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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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Wu L, Zhao B, Deng Z, Wang B, Yu Y. A biosynthetic network for protoberberine production in Coptis chinensis. HORTICULTURE RESEARCH 2024; 11:uhad259. [PMID: 38282690 PMCID: PMC10812381 DOI: 10.1093/hr/uhad259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/26/2023] [Indexed: 01/30/2024]
Abstract
Protoberberine alkaloids are a group of tetracyclic isoquinoline compounds known for their well-established antimicrobial and anti-inflammatory properties. The richness and diversity of protoberberine alkaloids accumulated in the Coptis genus necessitate a comprehensive examination of the biosynthetic machinery to understand their ecological significance. Here, from Coptis chinensis we identified CcCYP719A1, which could install a methylenedioxy bridge on either ring A or ring D of the protoberberine backbone, thus diverging metabolite flux towards the biosynthesis of various protoberberine components. We also obtained CcCYP719A2 and CcCYP719A3, which underwent positive selection after diverging from CcCYP719A1 and maintained specific catalytic activity on ring D. Further, we resolved the biosynthetic pathway of jatrorrhizine by identifying two demethylases, which could also modulate protoberberine composition by removing the C-3 methyl group and methylenedioxy bridge of ring D, allowing demethylated metabolites to be redirected into different routes. Moreover, we characterized 2-O-methyltransferase CcOMT1 and flavin-dependent oxidase CcTHBO, respectively responsible for the commonly observed 2-O-methylation and aromatic ring-C assembly in protoberberine alkaloids. Overall, this study reveals an interconnected metabolite network from which diverse protoberberine alkaloids originate. It provides valuable insights into the existence of undiscovered protoberberine components, and paves the way for the targeted production of desired protoberberine components for potential therapeutic development.
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Affiliation(s)
- Linrui Wu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, China
| | - Binxin Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, China
| | - Zixin Deng
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, China
| | - Bin Wang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Yi Yu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, China
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
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Park NI, Roy NS, Park Y, Choi BS, Jeon MJ, Oh JY, Kim BY, Kim YD, Kim YI, Um T, Kwak HJ, Kim NS, Kim S, Choi IY. Isolation and Characterization of the Genes Involved in the Berberine Synthesis Pathway in Asian Blue Cohosh, Caulophyllum robustum. PLANTS (BASEL, SWITZERLAND) 2023; 12:1483. [PMID: 37050109 PMCID: PMC10096549 DOI: 10.3390/plants12071483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
Caulophyllum robustum, commonly named Asian blue cohosh, is a perennial herb in the family Berberidaceae. It has traditionally been used for folk medicine in China. We isolated berberine from the leaves, stem, roots, and fruits of C. robustum, and this is the first report on berberine in this species. Transcriptome analysis was conducted for the characterization of berberine biosynthesis genes in C. robustum, in which, all the genes for berberine biosynthesis were identified. From 40,094 transcripts, using gene ontology (GO) analysis, 26,750 transcripts were assigned their functions in the categories of biological process, molecular function, and cellular component. In the analysis of genes expressed in different tissues, the numbers of genes in the categories of intrinsic component of membrane and transferase activity were up-regulated in leaves versus stem. The berberine synthesis genes in C. robustum were characterized by phylogenetic analysis with corresponding genes from other berberine-producing species. The co-existence of genes from different plant families in the deepest branch subclade implies that the differentiation of berberine synthesis genes occurred early in the evolution of berberine-producing plants. Furthermore, the copy number increment of the berberine synthesis genes was detected at the species level.
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Affiliation(s)
- Nam-Il Park
- Department of Plant Science, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
| | - Neha Samir Roy
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Yeri Park
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Beom-Soon Choi
- Next Bio Information Technology, Bodeumkwan 504, Kangwon National University, Gangwondaehakgil-1, Chuncheon 24341, Republic of Korea
| | - Mi Jin Jeon
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Ji Yeon Oh
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Bo-Yun Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Young-Dong Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Yong-In Kim
- On Biological Resource Research Institute, Chuncheon 24239, Republic of Korea
| | - Taeyoung Um
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hwan Jong Kwak
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Nam-Soo Kim
- Next Bio Information Technology, Bodeumkwan 504, Kangwon National University, Gangwondaehakgil-1, Chuncheon 24341, Republic of Korea
| | - Soonok Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Ik-Young Choi
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
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Pyne ME, Gold ND, Martin VJJ. Pathway elucidation and microbial synthesis of proaporphine and bis-benzylisoquinoline alkaloids from sacred lotus (Nelumbo nucifera). Metab Eng 2023; 77:162-173. [PMID: 37004909 DOI: 10.1016/j.ymben.2023.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/07/2023] [Accepted: 03/25/2023] [Indexed: 04/03/2023]
Abstract
Sacred lotus (Nelumbo nucifera) has been utilized as a food, medicine, and spiritual symbol for nearly 3000 years. The medicinal properties of lotus are largely attributed to its unique profile of benzylisoquinoline alkaloids (BIAs), which includes potential anti-cancer, anti-malarial and anti-arrhythmic compounds. BIA biosynthesis in sacred lotus differs markedly from that of opium poppy and other members of the Ranunculales, most notably in an abundance of BIAs possessing the (R)-stereochemical configuration and the absence of reticuline, a major branchpoint intermediate in most BIA producers. Owing to these unique metabolic features and the pharmacological potential of lotus, we set out to elucidate the BIA biosynthesis network in N. nucifera. Here we show that lotus CYP80G (NnCYP80G) and a superior ortholog from Peruvian nutmeg (Laurelia sempervirens; LsCYP80G) stereospecifically convert (R)-N-methylcoclaurine to the proaporphine alkaloid glaziovine, which is subsequently methylated to pronuciferine, the presumed precursor to nuciferine. While sacred lotus employs a dedicated (R)-route to aporphine alkaloids from (R)-norcoclaurine, we implemented an artificial stereochemical inversion approach to flip the stereochemistry of the core BIA pathway. Exploiting the unique substrate specificity of dehydroreticuline synthase from common poppy (Papaver rhoeas) and pairing it with dehydroreticuline reductase enabled de novo synthesis of (R)-N-methylcoclaurine from (S)-norcoclaurine and its subsequent conversion to pronuciferine. We leveraged our stereochemical inversion approach to also elucidate the role of NnCYP80A in sacred lotus metabolism, which we show catalyzes the stereospecific formation of the bis-BIA nelumboferine. Screening our collection of 66 plant O-methyltransferases enabled conversion of nelumboferine to liensinine, a potential anti-cancer bis-BIA from sacred lotus. Our work highlights the unique benzylisoquinoline metabolism of N. nucifera and enables the targeted overproduction of potential lotus pharmaceuticals using engineered microbial systems.
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Affiliation(s)
- Michael E Pyne
- Department of Biology, Concordia University, Montréal, Québec, Canada; Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada.
| | - Nicholas D Gold
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada; Concordia Genome Foundry, Concordia University, Montréal, Québec, Canada
| | - Vincent J J Martin
- Department of Biology, Concordia University, Montréal, Québec, Canada; Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada.
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5
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Yu Y, Liu Y, Dong G, Jiang J, Leng L, Liu X, Zhang J, Liu A, Chen S. Functional characterization and key residues engineering of a regiopromiscuity O-methyltransferase involved in benzylisoquinoline alkaloid biosynthesis in Nelumbo nucifera. HORTICULTURE RESEARCH 2023; 10:uhac276. [PMID: 36789257 PMCID: PMC9923211 DOI: 10.1093/hr/uhac276] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/09/2022] [Accepted: 12/02/2022] [Indexed: 06/18/2023]
Abstract
Lotus (Nelumbo nucifera), an ancient aquatic plant, possesses a unique pharmacological activity that is primarily contributed by benzylisoquinoline alkaloids (BIAs). However, only few genes and enzymes involved in BIA biosynthesis in N. nucifera have been isolated and characterized. In the present study we identified the regiopromiscuity of an O-methyltransferase, designated NnOMT6, isolated from N. nucifera; NnOMT6 was found to catalyze the methylation of monobenzylisoquinoline 6-O/7-O, aporphine skeleton 6-O, phenylpropanoid 3-O, and protoberberine 2-O. We further probed the key residues affecting NnOMT6 activity via molecular docking and molecular dynamics simulation. Verification using site-directed mutagenesis revealed that residues D316, N130, L135, N176A, D269, and E328 were critical for BIA O-methyltransferase activities; furthermore, N323A, a mutant of NnOMT6, demonstrated a substantial increase in catalytic efficiency for BIAs and a broader acceptor scope compared with wild-type NnOMT6. To the best of our knowledge, this is the first study to report the O-methyltransferase activity of an aporphine skeleton without benzyl moiety substitutions in N. nucifera. The study findings provide biocatalysts for the semisynthesis of related medical compounds and give insights into protein engineering to strengthen O-methyltransferase activity in plants.
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Affiliation(s)
- Yuetong Yu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Yan Liu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | | | - JinZhu Jiang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Liang Leng
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - XianJu Liu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - Jun Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16, Nanxiaojie, Dongzhimennei, Beijing 100700, China
| | - An Liu
- Corresponding author. E-mail: ;
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Lashley A, Miller R, Provenzano S, Jarecki SA, Erba P, Salim V. Functional Diversification and Structural Origins of Plant Natural Product Methyltransferases. Molecules 2022; 28:molecules28010043. [PMID: 36615239 PMCID: PMC9822479 DOI: 10.3390/molecules28010043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
In plants, methylation is a common step in specialized metabolic pathways, leading to a vast diversity of natural products. The methylation of these small molecules is catalyzed by S-adenosyl-l-methionine (SAM)-dependent methyltransferases, which are categorized based on the methyl-accepting atom (O, N, C, S, or Se). These methyltransferases are responsible for the transformation of metabolites involved in plant defense response, pigments, and cell signaling. Plant natural product methyltransferases are part of the Class I methyltransferase-superfamily containing the canonical Rossmann fold. Recent advances in genomics have accelerated the functional characterization of plant natural product methyltransferases, allowing for the determination of substrate specificities and regioselectivity and further realizing the potential for enzyme engineering. This review compiles known biochemically characterized plant natural product methyltransferases that have contributed to our knowledge in the diversification of small molecules mediated by methylation steps.
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Affiliation(s)
- Audrey Lashley
- Department of Biological Sciences, Louisiana State University, Shreveport, LA 71115, USA
| | - Ryan Miller
- Department of Biological Sciences, Louisiana State University, Shreveport, LA 71115, USA
- School of Medicine, Louisiana State University Health New Orleans, New Orleans, LA 70112, USA
| | - Stephanie Provenzano
- Department of Biological Sciences, Louisiana State University, Shreveport, LA 71115, USA
- School of Medicine, Louisiana State University Health Shreveport, Shreveport, LA 71103, USA
| | - Sara-Alexis Jarecki
- Department of Biological Sciences, Louisiana State University, Shreveport, LA 71115, USA
| | - Paul Erba
- Department of Biological Sciences, Louisiana State University, Shreveport, LA 71115, USA
- School of Medicine, Louisiana State University Health New Orleans, New Orleans, LA 70112, USA
| | - Vonny Salim
- Department of Biological Sciences, Louisiana State University, Shreveport, LA 71115, USA
- Correspondence:
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Cheng W, Yao Y, Wang Q, Chang X, Shi Z, Fang X, Chen F, Chen S, Zhang Y, Zhang F, Zhu D, Deng Z, Lu L. Characterization of benzylisoquinoline alkaloid methyltransferases in Liriodendron chinense provides insights into the phylogenic basis of angiosperm alkaloid diversity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:535-548. [PMID: 36062348 DOI: 10.1111/tpj.15966] [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: 04/12/2022] [Revised: 08/02/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Benzylisoquinoline alkaloids (BIAs) are a class of plant secondary metabolites with great pharmacological value. Their biosynthetic pathways have been extensively elucidated in the species from the Ranunculales order, such as poppy and Coptis japonica, in which methylation events play central roles and are directly responsible for BIA chemodiversity. Here, we combined BIA quantitative profiling and transcriptomic analyses to identify novel BIA methyltransferases (MTs) from Liriodendron chinense, a basal angiosperm plant. We identified an N-methyltransferase (LcNMT1) and two O-methyltransferases (LcOMT1 and LcOMT3), and characterized their biochemical functions in vitro. LcNMT1 methylates (S)-coclaurine to produce mono- and dimethylated products. Mutagenesis experiments revealed that a single-residue alteration is sufficient to change its substrate selectivity. LcOMT1 methylates (S)-norcoclaurine at the C6 site and LcOMT3 methylates (S)-coclaurine at the C7 site, respectively. Two key residues of LcOMT3, A115 and T301, are identified as important contributors to its catalytic activity. Compared with Ranunculales-derived NMTs, Magnoliales-derived NMTs were less abundant and had narrower substrate specificity, indicating that NMT expansion has contributed substantially to BIA chemodiversity in angiosperms, particularly in Ranunculales species. In summary, we not only characterized three novel enzymes that could be useful in the biosynthetic production of valuable BIAs but also shed light on the molecular origin of BIAs during angiosperm evolution.
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Affiliation(s)
- Weijia Cheng
- Department of Ophthalmology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yan Yao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Qiuxia Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Xiaosa Chang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Zhuolin Shi
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Xueting Fang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Fangfang Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Shixin Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yonghong Zhang
- Laboratory of Medicinal Plant, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, School of Basic Medicine, Hubei University of Medicine, Shiyan, 442000, China
| | - Fan Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Dongqing Zhu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Li Lu
- Department of Ophthalmology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
- Hubei Hongshan Laboratory, Wuhan, 430071, China
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8
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Bu J, Zhang X, Li Q, Ma Y, Hu Z, Yang J, Liu X, Wang R, Jiao X, Chen T, Lai C, Cui G, Tang J, Kong Y, Yang L, Lin S, Chen Y, Guo J, Huang L. Catalytic promiscuity of O-methyltransferases from Corydalis yanhusuo leading to the structural diversity of benzylisoquinoline alkaloids. HORTICULTURE RESEARCH 2022; 9:uhac152. [PMID: 36168544 PMCID: PMC9510826 DOI: 10.1093/hr/uhac152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/27/2022] [Indexed: 06/16/2023]
Abstract
O-methyltransferases play essential roles in producing structural diversity and improving the biological properties of benzylisoquinoline alkaloids (BIAs) in plants. In this study, Corydalis yanhusuo, a plant used in traditional Chinese medicine due to the analgesic effects of its BIA-active compounds, was employed to analyze the catalytic characteristics of O-methyltransferases in the formation of BIA diversity. Seven genes encoding O-methyltransferases were cloned, and functionally characterized using seven potential BIA substrates. Specifically, an O-methyltransferase (CyOMT2) with highly efficient catalytic activity of both 4'- and 6-O-methylations of 1-BIAs was found. CyOMT6 was found to perform two sequential methylations at both 9- and 2-positions of the essential intermediate of tetrahydroprotoberberines, (S)-scoulerine. Two O-methyltransferases (CyOMT5 and CyOMT7) with wide substrate promiscuity were found, with the 2-position of tetrahydroprotoberberines as the preferential catalytic site for CyOMT5 (named scoulerine 2-O-methyltransferase) and the 6-position of 1-BIAs as the preferential site for CyOMT7. In addition, results of integrated phylogenetic molecular docking analysis and site-directed mutation suggested that residues at sites 172, 306, 313, and 314 in CyOMT5 are important for enzyme promiscuity related to O-methylations at the 6- and 7-positions of isoquinoline. Cys at site 253 in CyOMT2 was proved to promote the methylation activity of the 6-position and to expand substrate scopes. This work provides insight into O-methyltransferases in producing BIA diversity in C. yanhusuo and genetic elements for producing BIAs by metabolic engineering and synthetic biology.
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Affiliation(s)
| | | | - Qishuang Li
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 South Side Street, Dongzhimen, Beijing 100700, China
| | - Ying Ma
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 South Side Street, Dongzhimen, Beijing 100700, China
| | - Zhimin Hu
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 South Side Street, Dongzhimen, Beijing 100700, China
| | - Jian Yang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 South Side Street, Dongzhimen, Beijing 100700, China
| | - Xiuyu Liu
- School of Pharmacy, Henan University of Chinese Medicine, No. 156 Jinshuidong Road, Zhengzhou 450008, China
| | - Ruishan Wang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 South Side Street, Dongzhimen, Beijing 100700, China
| | - Xiang Jiao
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden
| | - Tong Chen
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 South Side Street, Dongzhimen, Beijing 100700, China
| | - Changjiangsheng Lai
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 South Side Street, Dongzhimen, Beijing 100700, China
| | - Guanghong Cui
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 South Side Street, Dongzhimen, Beijing 100700, China
| | - Jinfu Tang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 South Side Street, Dongzhimen, Beijing 100700, China
| | - Yu Kong
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Lei Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Sheng Lin
- Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Yun Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE41296, Gothenburg, Sweden
| | - Juan Guo
- Corresponding authors. E-mail: ,
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Sun H, Song H, Deng X, Liu J, Yang D, Zhang M, Wang Y, Xin J, Chen L, Liu Y, Yang M. Transcriptome-Wide Characterization of Alkaloids and Chlorophyll Biosynthesis in Lotus Plumule. FRONTIERS IN PLANT SCIENCE 2022; 13:885503. [PMID: 35677240 PMCID: PMC9168470 DOI: 10.3389/fpls.2022.885503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Lotus plumule is a green tissue in the middle of seeds that predominantly accumulates bisbenzylisoquinoline alkaloids (bis-BIAs) and chlorophyll (Chl). However, the biosynthetic mechanisms of these two metabolites remain largely unknown in lotus. This study used physiological and RNA sequencing (RNA-Seq) approaches to characterize the development and molecular mechanisms of bis-BIAs and Chl biosynthesis in lotus plumule. Physiological analysis revealed that exponential plumule growth occurred between 9 and 15 days after pollination (DAP), which coincided with the onset of bis-BIAs biosynthesis and its subsequent rapid accumulation. Transcriptome analysis of lotus plumule identified a total of 8,725 differentially expressed genes (DEGs), representing ~27.7% of all transcripts in the lotus genome. Sixteen structural DEGs, potentially associated with bis-BIAs biosynthesis, were identified. Of these, 12 encoded O-methyltransferases (OMTs) are likely involved in the methylation and bis-BIAs diversity in lotus. In addition, functionally divergent paralogous and redundant homologous gene members of the BIAs biosynthesis pathway, as well as transcription factors co-expressed with bis-BIAs and Chl biosynthesis genes, were identified. Twenty-two genes encoding 16 conserved enzymes of the Chl biosynthesis pathway were identified, with the majority being significantly upregulated by Chl biosynthesis. Photosynthesis and Chl biosynthesis pathways were simultaneously activated during lotus plumule development. Moreover, our results showed that light-driven Pchlide reduction is essential for Chl biosynthesis in the lotus plumule. These results will be useful for enhancing our understanding of alkaloids and Chl biosynthesis in plants.
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Affiliation(s)
- Heng Sun
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Heyun Song
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xianbao Deng
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Juan Liu
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Dong Yang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Minghua Zhang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuxin Wang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jia Xin
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lin Chen
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, China
| | - Yanling Liu
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Mei Yang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
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10
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Diversification of Chemical Structures of Methoxylated Flavonoids and Genes Encoding Flavonoid-O-Methyltransferases. PLANTS 2022; 11:plants11040564. [PMID: 35214897 PMCID: PMC8876552 DOI: 10.3390/plants11040564] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 11/25/2022]
Abstract
The O-methylation of specialized metabolites in plants is a unique decoration that provides structural and functional diversity of the metabolites with changes in chemical properties and intracellular localizations. The O-methylation of flavonoids, which is a class of plant specialized metabolites, promotes their antimicrobial activities and liposolubility. Flavonoid O-methyltransferases (FOMTs), which are responsible for the O-methylation process of the flavonoid aglycone, generally accept a broad range of substrates across flavones, flavonols and lignin precursors, with different substrate preferences. Therefore, the characterization of FOMTs with the physiology roles of methoxylated flavonoids is useful for crop improvement and metabolic engineering. In this review, we summarized the chemodiversity and physiology roles of methoxylated flavonoids, which were already reported, and we performed a cross-species comparison to illustrate an overview of diversification and conserved catalytic sites of the flavonoid O-methyltransferases.
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11
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Cui X, Meng F, Pan X, Qiu X, Zhang S, Li C, Lu S. Chromosome-level genome assembly of Aristolochia contorta provides insights into the biosynthesis of benzylisoquinoline alkaloids and aristolochic acids. HORTICULTURE RESEARCH 2022; 9:uhac005. [PMID: 35147168 PMCID: PMC8973263 DOI: 10.1093/hr/uhac005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 05/11/2023]
Abstract
Aristolochic acids (AAs) and their derivatives exist in multiple Aristolochiaceae species which had been or are being used as medicinal materials. During the past decades, AAs have received increasing attention due to their nephrotoxicity and carcinogenecity. Elimination of AAs in medicinal materials using biotechnological approaches is important to improve medication safety. However, it has not been achieved because of the limited information of AA biosynthesis available. Here, we report a high-quality reference-grade genome assembly of the AA-containing vine, Aristolochia contorta. Total size of the assembly is 209.27 Mb, which is assembled into 7 pseudochromosomes. Synteny analysis, Ks distribution and 4DTv suggest absences of whole-genome duplication events in A. contorta after the angiosperm-wide WGD. Based on genomic, transcriptomic and metabolic data, pathways and candidate genes of benzylisoquinoline alkaloid (BIA) and AA biosynthesis in A. contorta were proposed. Five O-methyltransferase genes, including AcOMT1-3, AcOMT5 and AcOMT7, were cloned and functionally characterized. The results provide a high-quality reference genome for AA-containing species of Aristolochiaceae. It lays a solid foundation for further elucidation of AA biosynthesis and regulation and molecular breeding of Aristolochiaceae medicinal materials.
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Affiliation(s)
- Xinyun Cui
- Medicinal Plant Cultivation Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Haidian District, Beijing 100193, China
| | - Fanqi Meng
- Medicinal Plant Cultivation Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Haidian District, Beijing 100193, China
| | - Xian Pan
- Medicinal Plant Cultivation Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Haidian District, Beijing 100193, China
| | - Xiaoxiao Qiu
- Medicinal Plant Cultivation Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Haidian District, Beijing 100193, China
| | - Sixuan Zhang
- Medicinal Plant Cultivation Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Haidian District, Beijing 100193, China
| | - Caili Li
- Medicinal Plant Cultivation Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Medicinal Plant Cultivation Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Haidian District, Beijing 100193, China
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12
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Senn S, Pangell K, Bowerman AL. Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia. BIOTECH 2022; 11:biotech11010001. [PMID: 35822810 PMCID: PMC9245906 DOI: 10.3390/biotech11010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/20/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022] Open
Abstract
The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding fields in composition and function. We also hypothesized that rhizospheric and endophytic microbes would be associated with similar metabolic functions to the plant rootzone they inhabited. The methods employed were microbial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional analyses. A few of the main bacterial genera of interest that were differentially abundant in the Datura root microbiome were Flavobacterium (p = 0.007), Chitinophaga (p = 0.0007), Pedobacter (p = 6 × 10−5), Bradyhizobium (p = 1 × 10−8), and Paenibacillus (p = 1.46 × 10−6). There was significant evidence that the microbes associated with the Datura rootzone had elevated function related to bacterial chalcone synthase (p = 1.49 × 10−3) and permease genes (p < 0.003). There was some evidence that microbial functions in the Datura rootzone provided precursors to important plant bioactive molecules or were beneficial to plant growth. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is the first study to focus on the microbial ecology of the Datura rootzone. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.
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Affiliation(s)
- Savanah Senn
- Agriculture Sciences Department, Los Angeles Pierce College, 6201 Winnetka Avenue, PMB 553, Woodland Hills, CA 91304, USA; (K.P.); (A.L.B.)
- Environmental Sciences Graduate Program, Oregon State University, Corvallis, OR 97331, USA
- Correspondence:
| | - Kelly Pangell
- Agriculture Sciences Department, Los Angeles Pierce College, 6201 Winnetka Avenue, PMB 553, Woodland Hills, CA 91304, USA; (K.P.); (A.L.B.)
| | - Adrianna L. Bowerman
- Agriculture Sciences Department, Los Angeles Pierce College, 6201 Winnetka Avenue, PMB 553, Woodland Hills, CA 91304, USA; (K.P.); (A.L.B.)
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13
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Erythrina velutina Willd. alkaloids: Piecing biosynthesis together from transcriptome analysis and metabolite profiling of seeds and leaves. J Adv Res 2022; 34:123-136. [PMID: 35024185 PMCID: PMC8655131 DOI: 10.1016/j.jare.2021.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/01/2021] [Accepted: 01/30/2021] [Indexed: 12/27/2022] Open
Abstract
Introduction Natural products of pharmaceutical interest often do not reach the drug market due to the associated low yields and difficult extraction. Knowledge of biosynthetic pathways is a key element in the development of biotechnological strategies for plant specialized metabolite production. Erythrina species are mainly used as central nervous system depressants in folk medicine and are important sources of bioactive tetracyclic benzylisoquinoline alkaloids (BIAs), which can act on several pathology-related biological targets. Objectives In this sense, in an unprecedented approach used with a non-model Fabaceae species grown in its unique arid natural habitat, a combined transcriptome and metabolome analyses (seeds and leaves) is presented. Methods The Next Generation Sequencing-based transcriptome (de novo RNA sequencing) was carried out in a NextSeq 500 platform. Regarding metabolite profiling, the High-resolution Liquid Chromatography was coupled to DAD and a micrOTOF-QII mass spectrometer by using electrospray ionization (ESI) and Time of Flight (TOF) analyzer. The tandem MS/MS data were processed and analyzed through Molecular Networking approach. Results This detailed macro and micromolecular approach applied to seeds and leaves of E. velutina revealed 42 alkaloids, several of them unique. Based on the combined evidence, 24 gene candidates were put together in a putative pathway leading to the singular alkaloid diversity of this species. Conclusion Overall, these results could contribute by indicating potential biotechnological targets for modulation of erythrina alkaloids biosynthesis as well as improve molecular databases with omic data from a non-model medicinal plant, and reveal an interesting chemical diversity of Erythrina BIA harvested in Caatinga.
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14
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Hao DC, Li P, Xiao PG, He CN. Dissection of full-length transcriptome and metabolome of Dichocarpum (Ranunculaceae): implications in evolution of specialized metabolism of Ranunculales medicinal plants. PeerJ 2021; 9:e12428. [PMID: 34760397 PMCID: PMC8574218 DOI: 10.7717/peerj.12428] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/12/2021] [Indexed: 11/20/2022] Open
Abstract
Several main families of Ranunculales are rich in alkaloids and other medicinal compounds; many species of these families are used in traditional and folk medicine. Dichocarpum is a representative medicinal genus of Ranunculaceae, but the genetic basis of its metabolic phenotype has not been investigated, which hinders its sustainable conservation and utilization. We use the third-generation high-throughput sequencing and metabolomic techniques to decipher the full-length transcriptomes and metabolomes of five Dichocarpum species endemic in China, and 71,598 non-redundant full-length transcripts were obtained, many of which are involved in defense, stress response and immunity, especially those participating in the biosynthesis of specialized metabolites such as benzylisoquinoline alkaloids (BIAs). Twenty-seven orthologs extracted from trancriptome datasets were concatenated to reconstruct the phylogenetic tree, which was verified by the clustering analysis based on the metabolomic profile and agreed with the Pearson correlation between gene expression patterns of Dichocarpum species. The phylogenomic analysis of phytometabolite biosynthesis genes, e.g., (S)-norcoclaurine synthase, methyltransferases, cytochrome p450 monooxygenases, berberine bridge enzyme and (S)-tetrahydroprotoberberine oxidase, revealed the evolutionary trajectories leading to the chemodiversity, especially that of protoberberine type, aporphine type and bis-BIA abundant in Dichocarpum and related genera. The biosynthesis pathways of these BIAs are proposed based on full-length transcriptomes and metabolomes of Dichocarpum. Within Ranunculales, the gene duplications are common, and a unique whole genome duplication is possible in Dichocarpum. The extensive correlations between metabolite content and gene expression support the co-evolution of various genes essential for the production of different specialized metabolites. Our study provides insights into the transcriptomic and metabolomic landscapes of Dichocarpum, which will assist further studies on genomics and application of Ranunculales plants.
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Affiliation(s)
| | - Pei Li
- Chinese Academy of Medical Sciences, Beijing, China
| | - Pei-Gen Xiao
- Chinese Academy of Medical Sciences, Beijing, China
| | - Chun-Nian He
- Chinese Academy of Medical Sciences, Beijing, China
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15
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Cigan E, Eggbauer B, Schrittwieser JH, Kroutil W. The role of biocatalysis in the asymmetric synthesis of alkaloids - an update. RSC Adv 2021; 11:28223-28270. [PMID: 35480754 PMCID: PMC9038100 DOI: 10.1039/d1ra04181a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/30/2021] [Indexed: 12/19/2022] Open
Abstract
Alkaloids are a group of natural products with interesting pharmacological properties and a long history of medicinal application. Their complex molecular structures have fascinated chemists for decades, and their total synthesis still poses a considerable challenge. In a previous review, we have illustrated how biocatalysis can make valuable contributions to the asymmetric synthesis of alkaloids. The chemo-enzymatic strategies discussed therein have been further explored and improved in recent years, and advances in amine biocatalysis have vastly expanded the opportunities for incorporating enzymes into synthetic routes towards these important natural products. The present review summarises modern developments in chemo-enzymatic alkaloid synthesis since 2013, in which the biocatalytic transformations continue to take an increasingly 'central' role.
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Affiliation(s)
- Emmanuel Cigan
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth Heinrichstrasse 28/II 8010 Graz Austria
| | - Bettina Eggbauer
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth Heinrichstrasse 28/II 8010 Graz Austria
| | - Joerg H Schrittwieser
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth Heinrichstrasse 28/II 8010 Graz Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth Heinrichstrasse 28/II 8010 Graz Austria
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16
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Gao B, Yang B, Feng X, Li C. Recent advances in the biosynthesis strategies of nitrogen heterocyclic natural products. Nat Prod Rep 2021; 39:139-162. [PMID: 34374396 DOI: 10.1039/d1np00017a] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Covering: 2015 to 2020Nitrogen heterocyclic natural products (NHNPs) are primary or secondary metabolites containing nitrogen heterocyclic (N-heterocyclic) skeletons. Due to the existence of the N-heterocyclic structure, NHNPs exhibit various bioactivities such as anticancer and antibacterial, which makes them widely used in medicines, pesticides, and food additives. However, the low content of these NHNPs in native organisms severely restricts their commercial application. Although a variety of NHNPs have been produced through extraction or chemical synthesis strategies, these methods suffer from several problems. The development of biotechnology provides new options for the production of NHNPs. This review introduces the recent progress of two strategies for the biosynthesis of NHNPs: enzymatic biosynthesis and microbial cell factory. In the enzymatic biosynthesis part, the recent progress in the mining of enzymes that synthesize N-heterocyclic skeletons (e.g., pyrrole, piperidine, diketopiperazine, and isoquinoline), the engineering of tailoring enzymes, and enzyme cascades constructed to synthesize NHNPs are discussed. In the microbial cell factory part, with tropane alkaloids (TAs) and tetrahydroisoquinoline (THIQ) alkaloids as the representative compounds, the strategies of unraveling unknown natural biosynthesis pathways of NHNPs in plants are summarized, and various metabolic engineering strategies to enhance their production in microbes are introduced. Ultimately, future perspectives for accelerating the biosynthesis of NHNPs are discussed.
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Affiliation(s)
- Bo Gao
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.
| | - Bo Yang
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xudong Feng
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China. and SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China and Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
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17
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Diversity in Chemical Structures and Biological Properties of Plant Alkaloids. Molecules 2021; 26:molecules26113374. [PMID: 34204857 PMCID: PMC8199754 DOI: 10.3390/molecules26113374] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
Phytochemicals belonging to the group of alkaloids are signature specialized metabolites endowed with countless biological activities. Plants are armored with these naturally produced nitrogenous compounds to combat numerous challenging environmental stress conditions. Traditional and modern healthcare systems have harnessed the potential of these organic compounds for the treatment of many ailments. Various chemical entities (functional groups) attached to the central moiety are responsible for their diverse range of biological properties. The development of the characterization of these plant metabolites and the enzymes involved in their biosynthesis is of an utmost priority to deliver enhanced advantages in terms of biological properties and productivity. Further, the incorporation of whole/partial metabolic pathways in the heterologous system and/or the overexpression of biosynthetic steps in homologous systems have both become alternative and lucrative methods over chemical synthesis in recent times. Moreover, in-depth research on alkaloid biosynthetic pathways has revealed numerous chemical modifications that occur during alkaloidal conversions. These chemical reactions involve glycosylation, acylation, reduction, oxidation, and methylation steps, and they are usually responsible for conferring the biological activities possessed by alkaloids. In this review, we aim to discuss the alkaloidal group of plant specialized metabolites and their brief classification covering major categories. We also emphasize the diversity in the basic structures of plant alkaloids arising through enzymatically catalyzed structural modifications in certain plant species, as well as their emerging diverse biological activities. The role of alkaloids in plant defense and their mechanisms of action are also briefly discussed. Moreover, the commercial utilization of plant alkaloids in the marketplace displaying various applications has been enumerated.
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18
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Liu Y, Wang B, Shu S, Li Z, Song C, Liu D, Niu Y, Liu J, Zhang J, Liu H, Hu Z, Huang B, Liu X, Liu W, Jiang L, Alami MM, Zhou Y, Ma Y, He X, Yang Y, Zhang T, Hu H, Barker MS, Chen S, Wang X, Nie J. Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids. Nat Commun 2021; 12:3276. [PMID: 34078898 PMCID: PMC8172641 DOI: 10.1038/s41467-021-23611-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/07/2021] [Indexed: 02/04/2023] Open
Abstract
Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotation of C. chinensis. Phylogenetic and comparative genomic analyses reveal the phylogenetic placement of this species and identify a single round of ancient whole-genome duplication (WGD) shared by the Ranunculaceae. We characterize genes involved in the biosynthesis of protoberberine-type alkaloids in C. chinensis. In particular, local genomic tandem duplications contribute to member amplification of a Ranunculales clade-specific gene family of the cytochrome P450 (CYP) 719. The functional versatility of a key CYP719 gene that encodes the (S)-canadine synthase enzyme involved in the berberine biosynthesis pathway may play critical roles in the diversification of other berberine-related alkaloids in C. chinensis. Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model genome for genetic and applied studies of Ranunculales.
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Affiliation(s)
- Yifei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China.
| | - Bo Wang
- Hubei Institute for Drug Control, Wuhan, China
| | - Shaohua Shu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Chi Song
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Di Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yan Niu
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Jinxin Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jingjing Zhang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Heping Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Bisheng Huang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Xiuyu Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Liping Jiang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | | | - Yuxin Zhou
- Hubei Institute for Drug Control, Wuhan, China
| | - Yutao Ma
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiangxiang He
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Yicheng Yang
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Tianyuan Zhang
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Hui Hu
- Jing Brand Chizhengtang Pharmaceutical Company Limited, Huangshi, China
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Xuekui Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
| | - Jing Nie
- Hubei Institute for Drug Control, Wuhan, China.
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19
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Nguyen TD, O’Connor SE. The Progesterone 5β-Reductase/Iridoid Synthase Family: A Catalytic Reservoir for Specialized Metabolism across Land Plants. ACS Chem Biol 2020; 15:1780-1787. [PMID: 32501002 PMCID: PMC7467569 DOI: 10.1021/acschembio.0c00220] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Iridoids are plant-derived
terpenoids with a rich array of bioactivities.
The key step in iridoid skeleton formation is the reduction of 8-oxogeranial
by certain members of the progesterone 5β-reductase/iridoid
synthase (PRISE) family of short-chain alcohol dehydrogenases. Other
members of the PRISE family have previously been implicated in the
biosynthesis of the triterpenoid class of cardenolides, which requires
the reduction of progesterone. Here, we explore the occurrence and
activity of PRISE across major lineages of plants. We observed trace
activities toward either 8-oxogeranial or progesterone in all PRISEs,
including those from nonseed plants and green algae. Phylogenetic
analysis, coupled with enzymatic assays, show that these activities
appear to have become specialized in specific angiosperm lineages.
This broad analysis of the PRISE family provides insight into how
these enzymes evolved in plants and also suggests that iridoid synthase
activity is an ancestral trait in all land plants, which might have
contributed to the rise of iridoid metabolites.
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Affiliation(s)
- Trinh-Don Nguyen
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - 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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20
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Valentic TR, Payne JT, Smolke CD. Structure-Guided Engineering of a Scoulerine 9-O-Methyltransferase Enables the Biosynthesis of Tetrahydropalmatrubine and Tetrahydropalmatine in Yeast. ACS Catal 2020. [DOI: 10.1021/acscatal.9b05417] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Timothy R. Valentic
- Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, California 94305, United States
| | - James T. Payne
- Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, California 94305, United States
| | - Christina D. Smolke
- Department of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, California 94305, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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21
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Zhong F, Huang L, Qi L, Ma Y, Yan Z. Full-length transcriptome analysis of Coptis deltoidea and identification of putative genes involved in benzylisoquinoline alkaloids biosynthesis based on combined sequencing platforms. PLANT MOLECULAR BIOLOGY 2020; 102:477-499. [PMID: 31902069 DOI: 10.1007/s11103-019-00959-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/30/2019] [Indexed: 05/20/2023]
Abstract
The study carry out comprehensive transcriptome analysis of C. deltoidea and exploration of BIAs biosynthesis and accumulation based on UHPLC-MS/MS and combined sequencing platforms. Coptis deltoidea is an important medicinal plant with a long history of medicinal use, which is rich in benzylisoquinoline alkaloids (BIAs). In this study, Ultra performance liquid chromatography-electrospray ionization tandem mass spectrometry (UHPLC-ESI-MS/MS) and combined sequencing platforms were performed for exploration of BIAs biosynthesis, accumulation and comprehensive transcriptome analysis of C. deltoidea. By metabolism profiling, the accumulation of ten BIAs was analyzed using UHPLC-MS/MS and different contents were observed in different organs. From transcriptome sequencing result, we applied single-molecule real-time (SMRT) sequencing to C. deltoidea and generated a total of 75,438 full-length transcripts. We proposed the candidate biosynthetic pathway of tyrosine, precursor of BIAs, and identified 64 full length-transcripts encoding enzymes putatively involved in BIAs biosynthesis. RNA-Seq data indicated that the majority of genes exhibited relatively high expression level in roots. Transport of BIAs was also important for their accumulation. Here, 9 ABC transporters and 2 MATE transporters highly homologous to known alkaloid transporters related with BIAs transport in roots and rhizomes were identified. These findings based on the combined sequencing platforms provide valuable genetic information for C. deltoidea and the results of transcriptome combined with metabolome analysis can help us better understand BIAs biosynthesis and transport in this medicinal plant. The information will be critical for further characterization of C. deltoidea transcriptome and molecular-assisted breeding for this medicinal plant with scarce resources.
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Affiliation(s)
- Furong Zhong
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Ling Huang
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Luming Qi
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yuntong Ma
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Zhuyun Yan
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
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22
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Menéndez-Perdomo IM, Facchini PJ. Isolation and characterization of two O-methyltransferases involved in benzylisoquinoline alkaloid biosynthesis in sacred lotus ( Nelumbo nucifera). J Biol Chem 2020; 295:1598-1612. [PMID: 31914404 PMCID: PMC7008365 DOI: 10.1074/jbc.ra119.011547] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/28/2019] [Indexed: 12/15/2022] Open
Abstract
Benzylisoquinoline alkaloids (BIAs) are a major class of plant metabolites with many pharmacological benefits. Sacred lotus (Nelumbo nucifera) is an ancient aquatic plant of medicinal value because of antiviral and immunomodulatory activities linked to its constituent BIAs. Although more than 30 BIAs belonging to the 1-benzylisoquinoline, aporphine, and bisbenzylisoquinoline structural subclasses and displaying a predominant R-enantiomeric conformation have been isolated from N. nucifera, its BIA biosynthetic genes and enzymes remain unknown. Herein, we report the isolation and biochemical characterization of two O-methyltransferases (OMTs) involved in BIA biosynthesis in sacred lotus. Five homologous genes, designated NnOMT1-5 and encoding polypeptides sharing >40% amino acid sequence identity, were expressed in Escherichia coli Functional characterization of the purified recombinant proteins revealed that NnOMT1 is a regiospecific 1-benzylisoquinoline 6-O-methyltransferase (6OMT) accepting both R- and S-substrates, whereas NnOMT5 is mainly a 7-O-methyltransferase (7OMT), with relatively minor 6OMT activity and a strong stereospecific preference for S-enantiomers. Available aporphines were not accepted as substrates by either enzyme, suggesting that O-methylation precedes BIA formation from 1-benzylisoquinoline intermediates. Km values for NnOMT1 and NnOMT5 were 20 and 13 μm for (R,S)-norcoclaurine and (S)-N-methylcoclaurine, respectively, similar to those for OMTs from other BIA-producing plants. Organ-based correlations of alkaloid content, OMT activity in crude extracts, and OMT gene expression supported physiological roles for NnOMT1 and NnOMT5 in BIA metabolism, occurring primarily in young leaves and embryos of sacred lotus. In summary, our work identifies two OMTs involved in BIA metabolism in the medicinal plant N. nucifera.
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Affiliation(s)
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
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