1
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Eljounaidi K, Radzikowska BA, Whitehead CB, Taylor DJ, Conde S, Davis W, Dowle AA, Langer S, James S, Unsworth WP, Ezer D, Larson TR, Lichman BR. Variation of terpene alkaloids in Daphniphyllum macropodum across plants and tissues. THE NEW PHYTOLOGIST 2024; 243:299-313. [PMID: 38757546 DOI: 10.1111/nph.19814] [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: 02/08/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024]
Abstract
Daphniphyllum macropodum produces alkaloids that are structurally complex with polycyclic, stereochemically rich carbon skeletons. Understanding how these compounds are formed by the plant may enable exploration of their biological function and bioactivities. We employed multiple metabolomics techniques, including a workflow to annotate compounds in the absence of standards, to compare alkaloid content across plants and tissues. Different alkaloid structural types were found to have distinct distributions between genotypes, between tissues and within tissues. Alkaloid structural types also showed different isotope labelling enrichments that matched their biosynthetic relationships. The work suggests that mevalonate derived 30-carbon alkaloids are formed in the phloem region before their conversion to 22-carbon alkaloids which accumulate in the epidermis. This sets the stage for further investigation into the biosynthetic pathway.
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Affiliation(s)
- Kaouthar Eljounaidi
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Barbara A Radzikowska
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Caragh B Whitehead
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Danielle J Taylor
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Susana Conde
- Department of Biology, University of York, York, YO10 5DD, UK
| | - William Davis
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Adam A Dowle
- Biosciences Technology Facility, Department of Biology, University of York, York, YO10 5DD, UK
| | - Swen Langer
- Biosciences Technology Facility, Department of Biology, University of York, York, YO10 5DD, UK
| | - Sally James
- Biosciences Technology Facility, Department of Biology, University of York, York, YO10 5DD, UK
| | | | - Daphne Ezer
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Tony R Larson
- Biosciences Technology Facility, 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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2
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Swamidatta SH, Lichman BR. Beyond co-expression: pathway discovery for plant pharmaceuticals. Curr Opin Biotechnol 2024; 88:103147. [PMID: 38833915 DOI: 10.1016/j.copbio.2024.103147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024]
Abstract
Plant natural products have been an important source of medicinal molecules since ancient times. To gain access to the whole diversity of these molecules for pharmaceutical applications, it is important to understand their biosynthetic origins. Whilst co-expression is a reliable tool for identifying gene candidates, a variety of complementary methods can aid in screening or refining candidate selection. Here, we review recently employed plant biosynthetic pathway discovery approaches, and highlight future directions in the field.
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Affiliation(s)
- Sandesh H Swamidatta
- 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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3
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Lam HYI, Ong XE, Mutwil M. Large language models in plant biology. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00118-3. [PMID: 38797656 DOI: 10.1016/j.tplants.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024]
Abstract
Large language models (LLMs), such as ChatGPT, have taken the world by storm. However, LLMs are not limited to human language and can be used to analyze sequential data, such as DNA, protein, and gene expression. The resulting foundation models can be repurposed to identify the complex patterns within the data, resulting in powerful, multipurpose prediction tools able to predict the state of cellular systems. This review outlines the different types of LLMs and showcases their recent uses in biology. Since LLMs have not yet been embraced by the plant community, we also cover how these models can be deployed for the plant kingdom.
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Affiliation(s)
- Hilbert Yuen In Lam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Xing Er Ong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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4
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Barreda L, Brosse C, Boutet S, Perreau F, Rajjou L, Lepiniec L, Corso M. Specialized metabolite modifications in Brassicaceae seeds and plants: diversity, functions and related enzymes. Nat Prod Rep 2024; 41:834-859. [PMID: 38323463 DOI: 10.1039/d3np00043e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Covering: up to 2023Specialized metabolite (SM) modifications and/or decorations, corresponding to the addition or removal of functional groups (e.g. hydroxyl, methyl, glycosyl or acyl group) to SM structures, contribute to the huge diversity of structures, activities and functions of seed and plant SMs. This review summarizes available knowledge (up to 2023) on SM modifications in Brassicaceae and their contribution to SM plasticity. We give a comprehensive overview on enzymes involved in the addition or removal of these functional groups. Brassicaceae, including model (Arabidopsis thaliana) and crop (Brassica napus, Camelina sativa) plant species, present a large diversity of plant and seed SMs, which makes them valuable models to study SM modifications. In this review, particular attention is given to the environmental plasticity of SM and relative modification and/or decoration enzymes. Furthermore, a spotlight is given to SMs and related modification enzymes in seeds of Brassicaceae species. Seeds constitute a large reservoir of beneficial SMs and are one of the most important dietary sources, providing more than half of the world's intake of dietary proteins, oil and starch. The seed tissue- and stage-specific expressions of A. thaliana genes involved in SM modification are presented and discussed in the context of available literature. Given the major role in plant phytochemistry, biology and ecology, SM modifications constitute a subject of study contributing to the research and development in agroecology, pharmaceutical, cosmetics and food industrial sectors.
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Affiliation(s)
- Léa Barreda
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France.
| | - Céline Brosse
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France.
| | - Stéphanie Boutet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France.
| | - François Perreau
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France.
| | - Loïc Rajjou
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France.
| | - Loïc Lepiniec
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France.
| | - Massimiliano Corso
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France.
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5
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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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6
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Durand M, Besseau S, Papon N, Courdavault V. Unlocking plant bioactive pathways: omics data harnessing and machine learning assisting. Curr Opin Biotechnol 2024; 87:103135. [PMID: 38728826 DOI: 10.1016/j.copbio.2024.103135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/02/2024] [Accepted: 04/12/2024] [Indexed: 05/12/2024]
Abstract
Plant bioactives hold immense potential in the medicine and food industry. The recent advancements in omics applied in deciphering specialized metabolic pathways underscore the importance of high-quality genome releases and the wealth of data in metabolomics and transcriptomics. While harnessing data, whether integrated or standalone, has proven successful in unveiling plant natural product (PNP) biosynthetic pathways, the democratization of machine learning in biology opens exciting new opportunities for enhancing the exploration of these pathways. This review highlights the recent breakthroughs in disrupting plant-specialized biosynthetic pathways through the utilization of omics data harnessing and machine learning techniques.
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Affiliation(s)
- Mickael Durand
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France.
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7
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Li R, Du K, Zhang C, Shen X, Yun L, Wang S, Li Z, Sun Z, Wei J, Li Y, Guo B, Sun C. Single-cell transcriptome profiling reveals the spatiotemporal distribution of triterpenoid saponin biosynthesis and transposable element activity in Gynostemma pentaphyllum shoot apexes and leaves. FRONTIERS IN PLANT SCIENCE 2024; 15:1394587. [PMID: 38779067 PMCID: PMC11109411 DOI: 10.3389/fpls.2024.1394587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Gynostemma pentaphyllum (Thunb.) Makino is an important producer of dammarene-type triterpenoid saponins. These saponins (gypenosides) exhibit diverse pharmacological benefits such as anticancer, antidiabetic, and immunomodulatory effects, and have major potential in the pharmaceutical and health care industries. Here, we employed single-cell RNA sequencing (scRNA-seq) to profile the transcriptomes of more than 50,000 cells derived from G. pentaphyllum shoot apexes and leaves. Following cell clustering and annotation, we identified five major cell types in shoot apexes and four in leaves. Each cell type displayed substantial transcriptomic heterogeneity both within and between tissues. Examining gene expression patterns across various cell types revealed that gypenoside biosynthesis predominantly occurred in mesophyll cells, with heightened activity observed in shoot apexes compared to leaves. Furthermore, we explored the impact of transposable elements (TEs) on G. pentaphyllum transcriptomic landscapes. Our findings the highlighted the unbalanced expression of certain TE families across different cell types in shoot apexes and leaves, marking the first investigation of TE expression at the single-cell level in plants. Additionally, we observed dynamic expression of genes involved in gypenoside biosynthesis and specific TE families during epidermal and vascular cell development. The involvement of TE expression in regulating cell differentiation and gypenoside biosynthesis warrant further exploration. Overall, this study not only provides new insights into the spatiotemporal organization of gypenoside biosynthesis and TE activity in G. pentaphyllum shoot apexes and leaves but also offers valuable cellular and genetic resources for a deeper understanding of developmental and physiological processes at single-cell resolution in this species.
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Affiliation(s)
- Rucan Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ke Du
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chuyi Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaofeng Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lingling Yun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shu Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ziqin Li
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Zhiying Sun
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chao Sun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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8
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Chen C, Zhang X, Yue M. Spatial multi-omics in medicinal plants: from biosynthesis pathways to industrial applications. TRENDS IN PLANT SCIENCE 2024; 29:510-513. [PMID: 38485645 DOI: 10.1016/j.tplants.2024.02.008] [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: 01/05/2024] [Revised: 02/18/2024] [Accepted: 02/21/2024] [Indexed: 05/04/2024]
Abstract
With the rapid development of molecular sequencing and imaging technology, the multi-omics of medicinal plants enters the single-cell era. We discuss spatial multi-omics applied in medicinal plants, evaluate the special products' biosynthesis pathways, and highlight the applications, perspectives, and challenges of biomanufacturing natural products (NPs).
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Affiliation(s)
- Chen Chen
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, No. 17 Cuihua South Road, 710061 Xi'an, Shaanxi Province, China
| | - Xiao Zhang
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, No. 17 Cuihua South Road, 710061 Xi'an, Shaanxi Province, China
| | - Ming Yue
- College of Life Sciences, Northwest University, No. 229 Taibai North Road, 710069 Xi'an, Shaanxi Province, China.
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9
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Uzaki M, Mori T, Sato M, Wakazaki M, Takeda-Kamiya N, Yamamoto K, Murakami A, Guerrero DAS, Shichijo C, Ohnishi M, Ishizaki K, Fukaki H, O'Connor SE, Toyooka K, Mimura T, Hirai MY. Integration of cell differentiation and initiation of monoterpenoid indole alkaloid metabolism in seed germination of Catharanthus roseus. THE NEW PHYTOLOGIST 2024; 242:1156-1171. [PMID: 38513692 DOI: 10.1111/nph.19662] [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: 12/01/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
Abstract
In Catharanthus roseus, monoterpenoid indole alkaloids (MIAs) are produced through the cooperation of four cell types, with final products accumulating in specialized cells known as idioblasts and laticifers. To explore the relationship between cellular differentiation and cell type-specific MIA metabolism, we analyzed the expression of MIA biosynthesis in germinating seeds. Embryos from immature and mature seeds were observed via stereomicroscopy, fluorescence microscopy, and electron microscopy. Time-series MIA and iridoid quantification, along with transcriptome analysis, were conducted to determine the initiation of MIA biosynthesis. In addition, the localization of MIAs was examined using alkaloid staining and imaging mass spectrometry (IMS). Laticifers were present in embryos before seed maturation. MIA biosynthesis commenced 12 h after germination. MIAs accumulated in laticifers of embryos following seed germination, and MIA metabolism is induced after germination in a tissue-specific manner. These findings suggest that cellular morphological differentiation precedes metabolic differentiation. Considering the well-known toxicity and defense role of MIAs in matured plants, MIAs may be an important defense strategy already in the delicate developmental phase of seed germination, and biosynthesis and accumulation of MIAs may require the tissue and cellular differentiation.
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Affiliation(s)
- Mai Uzaki
- Graduate School of Bioagricultural Science, Nagoya University, Nagoya, Aichi, 464-8601, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Tetsuya Mori
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Mayumi Wakazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Noriko Takeda-Kamiya
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Kotaro Yamamoto
- School of Science, Yokohama City University, Yokohama, Kanagawa, 236-0027, Japan
| | - Akio Murakami
- Graduate School of Science, Kobe University, Kobe, Hyogo, 657-8501, Japan
| | - Delia Ayled Serna Guerrero
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, D-07745, Germany
| | - Chizuko Shichijo
- Graduate School of Science, Kobe University, Kobe, Hyogo, 657-8501, Japan
| | - Miwa Ohnishi
- Graduate School of Science, Kobe University, Kobe, Hyogo, 657-8501, Japan
- Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Kimitsune Ishizaki
- Graduate School of Science, Kobe University, Kobe, Hyogo, 657-8501, Japan
| | - Hidehiro Fukaki
- Graduate School of Science, Kobe University, Kobe, Hyogo, 657-8501, Japan
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, D-07745, Germany
| | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Tetsuro Mimura
- Graduate School of Science, Kobe University, Kobe, Hyogo, 657-8501, Japan
- College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan
- The Institute for Sustainable Agro-ecosystem Services, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 188-0002, Japan
- Faculty of Bioenvironmental Sciences, Kyoto University of Advanced Science, Kyoto, 621-8555, Japan
| | - Masami Yokota Hirai
- Graduate School of Bioagricultural Science, Nagoya University, Nagoya, Aichi, 464-8601, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
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10
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Tansley C, Patron NJ, Guiziou S. Engineering Plant Cell Fates and Functions for Agriculture and Industry. ACS Synth Biol 2024; 13:998-1005. [PMID: 38573786 PMCID: PMC11036505 DOI: 10.1021/acssynbio.4c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/06/2024]
Abstract
Many plant species are grown to enable access to specific organs or tissues, such as seeds, fruits, or stems. In some cases, a value is associated with a molecule that accumulates in a single type of cell. Domestication and subsequent breeding have often increased the yields of these target products by increasing the size, number, and quality of harvested organs and tissues but also via changes to overall plant growth architecture to suit large-scale cultivation. Many of the mutations that underlie these changes have been identified in key regulators of cellular identity and function. As key determinants of yield, these regulators are key targets for synthetic biology approaches to engineer new forms and functions. However, our understanding of many plant developmental programs and cell-type specific functions is still incomplete. In this Perspective, we discuss how advances in cellular genomics together with synthetic biology tools such as biosensors and DNA-recording devices are advancing our understanding of cell-specific programs and cell fates. We then discuss advances and emerging opportunities for cell-type-specific engineering to optimize plant morphology, responses to the environment, and the production of valuable compounds.
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Affiliation(s)
- Connor Tansley
- Engineering
Biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ United Kingdom
- Department
of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA United
Kingdom
| | - Nicola J. Patron
- Engineering
Biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ United Kingdom
- Department
of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA United
Kingdom
| | - Sarah Guiziou
- Engineering
Biology, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ United Kingdom
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11
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Lezin E, Carqueijeiro I, Cuello C, Durand M, Jansen HJ, Vergès V, Birer Williams C, Oudin A, Dugé de Bernonville T, Petrignet J, Celton N, St-Pierre B, Papon N, Sun C, Dirks RP, O'Connor SE, Jensen MK, Besseau S, Courdavault V. A chromosome-scale genome assembly of Rauvolfia tetraphylla facilitates identification of the complete ajmaline biosynthetic pathway. PLANT COMMUNICATIONS 2024; 5:100784. [PMID: 38155576 PMCID: PMC11009098 DOI: 10.1016/j.xplc.2023.100784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023]
Affiliation(s)
- Enzo Lezin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - 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
| | - Mickael Durand
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Hans J Jansen
- Future Genomics Technologies, 2333 BE Leiden, the Netherlands
| | - 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
| | | | - Julien Petrignet
- Laboratoire Synthèse et Isolement de Molécules BioActives (SIMBA, EA 7502), Université de Tours, 37200 Tours, France
| | - Noémie Celton
- Laboratoire de Cytogénetique Constitutionnelle, CHRU de Tours - Hôpital Bretonneau, 37044 Tours, France
| | - Benoit St-Pierre
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Nicolas Papon
- University Angers, University Brest, IRF, SFR ICAT, 49000 Angers, France; Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 2800, China
| | - Chao Sun
- University Angers, University Brest, IRF, SFR ICAT, 49000 Angers, France; Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 2800, China
| | - 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, 07745 Jena, Germany
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 100193 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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12
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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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13
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Holtz M, Acevedo-Rocha CG, Jensen MK. Combining enzyme and metabolic engineering for microbial supply of therapeutic phytochemicals. Curr Opin Biotechnol 2024; 87:103110. [PMID: 38503222 DOI: 10.1016/j.copbio.2024.103110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/21/2024]
Abstract
The history of pharmacology is deeply intertwined with plant-derived compounds, which continue to be crucial in drug development. However, their complex structures and limited availability in plants challenge drug discovery, optimization, development, and industrial production via chemical synthesis or natural extraction. This review delves into the integration of metabolic and enzyme engineering to leverage micro-organisms as platforms for the sustainable and reliable production of therapeutic phytochemicals. We argue that engineered microbes can serve a triple role in this paradigm: facilitating pathway discovery, acting as cell factories for scalable manufacturing, and functioning as platforms for chemical derivatization. Analyzing recent progress and outlining future directions, the review highlights microbial biotechnology's transformative potential in expanding plant-derived human therapeutics' discovery and supply chains.
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Affiliation(s)
- Maxence Holtz
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Carlos G Acevedo-Rocha
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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14
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Davis CC, Choisy P. Medicinal plants meet modern biodiversity science. Curr Biol 2024; 34:R158-R173. [PMID: 38412829 DOI: 10.1016/j.cub.2023.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Plants have been an essential source of human medicine for millennia. In this review, we argue that a holistic, interdisciplinary approach to the study of medicinal plants that combines methods and insights from three key disciplines - evolutionary ecology, molecular biology/biochemistry, and ethnopharmacology - is poised to facilitate new breakthroughs in science, including pharmacological discoveries and rapid advancements in human health and well-being. Such interdisciplinary research leverages data and methods spanning space, time, and species associated with medicinal plant species evolution, ecology, genomics, and metabolomic trait diversity, all of which build heavily on traditional Indigenous knowledge. Such an interdisciplinary approach contrasts sharply with most well-funded and successful medicinal plant research during the last half-century, which, despite notable advancements, has greatly oversimplified the dynamic relationships between plants and humans, kept hidden the larger human narratives about these relationships, and overlooked potentially important research and discoveries into life-saving medicines. We suggest that medicinal plants and people should be viewed as partners whose relationship involves a complicated and poorly explored set of (socio-)ecological interactions including not only domestication but also commensalisms and mutualisms. In short, medicinal plant species are not just chemical factories for extraction and exploitation. Rather, they may be symbiotic partners that have shaped modern societies, improved human health, and extended human lifespans.
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Affiliation(s)
- Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA.
| | - Patrick Choisy
- LVMH Research, 185 Avenue de Verdun, 45804 Saint Jean de Braye CEDEX, France
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15
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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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16
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Lin JL, Chen L, Wu WK, Guo XX, Yu CH, Xu M, Nie GB, Dun JL, Li Y, Xu B, Wang LJ, Chen XY, Gao W, Huang JQ. Single-cell RNA sequencing reveals a hierarchical transcriptional regulatory network of terpenoid biosynthesis in cotton secretory glandular cells. MOLECULAR PLANT 2023; 16:1990-2003. [PMID: 37849250 DOI: 10.1016/j.molp.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/24/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023]
Abstract
Plants can synthesize a wide range of terpenoids in response to various environmental cues. However, the specific regulatory mechanisms governing terpenoid biosynthesis at the cellular level remain largely elusive. In this study, we employed single-cell RNA sequencing to comprehensively characterize the transcriptome profile of cotton leaves and established a hierarchical transcriptional network regulating cell-specific terpenoid production. We observed substantial expression levels of genes associated with the biosynthesis of both volatile terpenes (such as β-caryophyllene and β-myrcene) and non-volatile gossypol-type terpenoids in secretory glandular cells. Moreover, two novel transcription factors, namely GoHSFA4a and GoNAC42, are identified to function downstream of the Gossypium PIGMENT GLAND FORMATION genes. Both transcription factors could directly regulate the expression of terpenoid biosynthetic genes in secretory glandular cells in response to developmental and environmental stimuli. For convenient retrieval of the single-cell RNA sequencing data generated in this study, we developed a user-friendly web server . Our findings not only offer valuable insights into the precise regulation of terpenoid biosynthesis genes in cotton leaves but also provide potential targets for cotton breeding endeavors.
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Affiliation(s)
- Jia-Ling Lin
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Longxian Chen
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wen-Kai Wu
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiao-Xiang Guo
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
| | - Cheng-Hui Yu
- Chongqing Key Laboratory of Micro-Nano Systems and Intelligent Transduction, Collaborative Innovation, National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Min Xu
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Gui-Bin Nie
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun-Ling Dun
- Analytical Applications Center, Shimadzu (China) Co., Ltd., Shanghai 200233, China
| | - Yan Li
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai 264117, Shandong, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Baofu Xu
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai 264117, Shandong, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ling-Jian Wang
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiao-Ya Chen
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Wei Gao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization (Henan University), Henan 475004, China.
| | - Jin-Quan Huang
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of CAS, Chinese Academy of Sciences, Shanghai 200032, China.
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17
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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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18
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Fang C, Hamilton JP, Vaillancourt B, Wang YW, Wood JC, Deans NC, Scroggs T, Carlton L, Mailloux K, Douches DS, Nadakuduti SS, Jiang J, Buell CR. Cold stress induces differential gene expression of retained homeologs in Camelina sativa cv Suneson. FRONTIERS IN PLANT SCIENCE 2023; 14:1271625. [PMID: 38034564 PMCID: PMC10687638 DOI: 10.3389/fpls.2023.1271625] [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: 08/02/2023] [Accepted: 10/26/2023] [Indexed: 12/02/2023]
Abstract
Camelina sativa (L.) Crantz, a member of the Brassicaceae, has potential as a biofuel feedstock which is attributable to the production of fatty acids in its seeds, its fast growth cycle, and low input requirements. While a genome assembly is available for camelina, it was generated from short sequence reads and is thus highly fragmented in nature. Using long read sequences, we generated a chromosome-scale, highly contiguous genome assembly (644,491,969 bp) for the spring biotype cultivar 'Suneson' with an N50 contig length of 12,031,512 bp and a scaffold N50 length of 32,184,682 bp. Annotation of protein-coding genes revealed 91,877 genes that encode 133,355 gene models. We identified a total of 4,467 genes that were significantly up-regulated under cold stress which were enriched in gene ontology terms associated with "response to cold" and "response to abiotic stress". Coexpression analyses revealed multiple coexpression modules that were enriched in genes differentially expressed following cold stress that had putative functions involved in stress adaptation, specifically within the plastid. With access to a highly contiguous genome assembly, comparative analyses with Arabidopsis thaliana revealed 23,625 A. thaliana genes syntenic with 45,453 Suneson genes. Of these, 24,960 Suneson genes were syntenic to 8,320 A. thaliana genes reflecting a 3 camelina homeolog to 1 Arabidopsis gene relationship and retention of all three homeologs. Some of the retained triplicated homeologs showed conserved gene expression patterns under control and cold-stressed conditions whereas other triplicated homeologs displayed diverged expression patterns revealing sub- and neo-functionalization of the homeologs at the transcription level. Access to the chromosome-scale assembly of Suneson will enable both basic and applied research efforts in the improvement of camelina as a sustainable biofuel feedstock.
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Affiliation(s)
- Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - John P. Hamilton
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Department of Crop & Soil Sciences, University of Georgia, Athens, GA, United States
| | - Brieanne Vaillancourt
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Yi-Wen Wang
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Joshua C. Wood
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Natalie C. Deans
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Taylor Scroggs
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Lemor Carlton
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Kathrine Mailloux
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - David S. Douches
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Satya Swathi Nadakuduti
- Department of Environmental Horticulture, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - C. Robin Buell
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Department of Crop & Soil Sciences, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA, United States
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19
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Wu M, Northen TR, Ding Y. Stressing the importance of plant specialized metabolites: omics-based approaches for discovering specialized metabolism in plant stress responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1272363. [PMID: 38023861 PMCID: PMC10663375 DOI: 10.3389/fpls.2023.1272363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
Plants produce a diverse range of specialized metabolites that play pivotal roles in mediating environmental interactions and stress adaptation. These unique chemical compounds also hold significant agricultural, medicinal, and industrial values. Despite the expanding knowledge of their functions in plant stress interactions, understanding the intricate biosynthetic pathways of these natural products remains challenging due to gene and pathway redundancy, multifunctionality of proteins, and the activity of enzymes with broad substrate specificity. In the past decade, substantial progress in genomics, transcriptomics, metabolomics, and proteomics has made the exploration of plant specialized metabolism more feasible than ever before. Notably, recent advances in integrative multi-omics and computational approaches, along with other technologies, are accelerating the discovery of plant specialized metabolism. In this review, we present a summary of the recent progress in the discovery of plant stress-related specialized metabolites. Emphasis is placed on the application of advanced omics-based approaches and other techniques in studying plant stress-related specialized metabolism. Additionally, we discuss the high-throughput methods for gene functional characterization. These advances hold great promise for harnessing the potential of specialized metabolites to enhance plant stress resilience in the future.
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Affiliation(s)
- Mengxi Wu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Trent R. Northen
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yezhang Ding
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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20
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Burlat V, Papon N, Courdavault V. Medicinal plants enter the single-cell multi-omics era. TRENDS IN PLANT SCIENCE 2023; 28:1205-1207. [PMID: 37625948 DOI: 10.1016/j.tplants.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023]
Abstract
Elucidating biosynthetic pathways of plant specialized metabolites is a tricky but essential task for the biotechnological production of plant drugs. In a new report, Li et al. used a single-cell multi-omics approach to provide an integrative view of the architecture and regulation of anticancer alkaloid routes in Madagascar periwinkle.
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Affiliation(s)
- Vincent Burlat
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier Toulouse 3, Institut National Polytechnique de Toulouse, 31320 Auzeville-Tolosane, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Université de Tours, Tours, France.
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Liu Y, Singh SK, Pattanaik S, Wang H, Yuan L. Light regulation of the biosynthesis of phenolics, terpenoids, and alkaloids in plants. Commun Biol 2023; 6:1055. [PMID: 37853112 PMCID: PMC10584869 DOI: 10.1038/s42003-023-05435-4] [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: 06/23/2023] [Accepted: 10/09/2023] [Indexed: 10/20/2023] Open
Abstract
Biosynthesis of specialized metabolites (SM), including phenolics, terpenoids, and alkaloids, is stimulated by many environmental factors including light. In recent years, significant progress has been made in understanding the regulatory mechanisms involved in light-stimulated SM biosynthesis at the transcriptional, posttranscriptional, and posttranslational levels of regulation. While several excellent recent reviews have primarily focused on the impacts of general environmental factors, including light, on biosynthesis of an individual class of SM, here we highlight the regulation of three major SM biosynthesis pathways by light-responsive gene expression, microRNA regulation, and posttranslational modification of regulatory proteins. In addition, we present our future perspectives on this topic.
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Affiliation(s)
- Yongliang Liu
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Sanjay K Singh
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Sitakanta Pattanaik
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
| | - Hongxia Wang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences Chenshan Botanical Garden, 3888 Chenhua Road, 201602, Songjiang, Shanghai, China.
| | - Ling Yuan
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
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Zhang J, Ahmad M, Gao H. Application of single-cell multi-omics approaches in horticulture research. MOLECULAR HORTICULTURE 2023; 3:18. [PMID: 37789394 PMCID: PMC10521458 DOI: 10.1186/s43897-023-00067-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023]
Abstract
Cell heterogeneity shapes the morphology and function of various tissues and organs in multicellular organisms. Elucidation of the differences among cells and the mechanism of intercellular regulation is essential for an in-depth understanding of the developmental process. In recent years, the rapid development of high-throughput single-cell transcriptome sequencing technologies has influenced the study of plant developmental biology. Additionally, the accuracy and sensitivity of tools used to study the epigenome and metabolome have significantly increased, thus enabling multi-omics analysis at single-cell resolution. Here, we summarize the currently available single-cell multi-omics approaches and their recent applications in plant research, review the single-cell based studies in fruit, vegetable, and ornamental crops, and discuss the potential of such approaches in future horticulture research.
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Affiliation(s)
- Jun Zhang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mayra Ahmad
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongbo Gao
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Salim V, Jarecki SA, Vick M, Miller R. Advances in Metabolic Engineering of Plant Monoterpene Indole Alkaloids. BIOLOGY 2023; 12:1056. [PMID: 37626942 PMCID: PMC10452178 DOI: 10.3390/biology12081056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023]
Abstract
Monoterpene indole alkaloids (MIAs) encompass a diverse family of over 3000 plant natural products with a wide range of medical applications. Further utilizations of these compounds, however, are hampered due to low levels of abundance in their natural sources, causing difficult isolation and complex multi-steps in uneconomical chemical syntheses. Metabolic engineering of MIA biosynthesis in heterologous hosts is attractive, particularly for increasing the yield of natural products of interest and expanding their chemical diversity. Here, we review recent advances and strategies which have been adopted to engineer microbial and plant systems for the purpose of generating MIAs and discuss the current issues and future developments of manufacturing MIAs by synthetic biology approaches.
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Affiliation(s)
- Vonny Salim
- Department of Biological Sciences, Louisiana State University Shreveport, Shreveport, LA 71115, USA; (S.-A.J.); (M.V.)
| | - Sara-Alexis Jarecki
- Department of Biological Sciences, Louisiana State University Shreveport, Shreveport, LA 71115, USA; (S.-A.J.); (M.V.)
| | - Marshall Vick
- Department of Biological Sciences, Louisiana State University Shreveport, Shreveport, LA 71115, USA; (S.-A.J.); (M.V.)
| | - Ryan Miller
- School of Medicine, Louisiana State University Health New Orleans, New Orleans, LA 70112, USA;
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