Phylogenomics revealed that, among the Apocynaceae whose genomes have been sequenced, the Madagascar palm is so far the species closest to the common ancestor between MIA producers/non-MIA producers. Transposable elements, constituting 72.48% of the genome, emerge as potential key players in shaping genomic architecture and influencing specialized metabolic pathways. The absence of crucial MIA biosynthetic genes such as strictosidine synthase in P. lamerei and non-Rauvolfioideae species hints at a transposon-mediated mechanism behind gene loss. Phylogenetic analysis not only showcases the evolutionary divergence of specialized metabolite biosynthesis within Apocynaceae but also underscores the role of transposable elements in this intricate process. Moreover, we shed light on the low conservation of enzymes involved in the final stages of MIA biosynthesis in the distinct MIA-producing plant families, inferring independent gains of these specialized enzymes along the evolution of these medicinal plant clades. Overall, this study marks a leap forward in understanding the genomic dynamics underpinning the evolution of specialized metabolites biosynthesis in the Apocynaceae family, with transposons emerging as potential architects of genomics restructuring and gene loss.
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Affiliation(s)
- Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Hans J. Jansen
- Future Genomics Technologies, 2333 BE, Leiden, the Netherlands
| | - Cécile Abdallah
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | | | - Caroline Birer Williams
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Mickael Durand
- 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, 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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4
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Tabatabaeipour SN, Shiran B, Ravash R, Niazi A, Ebrahimie E. Comprehensive transcriptomic meta-analysis unveils new responsive genes to methyl jasmonate and ethylene in Catharanthusroseus. Heliyon 2024; 10:e27132. [PMID: 38449649 PMCID: PMC10915408 DOI: 10.1016/j.heliyon.2024.e27132] [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: 02/17/2024] [Accepted: 02/23/2024] [Indexed: 03/08/2024] Open
Abstract
In Catharanthus roseus, vital plant hormones, namely methyl jasmonate (MeJA) and ethylene, serve as abiotic triggers, playing a crucial role in stimulating the production of specific secondary compounds with anticancer properties. Understanding how plants react to various stresses, stimuli, and the pathways involved in biosynthesis holds significant promise. The application of stressors like ethylene and MeJA induces the plant's defense mechanisms, leading to increased secondary metabolite production. To delve into the essential transcriptomic processes linked to hormonal responses, this study employed an integrated approach combining RNA-Seq data meta-analysis and system biology methodologies. Furthermore, the validity of the meta-analysis findings was confirmed using RT-qPCR. Within the meta-analysis, 903 genes exhibited differential expression (DEGs) when comparing normal conditions to those of the treatment. Subsequent analysis, encompassing gene ontology, KEGG, TF, and motifs, revealed that these DEGs were actively engaged in multiple biological processes, particularly in responding to various stresses and stimuli. Additionally, these genes were notably enriched in diverse biosynthetic pathways, including those related to TIAs, housing valuable medicinal compounds found in this plant. Furthermore, by conducting co-expression network analysis, we identified hub genes within modules associated with stress response and the production of TIAs. Most genes linked to the biosynthesis pathway of TIAs clustered within three specific modules. Noteworthy hub genes, including Helicase ATP-binding domain, hbdA, and ALP1 genes within the blue, turquoise, and green module networks, are presumed to play a role in the TIAs pathway. These identified candidate genes hold potential for forthcoming genetic and metabolic engineering initiatives aimed at augmenting the production of secondary metabolites and medicinal compounds within C. roseus.
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Affiliation(s)
- Seyede Nasim Tabatabaeipour
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Behrouz Shiran
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
- Institute of Biotechnology, Shahrekord University, P.O. Box 115, Shahrekord, Iran
| | - Rudabeh Ravash
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Ali Niazi
- Department of Biotechnology, Faculty of Agriculture, Shiraz University, Shiraz, Iran
| | - Esmaeil Ebrahimie
- Department of Biotechnology, Faculty of Agriculture, Shiraz University, Shiraz, Iran
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA 5371, Australia
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5
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Guedes JG, Ribeiro R, Carqueijeiro I, Guimarães AL, Bispo C, Archer J, Azevedo H, Fonseca NA, Sottomayor M. The leaf idioblastome of the medicinal plant Catharanthus roseus is associated with stress resistance and alkaloid metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:274-299. [PMID: 37804484 PMCID: PMC10735432 DOI: 10.1093/jxb/erad374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 10/06/2023] [Indexed: 10/09/2023]
Abstract
Catharanthus roseus leaves produce a range of monoterpenoid indole alkaloids (MIAs) that include low levels of the anticancer drugs vinblastine and vincristine. The MIA pathway displays a complex architecture spanning different subcellular and cell type localizations, and is under complex regulation. As a result, the development of strategies to increase the levels of the anticancer MIAs has remained elusive. The pathway involves mesophyll specialized idioblasts where the late unsolved biosynthetic steps are thought to occur. Here, protoplasts of C. roseus leaf idioblasts were isolated by fluorescence-activated cell sorting, and their differential alkaloid and transcriptomic profiles were characterized. This involved the assembly of an improved C. roseus transcriptome from short- and long-read data, IDIO+. It was observed that C. roseus mesophyll idioblasts possess a distinctive transcriptomic profile associated with protection against biotic and abiotic stresses, and indicative that this cell type is a carbon sink, in contrast to surrounding mesophyll cells. Moreover, it is shown that idioblasts are a hotspot of alkaloid accumulation, suggesting that their transcriptome may hold the key to the in-depth understanding of the MIA pathway and the success of strategies leading to higher levels of the anticancer drugs.
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Affiliation(s)
- Joana G Guedes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Programa Doutoral em Biologia Molecular e Celular (MCbiology), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
| | - Rogério Ribeiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Inês Carqueijeiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Ana Luísa Guimarães
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Cláudia Bispo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - John Archer
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Herlander Azevedo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Nuno A Fonseca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Mariana Sottomayor
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
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6
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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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7
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Li C, Wood JC, Vu AH, Hamilton JP, Rodriguez Lopez CE, Payne RME, Serna Guerrero DA, Gase K, Yamamoto K, Vaillancourt B, Caputi L, O'Connor SE, Robin Buell C. Single-cell multi-omics in the medicinal plant Catharanthus roseus. Nat Chem Biol 2023:10.1038/s41589-023-01327-0. [PMID: 37188960 PMCID: PMC10374443 DOI: 10.1038/s41589-023-01327-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
Advances in omics technologies now permit the generation of highly contiguous genome assemblies, detection of transcripts and metabolites at the level of single cells and high-resolution determination of gene regulatory features. Here, using a complementary, multi-omics approach, we interrogated the monoterpene indole alkaloid (MIA) biosynthetic pathway in Catharanthus roseus, a source of leading anticancer drugs. We identified clusters of genes involved in MIA biosynthesis on the eight C. roseus chromosomes and extensive gene duplication of MIA pathway genes. Clustering was not limited to the linear genome, and through chromatin interaction data, MIA pathway genes were present within the same topologically associated domain, permitting the identification of a secologanin transporter. Single-cell RNA-sequencing revealed sequential cell-type-specific partitioning of the leaf MIA biosynthetic pathway that, when coupled with a single-cell metabolomics approach, permitted the identification of a reductase that yields the bis-indole alkaloid anhydrovinblastine. We also revealed cell-type-specific expression in the root MIA pathway.
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Affiliation(s)
- Chenxin Li
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Joshua C Wood
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Anh Hai Vu
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - John P Hamilton
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | - Richard M E Payne
- The John Innes Centre, Department of Biological Chemistry, Norwich Research Park, Norwich, UK
| | | | - Klaus Gase
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Kotaro Yamamoto
- School of Science, Association of International Arts and Science, Yokohama City University, Yokohama, Japan
| | | | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany.
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany.
| | - C Robin Buell
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA.
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA.
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8
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Schotte C, Jiang Y, Grzech D, Dang TTT, Laforest LC, León F, Mottinelli M, Nadakuduti SS, McCurdy CR, O’Connor SE. Directed Biosynthesis of Mitragynine Stereoisomers. J Am Chem Soc 2023; 145:4957-4963. [PMID: 36883326 PMCID: PMC9999412 DOI: 10.1021/jacs.2c13644] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Indexed: 02/24/2023]
Abstract
Mitragyna speciosa ("kratom") is used as a natural remedy for pain and management of opioid dependence. The pharmacological properties of kratom have been linked to a complex mixture of monoterpene indole alkaloids, most notably mitragynine. Here, we report the central biosynthetic steps responsible for the scaffold formation of mitragynine and related corynanthe-type alkaloids. We illuminate the mechanistic basis by which the key stereogenic center of this scaffold is formed. These discoveries were leveraged for the enzymatic production of mitragynine, the C-20 epimer speciogynine, and fluorinated analogues.
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Affiliation(s)
- Carsten Schotte
- Department
of Natural Product Biosynthesis, Max Planck
Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Yindi Jiang
- Department
of Natural Product Biosynthesis, Max Planck
Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Dagny Grzech
- Department
of Natural Product Biosynthesis, Max Planck
Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Thu-Thuy T. Dang
- Department
of Natural Product Biosynthesis, Max Planck
Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Larissa C. Laforest
- Plant
Molecular and Cell Biology Program, University
of Florida, Gainesville, Florida 32606, United States
| | - Francisco León
- Department
of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Marco Mottinelli
- Department
of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Satya Swathi Nadakuduti
- Plant
Molecular and Cell Biology Program, University
of Florida, Gainesville, Florida 32606, United States
- Department
of Environmental Horticulture, University
of Florida, Gainesville, Florida 32606, United
States
| | - Christopher R. McCurdy
- Department
of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - 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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9
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Li H, Wu S, Lin R, Xiao Y, Malaco Morotti AL, Wang Y, Galilee M, Qin H, Huang T, Zhao Y, Zhou X, Yang J, Zhao Q, Kanellis AK, Martin C, Tatsis EC. The genomes of medicinal skullcaps reveal the polyphyletic origins of clerodane diterpene biosynthesis in the family Lamiaceae. MOLECULAR PLANT 2023; 16:549-570. [PMID: 36639870 DOI: 10.1016/j.molp.2023.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/21/2022] [Accepted: 01/09/2023] [Indexed: 06/09/2023]
Abstract
The presence of anticancer clerodane diterpenoids is a chemotaxonomic marker for the traditional Chinese medicinal plant Scutellaria barbata, although the molecular mechanisms behind clerodane biosynthesis are unknown. Here, we report a high-quality assembly of the 414.98 Mb genome of S. barbata into 13 pseudochromosomes. Using phylogenomic and biochemical data, we mapped the plastidial metabolism of kaurene (gibberellins), abietane, and clerodane diterpenes in three species of the family Lamiaceae (Scutellaria barbata, Scutellaria baicalensis, and Salvia splendens), facilitating the identification of genes involved in the biosynthesis of the clerodanes, kolavenol, and isokolavenol. We show that clerodane biosynthesis evolved through recruitment and neofunctionalization of genes from gibberellin and abietane metabolism. Despite the assumed monophyletic origin of clerodane biosynthesis, which is widespread in species of the Lamiaceae, our data show distinct evolutionary lineages and suggest polyphyletic origins of clerodane biosynthesis in the family Lamiaceae. Our study not only provides significant insights into the evolution of clerodane biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the production of anticancer clerodanes through future metabolic engineering efforts.
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Affiliation(s)
- Haixiu Li
- 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
| | - 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
| | - Ruoxi Lin
- 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
| | - 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
| | - 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
| | - Meytal Galilee
- 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
| | - Haowen Qin
- 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
| | - Tao Huang
- Novogene Bioinformatics Institute, Beijing, China
| | - Yong Zhao
- Novogene Bioinformatics Institute, Beijing, China
| | - Xun Zhou
- Novogene Bioinformatics Institute, Beijing, 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; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602, China
| | - Qing Zhao
- 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; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602, China
| | - Angelos K Kanellis
- Group of Biotechnology of Pharmaceutical Plants, Lab. of Pharmacognosy, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | | | - 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 200032, China.
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10
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Zhu M, Wang Z, Yang Y, Wang Z, Mu W, Liu J. Multi-omics reveal differentiation and maintenance of dimorphic flowers in an alpine plant on the Qinghai-Tibet Plateau. Mol Ecol 2023; 32:1411-1424. [PMID: 35363913 DOI: 10.1111/mec.16449] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/22/2022] [Accepted: 03/28/2022] [Indexed: 11/28/2022]
Abstract
Dimorphic flowers growing on a single individual plant play a critical role in extreme adaption and reproductive assurance in plants and have high ecological and evolutionary significance. However, the omics bases underlying such a differentiation and maintenance remain largely unknown. We aimed to investigate this through genomic, transcriptome and metabolomic analyses of dimorphic flowers in an alpine biennial, Sinoswertia tetraptera (Gentianaceae). A high-quality chromosome-level genome sequence (903 Mb) was first assembled for S. tetraptera with 31,359 protein-coding genes annotated. Two rounds of recent independent whole-genome duplication (WGD) were revealed. Numerous genes from the recent species-specific WGD were found to be differentially expressed in the two types of flowers, and this may have helped contribute to the origin of this innovative trait. The genes with contrasting expressions between flowers were related to biosynthesis of hormones, floral pigments (carotenoids and flavonoids) and iridoid compounds, which are involved in both flower development and colour. Metabolomic analyses similarly suggested differential concentrations of these chemicals in the two types of flowers. The expression interactions between multiple genes may together lead to contrasting morphology and chemical concentration and open versus closed pollination of the dimorphic flowers in this species for reproductive assurance.
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Affiliation(s)
- Mingjia Zhu
- State Key Laboratory of Grassland and Agro-ecosystems, Institute of Innovation Ecology, School of Life Science and the Supercomputing Center, Lanzhou University, Lanzhou, China
| | - Zhenyue Wang
- State Key Laboratory of Grassland and Agro-ecosystems, Institute of Innovation Ecology, School of Life Science and the Supercomputing Center, Lanzhou University, Lanzhou, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland and Agro-ecosystems, Institute of Innovation Ecology, School of Life Science and the Supercomputing Center, Lanzhou University, Lanzhou, China
| | - Zefu Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wenjie Mu
- State Key Laboratory of Grassland and Agro-ecosystems, Institute of Innovation Ecology, School of Life Science and the Supercomputing Center, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland and Agro-ecosystems, Institute of Innovation Ecology, School of Life Science and the Supercomputing Center, Lanzhou University, Lanzhou, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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11
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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] [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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12
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Wu Y, Gong FL, Li S. Leveraging yeast to characterize plant biosynthetic gene clusters. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102314. [PMID: 36463029 PMCID: PMC10664738 DOI: 10.1016/j.pbi.2022.102314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Plant biosynthetic gene clusters (BGCs) contain multiple physically clustered non-homologous genes that encode enzymes catalyzing diverse reactions in one plant natural product biosynthetic pathway. A growing number of plant BGCs have emerged as an underlying resource for understanding plant specialized metabolism and evolution, but the characterization remains challenging. Recent studies have demonstrated that baker's yeast can serve as a versatile platform for the characterization of plant BGCs, from single-gene characterization to multiple genes and hitherto unknown putative BGC validation and elucidation. In this review, we will summarize the strategies and examples of the applications of yeast in plant BGC characterization and share our perspective on the development of a systematic pipeline to fully leverage yeast to advance the understanding of plant BGCs and plant natural product biomanufacturing.
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Affiliation(s)
- Yinan Wu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Franklin L Gong
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Sijin Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA.
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13
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Liu X, Zhang P, Zhao Q, Huang AC. Making small molecules in plants: A chassis for synthetic biology-based production of plant natural products. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:417-443. [PMID: 35852486 DOI: 10.1111/jipb.13330] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Plant natural products have been extensively exploited in food, medicine, flavor, cosmetic, renewable fuel, and other industrial sectors. Synthetic biology has recently emerged as a promising means for the cost-effective and sustainable production of natural products. Compared with engineering microbes for the production of plant natural products, the potential of plants as chassis for producing these compounds is underestimated, largely due to challenges encountered in engineering plants. Knowledge in plant engineering is instrumental for enabling the effective and efficient production of valuable phytochemicals in plants, and also paves the way for a more sustainable future agriculture. In this manuscript, we briefly recap the biosynthesis of plant natural products, focusing primarily on industrially important terpenoids, alkaloids, and phenylpropanoids. We further summarize the plant hosts and strategies that have been used to engineer the production of natural products. The challenges and opportunities of using plant synthetic biology to achieve rapid and scalable production of high-value plant natural products are also discussed.
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Affiliation(s)
- Xinyu Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Peijun Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Qiao Zhao
- Shenzhen Institutes of Advanced Technology (SIAT), the Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Ancheng C Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
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14
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Zhao Z, Zhang Y, Shi M, Liu Z, Xu Y, Luo Z, Yuan S, Tu T, Sun Z, Zhang D, Barrett SCH. Genomic evidence supports the genetic convergence of a supergene controlling the distylous floral syndrome. THE NEW PHYTOLOGIST 2023; 237:601-614. [PMID: 36239093 DOI: 10.1111/nph.18540] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Heterostyly, a plant sexual polymorphism controlled by the S-locus supergene, has evolved numerous times among angiosperm lineages and represents a classic example of convergent evolution in form and function. Determining whether underlying molecular convergence occurs could provide insights on constraints to floral evolution. Here, we investigated S-locus genes in distylous Gelsemium (Gelsemiaceae) to determine whether there is evidence of molecular convergence with unrelated distylous species. We used several approaches, including anatomical measurements of sex-organ development and transcriptome and whole-genome sequencing, to identify components of the S-locus supergene. We also performed evolutionary analysis with candidate S-locus genes and compared them with those reported in Primula and Turnera. The candidate S-locus supergene of Gelsemium contained four genes, of which three appear to have originated from gene duplication events within Gelsemiaceae. The style-length genes GeCYP in Gelsemium and CYP734A50 in Primula likely arose from duplication of the same gene, CYP734A1. Three out of four S-locus genes in Gelsemium elegans were hemizygous, as previously reported in Primula and Turnera. We provide genomic evidence on the genetic convergence of the supergene underlying distyly among distantly related angiosperm lineages and help to illuminate the genetic architecture involved in the evolution of heterostyly.
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Affiliation(s)
- Zhongtao Zhao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- College of Life Sciences, Gannan Normal University, Ganzhou, 34100, China
| | - Yu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhaoying Liu
- Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha, 410128, China
| | - Yuanqing Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhonglai Luo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Shuai Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Tieyao Tu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhiliang Sun
- Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha, 410128, China
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- College of Life Sciences, Gannan Normal University, Ganzhou, 34100, China
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
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15
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Hao J, Zheng L, Han Y, Zhang H, Hou K, Liang X, Chen C, Wang Z, Qian J, Lin Z, Wang Z, Zeng H, Shen C. Genome-wide identification and expression analysis of TCP family genes in Catharanthus roseus. FRONTIERS IN PLANT SCIENCE 2023; 14:1161534. [PMID: 37123846 PMCID: PMC10130365 DOI: 10.3389/fpls.2023.1161534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
Introduction The anti-tumor vindoline and catharanthine alkaloids are naturally existed in Catharanthus roseus (C. roseus), an ornamental plant in many tropical countries. Plant-specific TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play important roles in various plant developmental processes. However, the roles of C. roseus TCPs (CrTCPs) in terpenoid indole alkaloid (TIA) biosynthesis are largely unknown. Methods Here, a total of 15 CrTCP genes were identified in the newly updated C. roseus genome and were grouped into three major classes (P-type, C-type and CYC/TB1). Results Gene structure and protein motif analyses showed that CrTCPs have diverse intron-exon patterns and protein motif distributions. A number of stress responsive cis-elements were identified in promoter regions of CrTCPs. Expression analysis showed that three CrTCP genes (CrTCP2, CrTCP4, and CrTCP7) were expressed specifically in leaves and four CrTCP genes (CrTCP13, CrTCP8, CrTCP6, and CrTCP10) were expressed specifically in flowers. HPLC analysis showed that the contents of three classic TIAs, vindoline, catharanthine and ajmalicine, were significantly increased by ultraviolet-B (UV-B) and methyl jasmonate (MeJA) in leaves. By analyzing the expression patterns under UV-B radiation and MeJA application with qRT-PCR, a number of CrTCP and TIA biosynthesis-related genes were identified to be responsive to UV-B and MeJA treatments. Interestingly, two TCP binding elements (GGNCCCAC and GTGGNCCC) were identified in several TIA biosynthesis-related genes, suggesting that they were potential target genes of CrTCPs. Discussion These results suggest that CrTCPs are involved in the regulation of the biosynthesis of TIAs, and provide a basis for further functional identification of CrTCPs.
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Affiliation(s)
- Juan Hao
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Lijun Zheng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Yidie Han
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Hongshan Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
- Kharkiv Institute, Hangzhou Normal University, Hangzhou, China
| | - Kailin Hou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Xueshuang Liang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Cheng Chen
- College of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Zhijing Wang
- College of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Jiayi Qian
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Zhihao Lin
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Zitong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Houqing Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Kharkiv Institute, Hangzhou Normal University, Hangzhou, China
- *Correspondence: Chenjia Shen, ; Houqing Zeng,
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
- Kharkiv Institute, Hangzhou Normal University, Hangzhou, China
- *Correspondence: Chenjia Shen, ; Houqing Zeng,
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16
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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] [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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17
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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, MD.) 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] [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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18
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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] [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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19
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Singh KS, van der Hooft JJJ, van Wees SCM, Medema MH. Integrative omics approaches for biosynthetic pathway discovery in plants. Nat Prod Rep 2022; 39:1876-1896. [PMID: 35997060 PMCID: PMC9491492 DOI: 10.1039/d2np00032f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/13/2022]
Abstract
Covering: up to 2022With the emergence of large amounts of omics data, computational approaches for the identification of plant natural product biosynthetic pathways and their genetic regulation have become increasingly important. While genomes provide clues regarding functional associations between genes based on gene clustering, metabolome mining provides a foundational technology to chart natural product structural diversity in plants, and transcriptomics has been successfully used to identify new members of their biosynthetic pathways based on coexpression. Thus far, most approaches utilizing transcriptomics and metabolomics have been targeted towards specific pathways and use one type of omics data at a time. Recent technological advances now provide new opportunities for integration of multiple omics types and untargeted pathway discovery. Here, we review advances in plant biosynthetic pathway discovery using genomics, transcriptomics, and metabolomics, as well as recent efforts towards omics integration. We highlight how transcriptomics and metabolomics provide complementary information to link genes to metabolites, by associating temporal and spatial gene expression levels with metabolite abundance levels across samples, and by matching mass-spectral features to enzyme families. Furthermore, we suggest that elucidation of gene regulatory networks using time-series data may prove useful for efforts to unwire the complexities of biosynthetic pathway components based on regulatory interactions and events.
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Affiliation(s)
- Kumar Saurabh Singh
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Saskia C M van Wees
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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20
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Qiao C, Chen F, Liu Z, Huang T, Li W, Zhang G, Luo Y. Functional characterization of a catalytically promiscuous tryptophan decarboxylase from camptothecin-producing Camptotheca acuminata. FRONTIERS IN PLANT SCIENCE 2022; 13:987348. [PMID: 36061783 PMCID: PMC9433702 DOI: 10.3389/fpls.2022.987348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Tryptophan decarboxylases (TDCs) are a group of pyridoxal 5'-phosphate-dependent enzymes involved in the enzymatic conversion of tryptophan into tryptamine, a critical biogenic amine. We herein mined and cloned a TDC-encoding gene, CaTDC3, from camptothecin-producing plant Camptotheca acuminata. The intact CaTDC3 was heterologously overexpressed in Escherichia coli and the recombinant CaTDC3 was purified to homogeneity. High-performance liquid chromatography (HPLC)-diode array detector (DAD) and high resolution mass spectrometry (HRMS) data analyses of the CaTDC3-catalyzed reaction mixture confirmed the catalytically decarboxylative activity of CaTDC3. CaTDC3 shows strict stereoselectivity for L-tryptophan. Homology modeling and molecular docking implied CaTDC3's recognition of L-tryptophan derivatives and analogs. Substrate scope investigations revealed that the appropriate substituent groups on the indole ring, i.e., hydroxylated and halogenated L-tryptophans, could be recognized by CaTDC3 and the decarboxylation reactions generated the corresponding tryptamines. The Cβ -methyl-L-tryptophans were decarboxylated by CaTDC3 efficiently. 1-Thio-L-tryptophan, the NH group of the indole ring replaced by an S atom, could be decarboxylated by CaTDC3. CaTDC3 catalyzed the decarboxylation of 7-aza-L-tryptophan, an N displacement of the C on the aromatic ring, to afford 7-aza-tryptamine. L-Kynurenine, an L-tryptophan degradation product, could be decarboxylated by CaTDC3. The present works uncover a catalytically promiscuous TDC and the TDC is a versatile decarboxylase in synthetic biology for specialized pharmaceutically important substances.
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Affiliation(s)
- Chong Qiao
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Chen
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhan Liu
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianfang Huang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Wei Li
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guolin Zhang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yinggang Luo
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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21
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Sirirungruang S, Markel K, Shih PM. Plant-based engineering for production of high-valued natural products. Nat Prod Rep 2022; 39:1492-1509. [PMID: 35674317 DOI: 10.1039/d2np00017b] [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
Covering: up to March 2022Plants are a unique source of complex specialized metabolites, many of which play significant roles in human society. In many cases, however, the availability of these metabolites from naturally occurring sources fails to meet current demands. Thus, there is much interest in expanding the production capacity of target plant molecules. Traditionally, plant breeding, chemical synthesis, and microbial fermentation are considered the primary routes towards large scale production of natural products. Here, we explore the advances, challenges, and future of plant engineering as a complementary path. Although plants are an integral part of our food and agricultural systems and sustain an extensive array of chemical constituents, their complex genetics and physiology have prevented the optimal exploitation of plants as a production chassis. We highlight emerging engineering tools and scientific advances developed in recent years that have improved the prospects of using plants as a sustainable and scalable production platform. We also discuss technological limitations and overall economic outlook of plant-based production of natural products.
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Affiliation(s)
- Sasilada Sirirungruang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. .,Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Kasey Markel
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. .,Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Patrick M Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. .,Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, CA, USA
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22
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Smit SJ, Lichman BR. Plant biosynthetic gene clusters in the context of metabolic evolution. Nat Prod Rep 2022; 39:1465-1482. [PMID: 35441651 PMCID: PMC9298681 DOI: 10.1039/d2np00005a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Indexed: 12/17/2022]
Abstract
Covering: up to 2022Plants produce a wide range of structurally and biosynthetically diverse natural products to interact with their environment. These specialised metabolites typically evolve in limited taxonomic groups presumably in response to specific selective pressures. With the increasing availability of sequencing data, it has become apparent that in many cases the genes encoding biosynthetic enzymes for specialised metabolic pathways are not randomly distributed on the genome. Instead they are physically linked in structures such as arrays, pairs and clusters. The exact function of these clusters is debated. In this review we take a broad view of gene arrangement in plant specialised metabolism, examining types of structures and variation. We discuss the evolution of biosynthetic gene clusters in the wider context of metabolism, populations and epigenetics. Finally, we synthesise our observations to propose a new hypothesis for biosynthetic gene cluster formation in plants.
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Affiliation(s)
- Samuel J Smit
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
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23
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Wu S, Malaco Morotti AL, Wang S, Wang Y, Xu X, Chen J, Wang G, Tatsis EC. Convergent gene clusters underpin hyperforin biosynthesis in St John's wort. THE NEW PHYTOLOGIST 2022; 235:646-661. [PMID: 35377483 DOI: 10.1111/nph.18138] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The meroterpenoid hyperforin is responsible for the antidepressant activity of St John's wort extracts, but the genes controlling its biosynthesis are unknown. Using genome mining and biochemical work, we characterize two biosynthetic gene clusters (BGCs) that encode the first three steps in the biosynthesis of hyperforin precursors. The findings of syntenic and phylogenetic analyses reveal the parallel assembly of the two BGCs. The syntenous BGC in Mesua ferrea indicates that the first cluster was assembled before the divergence of the Hypericaceae and Calophyllaceae families. The assembly of the second cluster is the result of a coalescence of genomic fragments after a major duplication event. The differences between the two BGCs - in terms of gene expression, response to methyl jasmonate, substrate specificity and subcellular localization of key enzymes - suggest that the presence of the two clusters could serve to generate separate pools of precursors. The parallel assembly of two BGCs with similar compositions in a single plant species is uncommon, and our work provides insights into how and when these gene clusters form. Our discovery helps to advance our understanding of the evolution of plant specialized metabolism and its genomic organization. Additionally, our results offer a foundation from which hyperforin biosynthesis can be more fully understood, and which can be used in future metabolic engineering applications.
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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, 300 Feng Lin Road, 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, 300 Feng Lin Road, 200032, China
| | - Shanshan 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, 300 Feng Lin Road, 200032, China
| | - 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, 300 Feng Lin Road, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyan Xu
- 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, 300 Feng Lin Road, 200032, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla County, 666303, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, 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, 300 Feng Lin Road, 200032, China
- CEPAMS - Centre of Excellence for Plant and Microbial Science, Shanghai, 200032, China
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24
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Božunović J, Milutinović M, Aničić N, Skorić M, Matekalo D, Živković S, Dragićević M, Filipović B, Banjanac T, Petrović L, Mišić D. Functional Characterization of Genes Coding for Novel β-D-Glucosidases Involved in the Initial Step of Secoiridoid Glucosides Catabolism in Centaurium erythraea Rafn. FRONTIERS IN PLANT SCIENCE 2022; 13:914138. [PMID: 35812935 PMCID: PMC9260424 DOI: 10.3389/fpls.2022.914138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Secoiridoid glucosides (SGs) are monoterpenoids derived from the iridoid cyclopentane-C-pyran skeleton with β-D glucose linked at C1 position. Coordinated metabolic processes, such as biosynthesis and catabolism of SGs, ensure constitutive presence of these bitter tasting compounds in plant tissues, which plays a decisive role in the defense against pathogens and herbivores. These compounds are susceptible to hydrolysis mediated by enzymes β-glucosidases, and the resulting aglycones are subsequently directed toward different metabolic pathways in plants. Function of two β-D-glucosidases (named CeBGlu1 and CeBGlu2) from centaury (Centaurium erythraea Rafn; fam. Gentianaceae), belonging to the glycoside hydrolase 1 (GH1) family, was confirmed using in vitro assays with recombinant proteins, following their heterologous expression in E. coli and His-tag affinity purification. Although they show slightly differential substrate preference, both isoforms display high specificity toward SGs and the organ-specific distribution of transcripts was positively correlated with the content of SGs in diploid and tetraploid C. erythraea plants. Transient overexpression of CeBGlu1 and CeBGlu2 in C. erythraea leaves induced changes in metabolite profiles. The effectiveness of transgene overexpression has been altered by plant ploidy. UHPLC/DAD/(±)HESI - MS2 profiling of leaves of diploid and tetraploid C. erythraea genotypes revealed that the amounts of major SGs; sweroside, swertiamarin, and gentiopicrin was decreased in agroinfiltrated leaves, especially when CeBGlu1 and CeBGlu2 were co-expressed with transgene silencing suppressor p19. The work demonstrates that in planta metabolic engineering adopting transient overexpression of CeBGlu1 and CeBGlu2 is a suitable tool for the modulation of SGs content and glucosides/aglycones ratio, which might have substantial effects on overall phytochemistry of C. erythraea.
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Affiliation(s)
| | | | | | | | - Dragana Matekalo
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”- National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | | | | | | | | | - Danijela Mišić
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”- National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
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25
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Li T, Yu X, Ren Y, Kang M, Yang W, Feng L, Hu Q. The chromosome-level genome assembly of Gentiana dahurica (Gentianaceae) provides insights into gentiopicroside biosynthesis. DNA Res 2022; 29:6563597. [PMID: 35380665 PMCID: PMC9019652 DOI: 10.1093/dnares/dsac008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 04/02/2022] [Indexed: 12/02/2022] Open
Abstract
Gentiana dahurica Fisch. is a perennial herb of the family Gentianaceae. This species is used as a traditional Tibetan medicine because of its rich gentiopicroside constituents. Here, we generate a high-quality, chromosome-level genome of G. dahurica with a total length of 1,416.54 Mb. Comparative genomic analyses showed that G. dahurica shared one whole-genome duplication (WGD) event with Gelsemium sempervirens of the family Gelsemiaceaei and had one additional species-specific WGD after the ancient whole-genome triplication with other eudicots. Further transcriptome analyses identified numerous enzyme coding genes and the transcription factors related to gentiopicroside biosynthesis. A set of candidate cytochrome P450 genes were identified for being involved in biosynthetic shifts from swertiamarin to gentiopicroside. Both gene expressions and the contents measured by high-performance liquid chromatography indicated that the gentiopicrosides were mainly synthesized in the rhizomes with the highest contents. In addition, we found that two above-mentioned WGDs, contributed greatly to the identified candidate genes involving in gentiopicroside biosynthesis. The first reference genome of Gentianaceae we generated here will definitely accelerate evolutionary, ecological, and pharmaceutical studies of this family.
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Affiliation(s)
- Ting Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xi Yu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yumeng Ren
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Minghui Kang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wenjie Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Landi Feng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Quanjun Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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26
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Koudounas K, Guirimand G, Hoyos LFR, Carqueijeiro I, Cruz PL, Stander E, Kulagina N, Perrin J, Oudin A, Besseau S, Lanoue A, Atehortùa L, St-Pierre B, Giglioli-Guivarc'h N, Papon N, O'Connor SE, Courdavault V. Tonoplast and Peroxisome Targeting of γ-tocopherol N-methyltransferase Homologs Involved in the Synthesis of Monoterpene Indole Alkaloids. PLANT & CELL PHYSIOLOGY 2022; 63:200-216. [PMID: 35166361 DOI: 10.1093/pcp/pcab160] [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: 07/02/2021] [Revised: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 06/14/2023]
Abstract
Many plant species from the Apocynaceae, Loganiaceae and Rubiaceae families evolved a specialized metabolism leading to the synthesis of a broad palette of monoterpene indole alkaloids (MIAs). These compounds are believed to constitute a cornerstone of the plant chemical arsenal but above all several MIAs display pharmacological properties that have been exploited for decades by humans to treat various diseases. It is established that MIAs are produced in planta due to complex biosynthetic pathways engaging a multitude of specialized enzymes but also a complex tissue and subcellular organization. In this context, N-methyltransferases (NMTs) represent an important family of enzymes indispensable for MIA biosynthesis but their characterization has always remained challenging. In particular, little is known about the subcellular localization of NMTs in MIA-producing plants. Here, we performed an extensive analysis on the subcellular localization of NMTs from four distinct medicinal plants but also experimentally validated that two putative NMTs from Catharanthus roseus exhibit NMT activity. Apart from providing unprecedented data regarding the targeting of these enzymes in planta, our results point out an additional layer of complexity to the subcellular organization of the MIA biosynthetic pathway by introducing tonoplast and peroxisome as new actors of the final steps of MIA biosynthesis.
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Affiliation(s)
- Konstantinos Koudounas
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | | | - Luisa Fernanda Rojas Hoyos
- Grupo de Biotransformación-Escuela de Microbiología, Universidad de Antioquia, Calle 70 No 52-21, A.A 1226, Medellín, Colombia
| | - Ines Carqueijeiro
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Pamela Lemos Cruz
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Emily Stander
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Natalja Kulagina
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Jennifer Perrin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Audrey Oudin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Sébastien Besseau
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Arnaud Lanoue
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Lucia Atehortùa
- Laboratorio de Biotecnología, Sede de Investigación Universitaria, Universidad de Antioquia, Medellin 50010, Colombia
| | - Benoit St-Pierre
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | | | - Nicolas Papon
- GEIHP, SFR ICAT, University of Angers, Université de Bretagne Occidentale, 4 rue de Larrey - F49933, Angers 49000, France
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
- Graduate School of Sciences, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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Lichman BR. Ancestral Sequence Reconstruction for Exploring Alkaloid Evolution. Methods Mol Biol 2022; 2505:165-179. [PMID: 35732944 DOI: 10.1007/978-1-0716-2349-7_12] [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] [Indexed: 06/15/2023]
Abstract
The complex and bioactive monoterpene indole alkaloids (MIAs) found in Catharanthus roseus and related species are the products of many millions of years of evolution through mutation and natural selection. Ancestral sequence reconstruction (ASR) is a method that combines phylogenetic analysis and experimental biochemistry to infer details about past events in protein evolution. Here, I propose that ASR could be leveraged to understand how enzymes catalyzing the formation of complex alkaloids arose over evolutionary time. I discuss the steps of ASR, including sequence selection, multiple sequence alignment, tree inference, and the generation and characterization of inferred ancestral enzymes.
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Affiliation(s)
- Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK.
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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] [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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29
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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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30
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Lin H, Qiu H, Cheng Y, Liu M, Chen M, Que Y, Que W. Gelsemium elegans Benth: Chemical Components, Pharmacological Effects, and Toxicity Mechanisms. Molecules 2021; 26:molecules26237145. [PMID: 34885727 PMCID: PMC8659130 DOI: 10.3390/molecules26237145] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/20/2021] [Accepted: 11/20/2021] [Indexed: 11/16/2022] Open
Abstract
Gelsemium elegans Benth (GEB), also known as heartbreak grass, is a highly poisonous plant belonging to the family Loganiaceae and genus Gelsemium that has broad application prospects in medicine. This article reviews its chemical components, pharmacological effects, toxicity mechanisms, and research progress in clinical applications in recent years. Indole alkaloids are the main active components of GEB and have a variety of pharmacological and biological functions. They have anti-tumor, anti-inflammatory, analgesic, and immunomodulation properties, with the therapeutic dose being close to the toxic dose. Application of small-dose indole alkaloids fails to work effectively, while high-dose usage is prone to poisoning, aggravating the patient’s conditions. Special caution is needed, especially to observe the changes in the disease condition of the patients in clinical practice. In-depth research on the chemical components and mechanisms of GEB is essential to the development of promising lead compounds and lays the foundation for extensive clinical application and safe usage of GEB in the future.
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Affiliation(s)
- Hailing Lin
- Department of Pharmacy, Fujian Medical University Union Hospital, 29 Xin Quan Rd, Gulou, Fuzhou 350001, China; (H.L.); (H.Q.); (Y.C.); (M.L.); (M.C.)
| | - Hongqiang Qiu
- Department of Pharmacy, Fujian Medical University Union Hospital, 29 Xin Quan Rd, Gulou, Fuzhou 350001, China; (H.L.); (H.Q.); (Y.C.); (M.L.); (M.C.)
| | - Yu Cheng
- Department of Pharmacy, Fujian Medical University Union Hospital, 29 Xin Quan Rd, Gulou, Fuzhou 350001, China; (H.L.); (H.Q.); (Y.C.); (M.L.); (M.C.)
| | - Maobai Liu
- Department of Pharmacy, Fujian Medical University Union Hospital, 29 Xin Quan Rd, Gulou, Fuzhou 350001, China; (H.L.); (H.Q.); (Y.C.); (M.L.); (M.C.)
| | - Maohua Chen
- Department of Pharmacy, Fujian Medical University Union Hospital, 29 Xin Quan Rd, Gulou, Fuzhou 350001, China; (H.L.); (H.Q.); (Y.C.); (M.L.); (M.C.)
| | - Youxiong Que
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (Y.Q.); (W.Q.)
| | - Wancai Que
- Department of Pharmacy, Fujian Medical University Union Hospital, 29 Xin Quan Rd, Gulou, Fuzhou 350001, China; (H.L.); (H.Q.); (Y.C.); (M.L.); (M.C.)
- Correspondence: (Y.Q.); (W.Q.)
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Yu B, Pan Y, Liu Y, Chen Q, Guo X, Tang Z. A comprehensive analysis of transcriptome and phenolic compound profiles suggests the role of flavonoids in cotyledon greening in Catharanthus roseus seedling. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:185-197. [PMID: 34365289 DOI: 10.1016/j.plaphy.2021.07.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 07/03/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
During seedling photo-morphogenesis, cotyledon greening is a vital developmental process and a moment of responding to light stress. An increasing number of reports suggest the function of natural antioxidant protection of phenolic compounds in plant growth and development processes. Due to the antioxidant functions, flavonoids allow plants to respond to abiotic or biotic stresses. As one of the plants rich in secondary metabolites, Catharanthus roseus has drawn great academic interest due to its richness of diverse secondary metabolites with medicinal values. To assess the distribution and function of phenolic compounds during cotyledon greening, combined phenolic profiling and transcriptome were applied in C. roseus seedling through ultra-high performance liquid chromatography quadrupole time-of-flight mass spectrometer (UPLC-Q-TOF/MS) and high throughput RNA sequencing, respectively. Results herein showed that light-exposed greening cotyledon accumulated large amounts of C6C3C6-type flavonoids, suggesting the function in repressing reactive oxygen species (ROS) generation to improve light adaptation and seedling survival. Moreover, synergistic up-regulation of relevant genes involved in flavonoids pathway, including PAL, C4H, CHS, FLS, and F3'H, was monitored in response to light. Several crucial candidate transcription factors including bHLH, MYB, and B-box families were likely to function, and thereinto, CrHY5 (CRO_T122304) and CRO_T137938 revealed a prompt response to light, supposing to induce flavonoids accumulation by targeting CHS and FLS. Therefore, this study provided new insight into the potential regulation and underlying roles of flavonoids to improve light acclimation during cotyledon greening.
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Affiliation(s)
- Bofan Yu
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China; Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Yajie Pan
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China; Department of Biology, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yang Liu
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China; Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Qi Chen
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Xiaorui Guo
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China; Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China.
| | - Zhonghua Tang
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China; Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China.
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Strictosidine synthase, an indispensable enzyme involved in the biosynthesis of terpenoid indole and β-carboline alkaloids. Chin J Nat Med 2021; 19:591-607. [PMID: 34419259 DOI: 10.1016/s1875-5364(21)60059-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Indexed: 11/21/2022]
Abstract
Terpenoid indole (TIAs) and β-carboline alkaloids (BCAs), such as suppressant reserpine, vasodilatory yohimbine, and antimalarial quinine, are natural compounds derived from strictosidine. These compounds can exert powerful pharmacological effects but be obtained from limited source in nature. the whole biosynthetic pathway of TIAs and BCAs, The Pictet-Spengler reaction catalyzed by strictosidine synthase (STR; EC: 4.3.3.2) is the rate-limiting step. Therefore, it is necessary to investigate their biosynthesis pathways, especially the role of STR, and related findings will support the biosynthetic generation of natural and unnatural compounds. This review summarizes the latest studies concerning the function of STR in TIA and BCA biosynthesis, and illustrates the compounds derived from strictosidine. The substrate specificity of STR based on its structure is also summarized. Proteins that contain six-bladed four-stranded β-propeller folds in many organisms, other than plants, are listed. The presence of these folds may lead to similar functions among organisms. The expression of STR gene can greatly influence the production of many compounds. STR is mainly applied to product various valuable drugs in plant cell suspension culture and biosynthesis in other carriers.
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Tang C. Exploring the evolutionary process of alkannin/shikonin O-acyltransferases by a reliable Lithospermum erythrorhizon genome. DNA Res 2021; 28:6356517. [PMID: 34424327 PMCID: PMC8435551 DOI: 10.1093/dnares/dsab015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023] Open
Abstract
Increasing genome data are coming out. Genome size estimation plays an essential role in guiding genome assembly. Several months ago, other researchers were the first to publish a draft genome of the red gromwell (i.e. Lithospermum erythrorhizon). However, we considered that the genome size they estimated and assembled was incorrect. This study meticulously estimated the L. erythrorhizon genome size to should be ∼708.74 Mb and further provided a reliable genome version (size ≈ 693.34 Mb; contigN50 length ≈ 238.08 Kb) to support our objection. Furthermore, according to our genome, we identified a gene family of the alkannin/shikonin O-acyltransferases (i.e. AAT/SAT) that catalysed enantiomer-specific acylations in the alkannin/shikonin biosynthesis (a characteristic metabolic pathway in L. erythrorhizon's roots) and further explored its evolutionary process. The results indicated that the existing AAT/SAT were not generated from only one round of gene duplication but three rounds; after different rounds of gene duplication, the existing AAT/SAT and their recent ancestors were under positive selection at different amino acid sites. These suggested that a combined power from gene duplication plus positive selection plausibly propelled AAT/SAT's functional differentiation in evolution.
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Affiliation(s)
- Chengyi Tang
- School of the Environment, Nanjing University, Nanjing, China,To whom correspondence should be addressed. Tel: +86-0510-87900134; Fax: +86-0510-87900134;
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Bharadwaj R, Kumar SR, Sharma A, Sathishkumar R. Plant Metabolic Gene Clusters: Evolution, Organization, and Their Applications in Synthetic Biology. FRONTIERS IN PLANT SCIENCE 2021; 12:697318. [PMID: 34490002 PMCID: PMC8418127 DOI: 10.3389/fpls.2021.697318] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/05/2021] [Indexed: 05/21/2023]
Abstract
Plants are a remarkable source of high-value specialized metabolites having significant physiological and ecological functions. Genes responsible for synthesizing specialized metabolites are often clustered together for a coordinated expression, which is commonly observed in bacteria and filamentous fungi. Similar to prokaryotic gene clustering, plants do have gene clusters encoding enzymes involved in the biosynthesis of specialized metabolites. More than 20 gene clusters involved in the biosynthesis of diverse metabolites have been identified across the plant kingdom. Recent studies demonstrate that gene clusters are evolved through gene duplications and neofunctionalization of primary metabolic pathway genes. Often, these clusters are tightly regulated at nucleosome level. The prevalence of gene clusters related to specialized metabolites offers an attractive possibility of an untapped source of highly useful biomolecules. Accordingly, the identification and functional characterization of novel biosynthetic pathways in plants need to be worked out. In this review, we summarize insights into the evolution of gene clusters and discuss the organization and importance of specific gene clusters in the biosynthesis of specialized metabolites. Regulatory mechanisms which operate in some of the important gene clusters have also been briefly described. Finally, we highlight the importance of gene clusters to develop future metabolic engineering or synthetic biology strategies for the heterologous production of novel metabolites.
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Affiliation(s)
- Revuru Bharadwaj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Sarma R. Kumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, Querétaro, Mexico
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
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35
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Antonelli A, Clarkson JJ, Kainulainen K, Maurin O, Brewer GE, Davis AP, Epitawalage N, Goyder DJ, Livshultz T, Persson C, Pokorny L, Straub SCK, Struwe L, Zuntini AR, Forest F, Baker WJ. Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes. AMERICAN JOURNAL OF BOTANY 2021; 108:1143-1165. [PMID: 34254285 DOI: 10.1002/ajb2.1697] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family-level relationships within Gentianales have been presented in previous studies. METHODS Here we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off-target reads for most taxa and infer phylogenetic trees for comparison with the nuclear-derived trees. RESULTS We recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order's classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae). CONCLUSIONS The higher-level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.
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Affiliation(s)
- Alexandre Antonelli
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | | | - Kent Kainulainen
- Gothenburg Botanical Garden, Carl Skottsbergs gata 22 A, Gothenburg, 413 19, Sweden
| | | | | | | | | | | | - Tatyana Livshultz
- Department of Biodiversity Earth and Environmental Sciences and Academy of Natural Sciences, Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA, 19103, USA
| | - Claes Persson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
| | | | - Shannon C K Straub
- Department of Biology, Hobart and William Smith Colleges, 300 Pulteney Street, Geneva, NY, 14456, USA
| | - Lena Struwe
- Department of Ecology, Evolution, and Natural Resources & Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, NJ, 08901, USA
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Computational biotechnology guides elucidation of the biosynthesis of the plant anticancer drug camptothecin. Comput Struct Biotechnol J 2021; 19:3659-3663. [PMID: 34257844 PMCID: PMC8254074 DOI: 10.1016/j.csbj.2021.06.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/18/2021] [Accepted: 06/18/2021] [Indexed: 11/09/2022] Open
Abstract
Camptothecin is a clinically important monoterpene indole alkaloid (MIAs) used for treating various cancers. Currently, the production of this biopharmaceutical hinges on its extraction from camptothecin-producing plants, leading to high market prices and supply bottlenecks. While synthetic biology combined with metabolic approaches could represent an attractive alternative approach to manufacturing, it requires firstly a complete biosynthetic pathway elucidation, which is, unfortunately, severely missing in species naturally accumulating camptothecin. This knowledge gap can be attributed to the lack of high-quality genomic resources of medicinal plant species. In such a perspective, Yamazaki and colleagues produced the first described and experimentally validated chromosome-level plant genome assembly of Ophiorrhiza pumila, a prominent source plant of camptothecin for the pharmaceutical industry. More specifically, they have developed a method incorporating Illumina reads, PacBio single-molecule reads, optical mapping and Hi-C sequencing, followed by the experimental validation of contig orientation within scaffolds, using fluorescence in situ hybridization (FISH) analysis. This relevant strategy resulted in the most contiguous and complete de novo plant reference genome described to date, which can streamline the sequencing of new plant genomes. Further mining approaches, including integrative omics analysis, phylogenetics, gene cluster evaluation and comparative genomics were successfully used to puzzle out the evolutionary origins of MIA metabolism and revealed a short-list of high confidence MIA biosynthetic genes for functional validation.
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Wang J, Xu S, Mei Y, Cai S, Gu Y, Sun M, Liang Z, Xiao Y, Zhang M, Yang S. A high-quality genome assembly of Morinda officinalis, a famous native southern herb in the Lingnan region of southern China. HORTICULTURE RESEARCH 2021; 8:135. [PMID: 34059651 PMCID: PMC8166937 DOI: 10.1038/s41438-021-00551-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/23/2021] [Accepted: 03/22/2021] [Indexed: 05/03/2023]
Abstract
Morinda officinalis is a well-known medicinal and edible plant that is widely cultivated in the Lingnan region of southern China. Its dried roots (called bajitian in traditional Chinese medicine) are broadly used to treat various diseases, such as impotence and rheumatism. Here, we report a high-quality chromosome-scale genome assembly of M. officinalis using Nanopore single-molecule sequencing and Hi-C technology. The assembled genome size was 484.85 Mb with a scaffold N50 of 40.97 Mb, and 90.77% of the assembled sequences were anchored on eleven pseudochromosomes. The genome includes 27,698 protein-coding genes, and most of the assemblies are repetitive sequences. Genome evolution analysis revealed that M. officinalis underwent core eudicot γ genome triplication events but no recent whole-genome duplication (WGD). Likewise, comparative genomic analysis showed no large-scale structural variation after species divergence between M. officinalis and Coffea canephora. Moreover, gene family analysis indicated that gene families associated with plant-pathogen interactions and sugar metabolism were significantly expanded in M. officinalis. Furthermore, we identified many candidate genes involved in the biosynthesis of major active components such as anthraquinones, iridoids and polysaccharides. In addition, we also found that the DHQS, GGPPS, TPS-Clin, TPS04, sacA, and UGDH gene families-which include the critical genes for active component biosynthesis-were expanded in M. officinalis. This study provides a valuable resource for understanding M. officinalis genome evolution and active component biosynthesis. This work will facilitate genetic improvement and molecular breeding of this commercially important plant.
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Affiliation(s)
- Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Shiqiang Xu
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Yu Mei
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Shike Cai
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Yan Gu
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Minyang Sun
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China
| | - Zhan Liang
- DongFuhang High-tech Agricultural Planting and Management Co., Ltd, 526000, Zhaoqing, China
| | - Yong Xiao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, 571339, Wenchang, China.
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources, Guangxi University, 530005, Nanning, China.
| | - Shaohai Yang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, China.
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Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis. Nat Commun 2021; 12:405. [PMID: 33452249 PMCID: PMC7810986 DOI: 10.1038/s41467-020-20508-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/07/2020] [Indexed: 01/29/2023] Open
Abstract
Plant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes' evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.
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Singh SK, Patra B, Paul P, Liu Y, Pattanaik S, Yuan L. BHLH IRIDOID SYNTHESIS 3 is a member of a bHLH gene cluster regulating terpenoid indole alkaloid biosynthesis in Catharanthus roseus. PLANT DIRECT 2021; 5:e00305. [PMID: 33532692 PMCID: PMC7833464 DOI: 10.1002/pld3.305] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/30/2020] [Accepted: 01/01/2021] [Indexed: 05/02/2023]
Abstract
Basic helix-loop-helix (bHLH) transcription factors (TFs) are key regulators of plant specialized metabolites, including terpenoid indole alkaloids (TIAs) in Catharanthus roseus. Two previously characterized subgroup-IVa bHLH TFs, BIS1 (bHLH Iridoid Synthesis 1) and BIS2 regulate iridoid biosynthesis in the TIA pathway. We reanalyzed the recently updated C. roseus genome sequence and discovered that BIS1 and BIS2 are clustered on the same genomic scaffold with a previously uncharacterized bHLH gene, designated as BIS3. Only a few bHLH gene clusters have been studied to date. Comparative analysis of 49 genome sequences from different plant lineages revealed the presence of analogous bHLH clusters in core angiosperms, including the medicinal plants Calotropis gigantea (giant milkweed) and Gelsemium sempervirens (yellow jessamine), but not in the analyzed basal angiosperm and lower plants. Similar to the iridoid pathway genes, BIS3 is highly expressed in roots and induced by methyl jasmonate. BIS3 activates the promoters of iridoid branch genes, geraniol synthase (GES), geraniol 10-hydroxylase (G10H), 8-hydroxygeraniol oxidoreductase (8HGO), iridoid synthase (IS), 7-deoxyloganetic acid glucosyl transferase (7-DLGT), and 7-deoxyloganic acid hydroxylase (7DLH), but not iridoid oxidase (IO). Transactivation of the promoters was abolished when BIS3 is converted to a dominant repressor by fusing with the ERF-associated amphiphilic repression (EAR) sequence. In addition, BIS3 acts synergistically with BIS1 and BIS2 to activate the G10H promoter in tobacco cells. Mutation of the known bHLH TF binding motif, G-box (CACGTG) in the G10H promoter significantly reduced but did not abolish the transactivation by BIS3. Promoter deletion analysis of G10H suggests that the sequences adjacent to the G-box are also involved in the regulation by BIS3. Overexpression of BIS3 in C. roseus flower petals significantly upregulated the expression of iridoid biosynthetic genes and increased loganic acid accumulation. BIS2 expression was significantly induced by BIS3 although BIS3 did not directly activate the BIS2 promoter. Our results advance our understanding of the regulation of plant specialized metabolites by bHLH TF clusters.
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Affiliation(s)
- Sanjay Kumar Singh
- Kentucky Tobacco Research & Development CenterUniversity of KentuckyLexingtonKYUSA
| | - Barunava Patra
- Kentucky Tobacco Research & Development CenterUniversity of KentuckyLexingtonKYUSA
| | - Priyanka Paul
- Department of Plant and Soil SciencesUniversity of KentuckyLexingtonKYUSA
| | - Yongliang Liu
- Kentucky Tobacco Research & Development CenterUniversity of KentuckyLexingtonKYUSA
- South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Sitakanta Pattanaik
- Kentucky Tobacco Research & Development CenterUniversity of KentuckyLexingtonKYUSA
| | - Ling Yuan
- Kentucky Tobacco Research & Development CenterUniversity of KentuckyLexingtonKYUSA
- Department of Plant and Soil SciencesUniversity of KentuckyLexingtonKYUSA
- South China Botanical GardenChinese Academy of SciencesGuangzhouChina
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Cheng QQ, Ouyang Y, Tang ZY, Lao CC, Zhang YY, Cheng CS, Zhou H. Review on the Development and Applications of Medicinal Plant Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:791219. [PMID: 35003182 PMCID: PMC8732986 DOI: 10.3389/fpls.2021.791219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 05/04/2023]
Abstract
With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.
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Affiliation(s)
- Qi-Qing Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yue Ouyang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Zi-Yu Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chi-Chou Lao
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yan-Yu Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chun-Song Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Hua Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, The Ministry of Education of the People’s Republic of China, Macau University of Science and Technology, Taipa, Macao SAR, China
- *Correspondence: Hua Zhou,
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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] [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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Romanowski S, Eustáquio AS. Synthetic biology for natural product drug production and engineering. Curr Opin Chem Biol 2020; 58:137-145. [DOI: 10.1016/j.cbpa.2020.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 12/23/2022]
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Beyond the semi-synthetic artemisinin: metabolic engineering of plant-derived anti-cancer drugs. Curr Opin Biotechnol 2020; 65:17-24. [DOI: 10.1016/j.copbio.2019.11.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/12/2019] [Accepted: 11/14/2019] [Indexed: 01/22/2023]
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Dugé de Bernonville T, Maury S, Delaunay A, Daviaud C, Chaparro C, Tost J, O’Connor SE, Courdavault V. Developmental Methylome of the Medicinal Plant Catharanthus roseus Unravels the Tissue-Specific Control of the Monoterpene Indole Alkaloid Pathway by DNA Methylation. Int J Mol Sci 2020; 21:E6028. [PMID: 32825765 PMCID: PMC7503379 DOI: 10.3390/ijms21176028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/06/2020] [Accepted: 08/18/2020] [Indexed: 02/07/2023] Open
Abstract
Catharanthus roseus produces a wide spectrum of monoterpene indole alkaloids (MIAs). MIA biosynthesis requires a tightly coordinated pathway involving more than 30 enzymatic steps that are spatio-temporally and environmentally regulated so that some MIAs specifically accumulate in restricted plant parts. The first regulatory layer involves a complex network of transcription factors from the basic Helix Loop Helix (bHLH) or AP2 families. In the present manuscript, we investigated whether an additional epigenetic layer could control the organ-, developmental- and environmental-specificity of MIA accumulation. We used Whole-Genome Bisulfite Sequencing (WGBS) together with RNA-seq to identify differentially methylated and expressed genes among nine samples reflecting different plant organs and experimental conditions. Tissue specific gene expression was associated with specific methylation signatures depending on cytosine contexts and gene parts. Some genes encoding key enzymatic steps from the MIA pathway were found to be simultaneously differentially expressed and methylated in agreement with the corresponding MIA accumulation. In addition, we found that transcription factors were strikingly concerned by DNA methylation variations. Altogether, our integrative analysis supports an epigenetic regulation of specialized metabolisms in plants and more likely targeting transcription factors which in turn may control the expression of enzyme-encoding genes.
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Affiliation(s)
- Thomas Dugé de Bernonville
- Faculté des Sciences et Techniques, Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, F-37200 Tours, France;
| | - Stéphane Maury
- INRA, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, F-45067 Orléans, France;
| | - Alain Delaunay
- INRA, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, F-45067 Orléans, France;
| | - Christian Daviaud
- Laboratoire Epigénétique et Environnement, LEE, Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, F-92265 Evry, France; (C.D.); (J.T.)
| | - Cristian Chaparro
- CNRS, IFREMER, UMR5244 Interactions Hôtes-Pathogènes-Environnments, Université de Montpellier, Université de Perpignan Via Domitia, F-66860 Perpignan, France;
| | - Jörg Tost
- Laboratoire Epigénétique et Environnement, LEE, Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, F-92265 Evry, France; (C.D.); (J.T.)
| | - Sarah Ellen O’Connor
- Max Planck Institute for Chemical Ecology, Department of Natural Product Biosynthesis, 07745 Jena, Germany;
| | - Vincent Courdavault
- Faculté des Sciences et Techniques, Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, F-37200 Tours, France;
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Lichman BR, Godden GT, Buell CR. Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:74-83. [PMID: 32344371 DOI: 10.1016/j.pbi.2020.03.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 02/19/2020] [Accepted: 03/04/2020] [Indexed: 05/28/2023]
Abstract
Plants are reservoirs of extreme chemical diversity, yet biosynthetic pathways remain underexplored in the majority of taxa. Access to improved, inexpensive genomic and computational technologies has recently enhanced our understanding of plant specialized metabolism at the biochemical and evolutionary levels including the elucidation of pathways leading to key metabolites. Furthermore, these approaches have provided insights into the mechanisms of chemical evolution, including neofunctionalization and subfunctionalization, structural variation, and modulation of gene expression. The broader utilization of genomic tools across the plant tree of life, and an expansion of genomic resources from multiple accessions within species or populations, will improve our overall understanding of chemodiversity. These data and knowledge will also lead to greater insight into the selective pressures contributing to and maintaining this diversity, which in turn will enable the development of more accurate predictive models of specialized metabolism in plants.
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Affiliation(s)
- Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Grant T Godden
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Carol Robin Buell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI 48824, USA.
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Jacobowitz JR, Weng JK. Exploring Uncharted Territories of Plant Specialized Metabolism in the Postgenomic Era. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:631-658. [PMID: 32176525 DOI: 10.1146/annurev-arplant-081519-035634] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
For millennia, humans have used plants for food, raw materials, and medicines, but only within the past two centuries have we begun to connect particular plant metabolites with specific properties and utilities. Since the utility of classical molecular genetics beyond model species is limited, the vast specialized metabolic systems present in the Earth's flora remain largely unstudied. With an explosion in genomics resources and a rapidly expanding toolbox over the past decade, exploration of plant specialized metabolism in nonmodel species is becoming more feasible than ever before. We review the state-of-the-art tools that have enabled this rapid progress. We present recent examples of de novo biosynthetic pathway discovery that employ various innovative approaches. We also draw attention to the higher-order organization of plant specialized metabolism at subcellular, cellular, tissue, interorgan, and interspecies levels, which will have important implications for the future design of comprehensive metabolic engineering strategies.
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Affiliation(s)
- Joseph R Jacobowitz
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Singh SK, Patra B, Paul P, Liu Y, Pattanaik S, Yuan L. Revisiting the ORCA gene cluster that regulates terpenoid indole alkaloid biosynthesis in Catharanthus roseus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 293:110408. [PMID: 32081258 DOI: 10.1016/j.plantsci.2020.110408] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/03/2020] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
Transcription factor (TF) gene clusters in plants, such as tomato, potato, petunia, tobacco, and almond, have been characterized for their roles in the biosynthesis of diverse array of specialized metabolites. In Catharanthus roseus, three AP2/ERF TFs, ORCA3, ORCA4, and ORCA5, have been shown to be present on the same genomic scaffold, forming a cluster that regulates the biosynthesis of pharmaceutically important terpenoid indole alkaloids (TIAs). Our analysis of the recently updated C. roseus genome sequence revealed that the ORCA cluster comprises two additional AP2/ERFs, the previously characterized ORCA2 and a newly identified member designated as ORCA6. Transcriptomic analysis revealed that the ORCAs are highly expressed in stems, followed by leaves, roots and flowers. Expression of ORCAs was differentially induced in response to methyl-jasmonate and ethylene treatment. In addition, ORCA6 activated the strictosidine synthase (STR) promoter in tobacco cells. Activation of the STR promoter was significantly higher when ORCA2 or ORCA6 was coexpressed with the mitogen-activated protein kinase kinase, CrMPKK1. Furthermore, transient overexpression of ORCA6 in C. roseus flower petals activated TIA pathway gene expression and TIA accumulation. The results described here advance our understanding of regulation of TIA pathway by the ORCA gene cluster and the evolution for plant ERF gene clusters.
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Affiliation(s)
- Sanjay Kumar Singh
- Department of Plant and Soil Sciences and the Kentucky Tobacco Research and Development Center, University of Kentucky, 1401 University Drive, Lexington, KY 40546 USA
| | - Barunava Patra
- Department of Plant and Soil Sciences and the Kentucky Tobacco Research and Development Center, University of Kentucky, 1401 University Drive, Lexington, KY 40546 USA
| | - Priyanka Paul
- Department of Plant and Soil Sciences and the Kentucky Tobacco Research and Development Center, University of Kentucky, 1401 University Drive, Lexington, KY 40546 USA
| | - Yongliang Liu
- Department of Plant and Soil Sciences and the Kentucky Tobacco Research and Development Center, University of Kentucky, 1401 University Drive, Lexington, KY 40546 USA; South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Sitakanta Pattanaik
- Department of Plant and Soil Sciences and the Kentucky Tobacco Research and Development Center, University of Kentucky, 1401 University Drive, Lexington, KY 40546 USA.
| | - Ling Yuan
- Department of Plant and Soil Sciences and the Kentucky Tobacco Research and Development Center, University of Kentucky, 1401 University Drive, Lexington, KY 40546 USA; South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
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Liu Y, Tang Q, Cheng P, Zhu M, Zhang H, Liu J, Zuo M, Huang C, Wu C, Sun Z, Liu Z. Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans. Acta Pharm Sin B 2020; 10:374-382. [PMID: 32082980 PMCID: PMC7016290 DOI: 10.1016/j.apsb.2019.08.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/27/2019] [Accepted: 07/26/2019] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Gelsemium elegans (G. elegans) (2n = 2x = 16) is genus of flowering plants belonging to the Gelsemicaeae family. METHOD Here, a high-quality genome assembly using the Oxford Nanopore Technologies (ONT) platform and high-throughput chromosome conformation capture techniques (Hi-C) were used. RESULTS A total of 56.11 Gb of raw GridION X5 platform ONT reads (6.23 Gb per cell) were generated. After filtering, 53.45 Gb of clean reads were obtained, giving 160 × coverage depth. The de novo genome assemblies 335.13 Mb, close to the 338 Mb estimated by k-mer analysis, was generated with contig N50 of 10.23 Mb. The vast majority (99.2%) of the G. elegans assembled sequence was anchored onto 8 pseudo-chromosomes. The genome completeness was then evaluated and 1338 of the 1440 conserved genes (92.9%) could be found in the assembly. Genome annotation revealed that 43.16% of the G. elegans genome is composed of repetitive elements and 23.9% is composed of long terminal repeat elements. We predicted 26,768 protein-coding genes, of which 84.56% were functionally annotated. CONCLUSION The genomic sequences of G. elegans could be a valuable source for comparative genomic analysis in the Gelsemicaeae family and will be useful for understanding the phylogenetic relationships of the indole alkaloid metabolism.
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Mortensen S, Weaver JD, Sathitloetsakun S, Cole LF, Rizvi NF, Cram EJ, Lee‐Parsons CWT. The regulation of ZCT1, a transcriptional repressor of monoterpenoid indole alkaloid biosynthetic genes in Catharanthus roseus. PLANT DIRECT 2019; 3:e00193. [PMID: 31909362 PMCID: PMC6937483 DOI: 10.1002/pld3.193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/13/2019] [Accepted: 12/02/2019] [Indexed: 05/19/2023]
Abstract
Cys2/His2-type (C2H2) zinc finger proteins, such as ZCT1, are an important class of transcription factors involved in growth, development, and stress responses in plants. In the medicinal plant Catharanthus roseus, the zinc finger Catharanthus transcription factor (ZCT) family represses monoterpenoid indole alkaloid (MIA) biosynthetic gene expression. Here, we report the analysis of the ZCT1 promoter, which contains several hormone-responsive elements. ZCT1 is responsive to not only jasmonate, as was previously known, but is also induced by the synthetic auxin, 1-naphthalene acetic acid (1-NAA). Through promoter deletion analysis, we show that an activation sequence-1-like (as-1-like)-motif and other motifs contribute significantly to ZCT1 expression in seedlings. We also show that the activator ORCA3 does not transactivate the expression of ZCT1 in seedlings, but ZCT1 represses its own promoter, suggesting a feedback mechanism by which the expression of ZCT1 can be limited.
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Affiliation(s)
| | | | - Suphinya Sathitloetsakun
- Department of BiologyNortheastern UniversityBostonMAUSA
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMAUSA
| | - Lauren F. Cole
- Department of BioengineeringNortheastern UniversityBostonMAUSA
| | - Noreen F. Rizvi
- Department of Chemical EngineeringNortheastern UniversityBostonMAUSA
| | - Erin J. Cram
- Department of BiologyNortheastern UniversityBostonMAUSA
| | - Carolyn W. T. Lee‐Parsons
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMAUSA
- Department of Chemical EngineeringNortheastern UniversityBostonMAUSA
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Zhong Z, Liu S, Zhu W, Ou Y, Yamaguchi H, Hitachi K, Tsuchida K, Tian J, Komatsu S. Phosphoproteomics Reveals the Biosynthesis of Secondary Metabolites in Catharanthus roseus under Ultraviolet-B Radiation. J Proteome Res 2019; 18:3328-3341. [PMID: 31356092 DOI: 10.1021/acs.jproteome.9b00267] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ultraviolet (UV)-B radiation acts as an elicitor to enhance the production of secondary metabolites in medicinal plants. To investigate the mechanisms, which lead to secondary metabolites in Catharanthus roseus under UVB radiation, a phosphoproteomic technique was used. ATP content increased in the leaves of C. roseus under UVB radiation. Phosphoproteins related to calcium such as calmodulin, calcium-dependent kinase, and heat shock proteins increased. Phosphoproteins related to protein synthesis/modification/degradation and signaling intensively changed. Metabolomic analysis indicated that the metabolites classified with pentoses, aromatic amino acids, and phenylpropanoids accumulated under UVB radiation. Phosphoproteomic and immunoblot analyses indicated that proteins related to glycolysis and the reactive-oxygen species scavenging system were changed under UVB radiation. These results suggest that UVB radiation activates the calcium-related pathway and reactive-oxygen species scavenging system in C. roseus. These changes lead to the upregulation of proteins, which are responsible for the redox reactions in secondary metabolism and are important for the accumulation of secondary metabolites in C. roseus under UVB radiation.
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Affiliation(s)
- Zhuoheng Zhong
- College of Biomedical Engineering & Instrument Science , Zhejiang University , Hangzhou 310027 , P. R. China.,Faculty of Life and Environmental and Information Sciences , Fukui University of Technology , Fukui 910-8505 , Japan
| | - Shengzhi Liu
- College of Biomedical Engineering & Instrument Science , Zhejiang University , Hangzhou 310027 , P. R. China
| | - Wei Zhu
- College of Biomedical Engineering & Instrument Science , Zhejiang University , Hangzhou 310027 , P. R. China
| | - Yuting Ou
- College of Biomedical Engineering & Instrument Science , Zhejiang University , Hangzhou 310027 , P. R. China
| | - Hisateru Yamaguchi
- Institute for Comprehensive Medical Science , Fujita Health University , Toyoake 470-1192 , Japan
| | - Keisuke Hitachi
- Institute for Comprehensive Medical Science , Fujita Health University , Toyoake 470-1192 , Japan
| | - Kunihiro Tsuchida
- Institute for Comprehensive Medical Science , Fujita Health University , Toyoake 470-1192 , Japan
| | - Jingkui Tian
- College of Biomedical Engineering & Instrument Science , Zhejiang University , Hangzhou 310027 , P. R. China
| | - Setsuko Komatsu
- Faculty of Life and Environmental and Information Sciences , Fukui University of Technology , Fukui 910-8505 , Japan
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