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Salvatti BA, Chagas MA, Fernandes PO, Ladeira YFX, Bozzi AS, Valadares VS, Valente AP, de Miranda AS, Rocha WR, Maltarollo VG, Moraes AH. Understanding the Enzyme ( S)-Norcoclaurine Synthase Promiscuity to Aldehydes and Ketones. J Chem Inf Model 2024; 64:4462-4474. [PMID: 38776464 DOI: 10.1021/acs.jcim.3c01773] [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: 05/25/2024]
Abstract
The (S)-norcoclaurine synthase from Thalictrum flavum (TfNCS) stereoselectively catalyzes the Pictet-Spengler reaction between dopamine and 4-hydroxyphenylacetaldehyde to give (S)-norcoclaurine. TfNCS can catalyze the Pictet-Spengler reaction with various aldehydes and ketones, leading to diverse tetrahydroisoquinolines. This substrate promiscuity positions TfNCS as a highly promising enzyme for synthesizing fine chemicals. Understanding carbonyl-containing substrates' structural and electronic signatures that influence TfNCS activity can help expand its applications in the synthesis of different compounds and aid in protein optimization strategies. In this study, we investigated the influence of the molecular properties of aldehydes and ketones on their reactivity in the TfNCS-catalyzed Pictet-Spengler reaction. Initially, we compiled a library of reactive and unreactive compounds from previous publications. We also performed enzymatic assays using nuclear magnetic resonance to identify some reactive and unreactive carbonyl compounds, which were then included in the library. Subsequently, we employed QSAR and DFT calculations to establish correlations between substrate-candidate structures and reactivity. Our findings highlight correlations of structural and stereoelectronic features, including the electrophilicity of the carbonyl group, to the reactivity of aldehydes and ketones toward the TfNCS-catalyzed Pictet-Spengler reaction. Interestingly, experimental data of seven compounds out of fifty-three did not correlate with the electrophilicity of the carbonyl group. For these seven compounds, we identified unfavorable interactions between them and the TfNCS. Our results demonstrate the applications of in silico techniques in understanding enzyme promiscuity and specificity, with a particular emphasis on machine learning methodologies, DFT electronic structure calculations, and molecular dynamic (MD) simulations.
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Affiliation(s)
- Brunno A Salvatti
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Marcelo A Chagas
- Departamento de Ciências Exatas, Universidade do Estado de Minas Gerais, João Monlevade, Minas Gerais 35930-314, Brazil
| | - Phillipe O Fernandes
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Yan F X Ladeira
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Aline S Bozzi
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Veronica S Valadares
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Ana Paula Valente
- Centro Nacional de Ressonância Magnética Nuclear, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil
| | - Amanda S de Miranda
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Willian R Rocha
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Vinicius G Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Adolfo H Moraes
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
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2
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Hohenfeld CS, de Oliveira SAS, Ferreira CF, Mello VH, Margarido GRA, Passos AR, de Oliveira EJ. Comparative analysis of infected cassava root transcriptomics reveals candidate genes for root rot disease resistance. Sci Rep 2024; 14:10587. [PMID: 38719851 PMCID: PMC11078935 DOI: 10.1038/s41598-024-60847-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
Cassava root-rot incited by soil-borne pathogens is one of the major diseases that reduces root yield. Although the use of resistant cultivars is the most effective method of management, the genetic basis for root-rot resistance remains poorly understood. Therefore, our work analyzed the transcriptome of two contrasting genotypes (BRS Kiriris/resistant and BGM-1345/susceptible) using RNA-Seq to understand the molecular response and identify candidate genes for resistance. Cassava seedlings (resistant and susceptible to root-rot) were both planted in infested and sterilized soil and samples from Initial-time and Final-time periods, pooled. Two controls were used: (i) seedlings collected before planting in infested soil (absolute control) and, (ii) plants grown in sterilized soil (mock treatments). For the differentially expressed genes (DEGs) analysis 23.912 were expressed in the resistant genotype, where 10.307 were differentially expressed in the control treatment, 15 DEGs in the Initial Time-period and 366 DEGs in the Final Time-period. Eighteen candidate genes from the resistant genotype were related to plant defense, such as the MLP-like protein 31 and the peroxidase A2-like gene. This is the first model of resistance at the transcriptional level proposed for the cassava × root-rot pathosystem. Gene validation will contribute to screening for resistance of germplasm, segregating populations and/or use in gene editing in the pursuit to develop most promising cassava clones with resistance to root-rot.
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Affiliation(s)
- Camila Santiago Hohenfeld
- Universidade Estadual de Feira de Santana, Av. Transnordestina, S/N - 44036-900, Novo Horizonte, Feira de Santana, BA, Brazil
| | | | - Claudia Fortes Ferreira
- Embrapa Mandioca e Fruticultura, Rua da Embrapa, Caixa Postal 007, Cruz das Almas, BA, 44380-000, Brazil
| | - Victor Hugo Mello
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba, SP, 13418-900, Brazil
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba, SP, 13418-900, Brazil
| | - Adriana Rodrigues Passos
- Universidade Estadual de Feira de Santana, Av. Transnordestina, S/N - 44036-900, Novo Horizonte, Feira de Santana, BA, Brazil
| | - Eder Jorge de Oliveira
- Embrapa Mandioca e Fruticultura, Rua da Embrapa, Caixa Postal 007, Cruz das Almas, BA, 44380-000, Brazil.
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3
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Majhi BB, Gélinas SE, Mérindol N, Ricard S, Desgagné-Penix I. Characterization of norbelladine synthase and noroxomaritidine/norcraugsodine reductase reveals a novel catalytic route for the biosynthesis of Amaryllidaceae alkaloids including the Alzheimer's drug galanthamine. FRONTIERS IN PLANT SCIENCE 2023; 14:1231809. [PMID: 37711303 PMCID: PMC10499049 DOI: 10.3389/fpls.2023.1231809] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Amaryllidaceae alkaloids (AAs) are a large group of plant specialized metabolites with diverse pharmacological properties. Norbelladine is the entry compound in AAs biosynthesis and is produced from the condensation of tyramine and 3,4-dihydroxybenzaldehyde (3,4-DHBA). There are two reported enzymes capable of catalyzing this reaction in-vitro, both with low yield. The first one, norbelladine synthase (NBS), was shown to condense tyramine and 3,4-DHBA, while noroxomaritidine/norcraugsodine reductase (NR), catalyzes a reduction reaction to produce norbelladine. To clarify the mechanisms involved in this controversial step, both NBS and NR homologs were identified from the transcriptome of Narcissus papyraceus and Leucojum aestivum, cloned and expressed in Escherichia coli. Enzymatic assays performed with tyramine and 3,4-DHBA with each enzyme separately or combined, suggested that NBS and NR function together for the condensation of tyramine and 3,4-DHBA into norcraugsodine and further reduction into norbelladine. Using molecular homology modeling and docking studies, we predicted models for the binding of tyramine and 3,4-DHBA to NBS, and of the intermediate norcraugsodine to NR. Moreover, we show that NBS and NR physically interact in yeast and in-planta, that both localize to the cytoplasm and nucleus and are expressed at high levels in bulbs, confirming their colocalization and co-expression thus their ability to work together in the same catalytic route. Finally, their co-expression in yeast led to the production of norbelladine. In all, our study establishes that both NBS and NR participate in the biosynthesis of norbelladine by catalyzing the first key steps associated in the biosynthesis of the Alzheimer's drug galanthamine.
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Affiliation(s)
- Bharat Bhusan Majhi
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, QC, Canada
| | - Sarah-Eve Gélinas
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, QC, Canada
| | - Natacha Mérindol
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, QC, Canada
| | - Simon Ricard
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, QC, Canada
| | - Isabel Desgagné-Penix
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, QC, Canada
- Plant Biology Research Group, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, QC, Canada
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4
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Elucidation of the (R)-enantiospecific benzylisoquinoline alkaloid biosynthetic pathways in sacred lotus (Nelumbo nucifera). Sci Rep 2023; 13:2955. [PMID: 36805479 PMCID: PMC9940101 DOI: 10.1038/s41598-023-29415-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/03/2023] [Indexed: 02/22/2023] Open
Abstract
Benzylisoquinoline alkaloids (BIAs) are a structurally diverse group of plant specialized metabolites found mainly in members of the order Ranunculales, including opium poppy (Papaver somniferum), for which BIA biosynthetic pathways leading to the critical drugs morphine, noscapine, and sanguinarine have been elucidated. Sacred lotus (Nelumbo nucifera), in the order Proteales, accumulates medicinal BIAs in the proaporphine, aporphine, and bisbenzylisoquinoline structural subgroups with a prevalence of R enantiomers, opposed to the dominant S configuration occurring in the Ranunculales. Nevertheless, distinctive BIA biosynthetic routes in sacred lotus have not been explored. In planta labeling experiments and in vitro assays with recombinant enzymes and plant protein extracts showed that dopamine and 4-hydroxyphenylacetaldehyde derived from L-tyrosine serve as precursors for the formation of (R,S)-norcoclaurine in sacred lotus, whereas only (R)-norcoclaurine byproducts are favored in the plant by action of R-enantiospecific methyltransferases and cytochrome P450 oxidoreductases (CYPs). Enzymes responsible for the R-enantiospecific formation of proaporphine (NnCYP80Q1) and bisbenzylisoquinoline (NnCYP80Q2) scaffolds, and a methylenedioxy bridge introduction on aporphine substrates (NnCYP719A22) were identified, whereas additional aspects of the biosynthetic pathways leading to the distinctive alkaloid profile are discussed. This work expands the availability of molecular tools that can be deployed in synthetic biology platforms for the production of high-value alkaloids.
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5
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Li J, Li Y, Dang M, Li S, Chen S, Liu R, Zhang Z, Li G, Zhang M, Yang D, Yang M, Liu Y, Tian D, Deng X. Jasmonate-Responsive Transcription Factors NnWRKY70a and NnWRKY70b Positively Regulate Benzylisoquinoline Alkaloid Biosynthesis in Lotus ( Nelumbo nucifera). FRONTIERS IN PLANT SCIENCE 2022; 13:862915. [PMID: 35783938 PMCID: PMC9240598 DOI: 10.3389/fpls.2022.862915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/17/2022] [Indexed: 05/20/2023]
Abstract
Lotus (Nelumbo nucifera) is a large aquatic plant that accumulates pharmacologically significant benzylisoquinoline alkaloids (BIAs). However, little is known about their biosynthesis and regulation. Here, we show that the two group III WRKY transcription factors (TFs), NnWRKY70a and NnWRKY70b, positively regulate the BIA biosynthesis in lotus. Both NnWRKY70s are jasmonic acid (JA) responsive, with their expression profiles highly correlated to the BIA concentration and BIA pathway gene expression. A dual-luciferase assay showed that NnWRKY70a could transactivate the NnTYDC promoter, whereas NnWRKY70b could activate promoters of the three BIA structural genes, including NnTYDC, NnCYP80G, and Nn7OMT. In addition, the transient overexpression of NnWRKY70a and NnWRKY70b in lotus petals significantly elevated the BIA alkaloid concentrations. Notably, NnWRKY70b seems to be a stronger BIA biosynthesis regulator, because it dramatically induced more BIA structural gene expressions and BIA accumulation than NnWRKY70a. A yeast two-hybrid assay further revealed that NnWRKY70b physically interacted with NnJAZ1 and two other group III WRKY TFs (NnWRKY53b and NnWRKY70a), suggesting that it may cooperate with the other group III WRKYs to adjust the lotus BIA biosynthesis via the JA-signaling pathway. To illustrate the mechanism underlying NnWRKY70b-mediated BIA regulation in the lotus, a simplified model is proposed. Our study provides useful insights into the regulatory roles of WRKY TFs in the biosynthesis of secondary metabolites.
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Affiliation(s)
- Jing Li
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Yi Li
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Mingjing Dang
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Shang Li
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Simeng Chen
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Ruizhen Liu
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Zeyu Zhang
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Guoqian Li
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Minghua Zhang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Dong Yang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Mei Yang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yanling Liu
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Daike Tian
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Xianbao Deng
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- *Correspondence: Xianbao Deng
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6
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Wang Z, Li Y, Ma D, Zeng M, Wang Z, Qin F, Chen J, Christian M, He Z. Alkaloids from lotus ( Nelumbo nucifera): recent advances in biosynthesis, pharmacokinetics, bioactivity, safety, and industrial applications. Crit Rev Food Sci Nutr 2021:1-34. [PMID: 34845950 DOI: 10.1080/10408398.2021.2009436] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Different parts of lotus (Nelumbo nucifera Gaertn.) including the seeds, rhizomes, leaves, and flowers, are used for medicinal purposes with health promoting and illness preventing benefits. The presence of active chemicals such as alkaloids, phenolic acids, flavonoids, and terpenoids (particularly alkaloids) may account for this plant's pharmacological effects. In this review, we provide a comprehensive overview and summarize up-to-date research on the biosynthesis, pharmacokinetics, and bioactivity of lotus alkaloids as well as their safety. Moreover, the potential uses of lotus alkaloids in the food, pharmaceutical, and cosmetic sectors are explored. Current evidence shows that alkaloids, mainly consisting of aporphines, 1-benzylisoquinolines, and bisbenzylisoquinolines, are present in different parts of lotus. The bioavailability of these alkaloids is relatively low in vivo but can be enhanced by technological modification using nanoliposomes, liposomes, microcapsules, and emulsions. Available data highlights their therapeutic and preventive effects on obesity, diabetes, neurodegeneration, cancer, cardiovascular disease, etc. Additionally, industrial applications of lotus alkaloids include their use as food, medical, and cosmetic ingredients in tea, other beverages, and healthcare products; as lipid-lowering, anticancer, and antipsychotic drugs; and in facial masks, toothpastes, and shower gels. However, their clinical efficacy and safety remains unclear; hence, larger and longer human trials are needed to achieve their safe and effective use with minimal side effects.
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Affiliation(s)
- Zhenyu Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Yong Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Dandan Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Maomao Zeng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhaojun Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Fang Qin
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Jie Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
| | - Mark Christian
- School of Science and Technology, Nottingham Trent University, Clifton, Nottingham, UK
| | - Zhiyong He
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
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7
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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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8
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Qin L, Hu Y, Wang J, Wang X, Zhao R, Shan H, Li K, Xu P, Wu H, Yan X, Liu L, Yi X, Wanke S, Bowers JE, Leebens-Mack JH, dePamphilis CW, Soltis PS, Soltis DE, Kong H, Jiao Y. Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome. NATURE PLANTS 2021; 7:1239-1253. [PMID: 34475528 PMCID: PMC8445822 DOI: 10.1038/s41477-021-00990-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 07/22/2021] [Indexed: 05/04/2023]
Abstract
Aristolochia, a genus in the magnoliid order Piperales, has been famous for centuries for its highly specialized flowers and wide medicinal applications. Here, we present a new, high-quality genome sequence of Aristolochia fimbriata, a species that, similar to Amborella trichopoda, lacks further whole-genome duplications since the origin of extant angiosperms. As such, the A. fimbriata genome is an excellent reference for inferences of angiosperm genome evolution, enabling detection of two novel whole-genome duplications in Piperales and dating of previously reported whole-genome duplications in other magnoliids. Genomic comparisons between A. fimbriata and other angiosperms facilitated the identification of ancient genomic rearrangements suggesting the placement of magnoliids as sister to monocots, whereas phylogenetic inferences based on sequence data we compiled yielded ambiguous relationships. By identifying associated homologues and investigating their evolutionary histories and expression patterns, we revealed highly conserved floral developmental genes and their distinct downstream regulatory network that may contribute to the complex flower morphology in A. fimbriata. Finally, we elucidated the genetic basis underlying the biosynthesis of terpenoids and aristolochic acids in A. fimbriata.
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Affiliation(s)
- Liuyu Qin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiheng Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinpeng Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xiaoliang Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ran Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Kunpeng Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hanying Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Xueqing Yan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lumei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Yi
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Stefan Wanke
- Institute of Botany, Dresden University of Technology, Dresden, Germany
| | - John E Bowers
- Department of Plant Biology, University of Georgia, Athens, GA, USA
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | | | - Claude W dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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9
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Torrens-Spence MP, Glinkerman CM, Günther J, Weng JK. Imine chemistry in plant metabolism. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:101999. [PMID: 33450608 DOI: 10.1016/j.pbi.2020.101999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/25/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
Imine chemistry represents an important category of chemical reactions involved in the biosynthesis of plant natural products, ranging from the newly discovered mobile defense hormone N-hydroxy-pipecolic acid to the red-to-yellow tyrosine-derived betalain pigments. Spontaneous imine formation reactions have also served as the basis for the evolution of numerous plant metabolic enzymes, such as specialized Pictet-Spenglerases that produce the backbone structures of benzylisoquinoline and monoterpene indole alkaloids and pyridoxal 5'-phosphate-dependent enzymes of diverse functions. Here, we review occurrences of imine chemistry in plant metabolism and their chemical and biochemical mechanisms. A better understanding of plant imine chemistry will ultimately facilitate synthetic biology approaches to further expand the scope of imine natural product biosynthesis for broad biotechnological applications.
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Affiliation(s)
| | | | - Jan Günther
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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10
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Lichman BR. The scaffold-forming steps of plant alkaloid biosynthesis. Nat Prod Rep 2020; 38:103-129. [PMID: 32745157 DOI: 10.1039/d0np00031k] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Alkaloids from plants are characterised by structural diversity and bioactivity, and maintain a privileged position in both modern and traditional medicines. In recent years, there have been significant advances in elucidating the biosynthetic origins of plant alkaloids. In this review, I will describe the progress made in determining the metabolic origins of the so-called true alkaloids, specialised metabolites derived from amino acids containing a nitrogen heterocycle. By identifying key biosynthetic steps that feature in the majority of pathways, I highlight the key roles played by modifications to primary metabolism, iminium reactivity and spontaneous reactions in the molecular and evolutionary origins of these pathways.
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Affiliation(s)
- Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.
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11
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Li Y, Winzer T, He Z, Graham IA. Over 100 Million Years of Enzyme Evolution Underpinning the Production of Morphine in the Papaveraceae Family of Flowering Plants. PLANT COMMUNICATIONS 2020; 1:100029. [PMID: 32685922 PMCID: PMC7357826 DOI: 10.1016/j.xplc.2020.100029] [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: 09/17/2019] [Revised: 11/06/2019] [Accepted: 02/03/2020] [Indexed: 05/06/2023]
Abstract
Phylogenomic analysis of whole genome sequences of five benzylisoquinoline alkaloid (BIA)-producing species from the Ranunculales and Proteales orders of flowering plants revealed the sequence and timing of evolutionary events leading to the diversification of these compounds. (S)-Reticuline is a pivotal intermediate in the synthesis of many BIAs and our analyses revealed parallel evolution between the two orders, which diverged ∼122 million years ago (MYA). Berberine is present in species across the entire Ranunculales, and we found co-evolution of genes essential for production of the protoberberine class. The benzophenanthridine class, which includes the antimicrobial compound sanguinarine, is specific to the Papaveraceae family of Ranunculales, and biosynthetic genes emerged after the split with the Ranunculaceae family ∼110 MYA but before the split of the three Papaveraceae species used in this study at ∼77 MYA. The phthalideisoquinoline noscapine and morphinan class of BIAs are exclusive to the opium poppy lineage. Ks estimation of paralogous pairs indicates that morphine biosynthesis evolved more recently than 18 MYA in the Papaver genus. In the preceding 100 million years gene duplication, neofunctionalization and recruitment of additional enzyme classes, combined with gene clustering, gene fusion, and gene amplification, resulted in emergence of medicinally valuable BIAs including morphine and noscapine.
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Affiliation(s)
- Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, UK
| | - Thilo Winzer
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, UK
| | - Zhesi He
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, UK
| | - Ian A. Graham
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, UK
- Corresponding author
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12
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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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13
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Oogai S, Fukuta M, Watanabe K, Inafuku M, Oku H. Molecular characterization of mimosinase and cystathionine β-lyase in the Mimosoideae subfamily member Mimosa pudica. JOURNAL OF PLANT RESEARCH 2019; 132:667-680. [PMID: 31368041 DOI: 10.1007/s10265-019-01128-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/27/2019] [Indexed: 06/10/2023]
Abstract
Mimosinase degrades the non-protein amino acid mimosine and is thought to have evolved from cystathionine β-lyase (CBL) via gene duplication. However, no study has, to date, compared the molecular characteristics of mimosinase and CBL. We therefore cloned mimosinase and CBL from the Mimosoideae subfamily member Mimosa pudica (Mp) and explored the molecular relationship between mimosinase and CBL for the first time. The recombinant Mp mimosinase degraded both mimosine and cystathionine with a much higher turnover number (kcat) for mimosine compared with cystathionine, and Mp CBL utilized only cystathionine as a substrate. The critical residues implicated in the substrate binding of Arabidopsis thaliana CBL (Tyr-127, Arg-129, Tyr-181, and Arg-440) were highly conserved in both Mp mimosinase and CBL. However, homology modeling and molecular simulation of these enzymes predicted variations in the residues that interact with substrates. A mutation experiment on Mp mimosinase revealed that the disruption of a disulfide bond in the vicinity of the pyridoxal-5'-phosphate domain increased the enzyme's preference toward cystathionine. Treatment of Mp mimosinase with a disulfide-cleavage agent also decreased mimosinase activity. Furthermore, mutation near the conserved binding residue altered the substrate preference between mimosine and cystathionine. Molecular dynamics simulations of Mp mimosinase suggested a closer coordination of the residues that interact with mimosine at the active site compared with cystathionine, indicating a more compact pocket size for mimosine degradation. This study thus may provide new insights into the molecular diversification of CBL, a C-S lyase, into the C-N lyase mimosinase in the Mimosoideae subfamily.
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Affiliation(s)
- Shigeki Oogai
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Ko-rimoto, Kagoshima, 890-8580, Japan
| | - Masakazu Fukuta
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Ko-rimoto, Kagoshima, 890-8580, Japan
- Faculty of Agriculture, University of the Ryukyus, 1 Senbaru, Nishihara-cho, Nakagami-gun, Okinawa, 903-0213, Japan
| | - Keiichi Watanabe
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Ko-rimoto, Kagoshima, 890-8580, Japan
- Faculty of Agriculture, Saga University, 1, Honjo-machi, Saga, 840-8502, Japan
| | - Masashi Inafuku
- Molecular Biotechnology Group, Center of Molecular Bioscience, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa, 903-0213, Japan
| | - Hirosuke Oku
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Ko-rimoto, Kagoshima, 890-8580, Japan.
- Molecular Biotechnology Group, Center of Molecular Bioscience, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa, 903-0213, Japan.
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14
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Menéndez-Perdomo IM, Facchini PJ. Benzylisoquinoline Alkaloids Biosynthesis in Sacred Lotus. Molecules 2018; 23:E2899. [PMID: 30404216 PMCID: PMC6278464 DOI: 10.3390/molecules23112899] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/01/2018] [Accepted: 11/04/2018] [Indexed: 12/30/2022] Open
Abstract
Sacred lotus (Nelumbo nucifera Gaertn.) is an ancient aquatic plant used throughout Asia for its nutritional and medicinal properties. Benzylisoquinoline alkaloids (BIAs), mostly within the aporphine and bisbenzylisoquinoline structural categories, are among the main bioactive constituents in the plant. The alkaloids of sacred lotus exhibit promising anti-cancer, anti-arrhythmic, anti-HIV, and anti-malarial properties. Despite their pharmacological significance, BIA metabolism in this non-model plant has not been extensively investigated. In this review, we examine the diversity of BIAs in sacred lotus, with an emphasis on the distinctive stereochemistry of alkaloids found in this species. Additionally, we discuss our current understanding of the biosynthetic genes and enzymes involved in the formation of 1-benzylisoquinoline, aporphine, and bisbenzylisoquinoline alkaloids in the plant. We conclude that a comprehensive functional characterization of alkaloid biosynthetic enzymes using both in vitro and in vivo methods is required to advance our limited knowledge of BIA metabolism in the sacred lotus.
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Affiliation(s)
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada.
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15
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Patil MD, Grogan G, Yun H. Biocatalyzed C−C Bond Formation for the Production of Alkaloids. ChemCatChem 2018. [DOI: 10.1002/cctc.201801130] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mahesh D. Patil
- Department of Systems BiotechnologyKonkuk University Seoul 143-701 Korea
| | - Gideon Grogan
- Department of ChemistryUniversity of York Heslington York, YO10 5DD UK
| | - Hyungdon Yun
- Department of Systems BiotechnologyKonkuk University Seoul 143-701 Korea
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16
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Meelaph T, Kobtrakul K, Chansilpa NN, Han Y, Rani D, De-Eknamkul W, Vimolmangkang S. Coregulation of Biosynthetic Genes and Transcription Factors for Aporphine-Type Alkaloid Production in Wounded Lotus Provides Insight into the Biosynthetic Pathway of Nuciferine. ACS OMEGA 2018; 3:8794-8802. [PMID: 31459012 PMCID: PMC6644620 DOI: 10.1021/acsomega.8b00827] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/30/2018] [Indexed: 05/24/2023]
Abstract
Lotus (Nelumbo nucifera Gaertn.) contains various bioactive compounds, with benzylisoquinoline alkaloids (BIAs) as one of the major groups. The biosynthetic pathways of two major bioactive BIAs in this plant, nuciferine and N-nornuciferine, are still not clear. Therefore, several genes related to BIA biosynthesis were searched from the lotus database to study the role of key genes in regulating these pathways. In this study, the expression profiles of NCS, CNMT, 6OMT, CYP80G2, and WRKY TFs were investigated in mechanically wounded lotus leaves. It was found that the accumulation of nuciferine and N-nornuciferine significantly increased in the mechanically wounded lotus leaves in accordance with the relative expression of putative CYP80G2 and one WRKY transcription factor (NNU_24385), with the coregulation of CNMT. Furthermore, the role of methyltransferase-related genes in this study suggested that methylation of the isoquinoline nucleus to yield a methylated-BIA structure may occur at the N position before the O position. Altogether, this study provides improved understanding of the genes regulating BIA biosynthesis under stressed conditions, which could lead to improvements in BIA production from the commercial lotus.
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Affiliation(s)
- Thitirat Meelaph
- Research
Unit for Natural Product Biotechnology, Faculty of Pharmaceutical
Sciences, Department of Biochemistry and Microbiology, Faculty of Pharmaceutical
Sciences, and Department of Pharmacognosy and Pharmaceutical Botany, Faculty of
Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Khwanlada Kobtrakul
- Research
Unit for Natural Product Biotechnology, Faculty of Pharmaceutical
Sciences, Department of Biochemistry and Microbiology, Faculty of Pharmaceutical
Sciences, and Department of Pharmacognosy and Pharmaceutical Botany, Faculty of
Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - N. Nopchai Chansilpa
- Faculty of Agriculture and Natural Resources, Rajamangala University of Technology Tawan-ok, Chonburi 20110, Thailand
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement
and Specialty Agriculture, Wuhan Botanical
Garden of the Chinese Academy of Sciences, Wuhan 430074, P. R. China
| | - Dolly Rani
- Research
Unit for Natural Product Biotechnology, Faculty of Pharmaceutical
Sciences, Department of Biochemistry and Microbiology, Faculty of Pharmaceutical
Sciences, and Department of Pharmacognosy and Pharmaceutical Botany, Faculty of
Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wanchai De-Eknamkul
- Research
Unit for Natural Product Biotechnology, Faculty of Pharmaceutical
Sciences, Department of Biochemistry and Microbiology, Faculty of Pharmaceutical
Sciences, and Department of Pharmacognosy and Pharmaceutical Botany, Faculty of
Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sornkanok Vimolmangkang
- Research
Unit for Natural Product Biotechnology, Faculty of Pharmaceutical
Sciences, Department of Biochemistry and Microbiology, Faculty of Pharmaceutical
Sciences, and Department of Pharmacognosy and Pharmaceutical Botany, Faculty of
Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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17
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Deng X, Zhao L, Fang T, Xiong Y, Ogutu C, Yang D, Vimolmangkang S, Liu Y, Han Y. Investigation of benzylisoquinoline alkaloid biosynthetic pathway and its transcriptional regulation in lotus. HORTICULTURE RESEARCH 2018; 5:29. [PMID: 29872534 PMCID: PMC5981371 DOI: 10.1038/s41438-018-0035-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 05/10/2023]
Abstract
Lotus predominantly accumulates benzylisoquinoline alkaloids (BIAs), but their biosynthesis and regulation remain unclear. Here, we investigated structural and regulatory genes involved in BIA accumulation in lotus. Two clustered CYP80 genes were identified to be responsible for the biosynthesis of bis-BIAs and aporphine-type BIAs, respectively, and their tissue-specific expression causes divergence in alkaloid component between leaf and embryo. In contrast with the common (S)-reticuline precursor for most BIAs, aporphine alkaloids in lotus leaf may result from the (S)-N-methylcoclaurine precursor. Structural diversity of BIA alkaloids in the leaf is attributed to enzymatic modifications, including intramolecular C-C phenol coupling on ring A and methylation and demethylation at certain positions. Additionally, most BIA biosynthetic pathway genes show higher levels of expression in the leaf of high-BIA cultivar compared with low-BIA cultivar, suggesting transcriptional regulation of BIA accumulation in lotus. Five transcription factors, including three MYBs, one ethylene-responsive factor, and one basic helix-loop-helix (bHLH), were identified to be candidate regulators of BIA biosynthesis in lotus. Our study reveals a BIA biosynthetic pathway and its transcriptional regulation in lotus, which will enable a deeper understanding of BIA biosynthesis in plants.
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Affiliation(s)
- Xianbao Deng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
| | - Li Zhao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Ting Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Yaqian Xiong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
| | - Collins Ogutu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Dong Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
| | - Sornkanok Vimolmangkang
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Yanling Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074 China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
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18
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Hagel JM, Facchini PJ. Tying the knot: occurrence and possible significance of gene fusions in plant metabolism and beyond. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4029-4043. [PMID: 28521055 DOI: 10.1093/jxb/erx152] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Gene fusions have recently attracted attention especially in the field of plant specialized metabolism. The occurrence of a gene fusion, in which originally separate gene products are combined into a single polypeptide, often corresponds to the functional association of individual components within a single metabolic pathway. Examples include gene fusions implicated in benzylisoquinoline alkaloid (BIA), terpenoid, and amino acid biosynthetic pathways, in which distinct domains within a fusion catalyze consecutive, yet independent reactions. Both genomic and transcriptional mechanisms result in the fusion of gene products, which can include partial or complete domain repeats and extensive domain shuffling as evident in the BIA biosynthetic enzyme norcoclaurine synthase. Artificial gene fusions are commonly deployed in attempts to engineer new or improved pathways in plants or microorganisms, based on the premise that fusions are advantageous. However, a survey of functionally characterized fusions in microbial systems shows that the functional impact of fused gene products is not straightforward. For example, whereas enzyme fusions might facilitate the metabolic channeling of unstable intermediates, this channeling can also occur between tightly associated independent enzymes. The frequent occurrence of both fused and unfused enzymes in plant and microbial metabolism adds additional complexity, in terms of both pathway functionality and evolution.
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Affiliation(s)
- Jillian M Hagel
- Department of Biological Sciences, University of Calgary, 2500 University Dr N.W., Alberta T2N 1N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, 2500 University Dr N.W., Alberta T2N 1N4, Canada
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19
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Yang M, Zhu L, Li L, Li J, Xu L, Feng J, Liu Y. Digital Gene Expression Analysis Provides Insight into the Transcript Profile of the Genes Involved in Aporphine Alkaloid Biosynthesis in Lotus ( Nelumbo nucifera). FRONTIERS IN PLANT SCIENCE 2017; 8:80. [PMID: 28197160 PMCID: PMC5281601 DOI: 10.3389/fpls.2017.00080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/13/2017] [Indexed: 05/21/2023]
Abstract
The predominant alkaloids in lotus leaves are aporphine alkaloids. These are the most important active components and have many pharmacological properties, but little is known about their biosynthesis. We used digital gene expression (DGE) technology to identify differentially-expressed genes (DEGs) between two lotus cultivars with different alkaloid contents at four leaf development stages. We also predicted potential genes involved in aporphine alkaloid biosynthesis by weighted gene co-expression network analysis (WGCNA). Approximately 335 billion nucleotides were generated; and 94% of which were aligned against the reference genome. Of 22 thousand expressed genes, 19,000 were differentially expressed between the two cultivars at the four stages. Gene Ontology (GO) enrichment analysis revealed that catalytic activity and oxidoreductase activity were enriched significantly in most pairwise comparisons. In Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, dozens of DEGs were assigned to the categories of biosynthesis of secondary metabolites, isoquinoline alkaloid biosynthesis, and flavonoid biosynthesis. The genes encoding norcoclaurine synthase (NCS), norcoclaurine 6-O-methyltransferase (6OMT), coclaurine N-methyltransferase (CNMT), N-methylcoclaurine 3'-hydroxylase (NMCH), and 3'-hydroxy-N-methylcoclaurine 4'-O-methyltransferase (4'OMT) in the common pathways of benzylisoquinoline alkaloid biosynthesis and the ones encoding corytuberine synthase (CTS) in aporphine alkaloid biosynthetic pathway, which have been characterized in other plants, were identified in lotus. These genes had positive effects on alkaloid content, albeit with phenotypic lag. The WGCNA of DEGs revealed that one network module was associated with the dynamic change of alkaloid content. Eleven genes encoding proteins with methyltransferase, oxidoreductase and CYP450 activities were identified. These were surmised to be genes involved in aporphine alkaloid biosynthesis. This transcriptomic database provides new directions for future studies on clarifying the aporphine alkaloid pathway.
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Affiliation(s)
- Mei Yang
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Lingping Zhu
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
- Department of Agricultural Sciences, Viikki Plant Science Center, University of HelsinkiHelsinki, Finland
| | - Ling Li
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
- College of Life Science, University of Chinese Academy of SciencesBeijing, China
| | - Juanjuan Li
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
- College of Life Science, University of Chinese Academy of SciencesBeijing, China
| | - Liming Xu
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Ji Feng
- Tobacco Research Institute of Hubei ProvinceWuhan, China
| | - Yanling Liu
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
- *Correspondence: Yanling Liu
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