1
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Garza-Garcia JJO, Qu Y. Chemical, pharmacological properties and biosynthesis of opioid mitragynine in Mitragyna speciosa (kratom). CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102600. [PMID: 39002353 DOI: 10.1016/j.pbi.2024.102600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/15/2024]
Abstract
Mitragynine, an alkaloid found in Mitragyna speciosa (kratom), shows promise as a potential alternative to opioids owing to its distinctive indole alkaloid structure and its capacity for pain relief, alleviation of opioid withdrawal symptoms, and anti-inflammatory effects. Recently the intricate process of mitragynine biosynthesis from the precursor strictosidine was elucidated, providing insights into the complex pathways responsible for synthesizing this opioid compound and its related diastereomers. As the search continues for the authentic hydroxylase and methyltransferase crucial for mitragynine formation, leveraging enzymes from other species and exploiting enzyme promiscuity has facilitated heterologous mitragynine biosynthesis in microbes. This highlights the extraordinary flexibility of enzymes in generating a spectrum of variations and analogs of kratom opioids within alternative biological systems.
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Affiliation(s)
| | - Yang Qu
- Department of Chemistry, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada.
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2
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Holtz M, Acevedo-Rocha CG, Jensen MK. Combining enzyme and metabolic engineering for microbial supply of therapeutic phytochemicals. Curr Opin Biotechnol 2024; 87:103110. [PMID: 38503222 DOI: 10.1016/j.copbio.2024.103110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/21/2024]
Abstract
The history of pharmacology is deeply intertwined with plant-derived compounds, which continue to be crucial in drug development. However, their complex structures and limited availability in plants challenge drug discovery, optimization, development, and industrial production via chemical synthesis or natural extraction. This review delves into the integration of metabolic and enzyme engineering to leverage micro-organisms as platforms for the sustainable and reliable production of therapeutic phytochemicals. We argue that engineered microbes can serve a triple role in this paradigm: facilitating pathway discovery, acting as cell factories for scalable manufacturing, and functioning as platforms for chemical derivatization. Analyzing recent progress and outlining future directions, the review highlights microbial biotechnology's transformative potential in expanding plant-derived human therapeutics' discovery and supply chains.
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Affiliation(s)
- Maxence Holtz
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Carlos G Acevedo-Rocha
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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3
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Cuello C, Jansen HJ, Abdallah C, Zamar Mbadinga DL, Birer Williams C, Durand M, Oudin A, Papon N, Giglioli-Guivarc'h N, Dirks RP, Jensen MK, O'Connor SE, Besseau S, Courdavault V. The Madagascar palm genome provides new insights on the evolution of Apocynaceae specialized metabolism. Heliyon 2024; 10:e28078. [PMID: 38533072 PMCID: PMC10963385 DOI: 10.1016/j.heliyon.2024.e28078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Specialized metabolites possess diverse interesting biological activities and some cardenolides- and monoterpene indole alkaloids- (MIAs) derived pharmaceuticals are currently used to treat human diseases such as cancers or hypertension. While these two families of biocompounds are produced by specific subfamilies of Apocynaceae, one member of this medicinal plant family, the succulent tree Pachypodium lamerei Drake (also known as Madagascar palm), does not produce such specialized metabolites. To explore the evolutionary paths that have led to the emergence and loss of cardenolide and MIA biosynthesis in Apocynaceae, we sequenced and assembled the P. lamerei genome by combining Oxford Nanopore Technologies long-reads and Illumina short-reads. Phylogenomics revealed that, among the Apocynaceae whose genomes have been sequenced, the Madagascar palm is so far the species closest to the common ancestor between MIA producers/non-MIA producers. Transposable elements, constituting 72.48% of the genome, emerge as potential key players in shaping genomic architecture and influencing specialized metabolic pathways. The absence of crucial MIA biosynthetic genes such as strictosidine synthase in P. lamerei and non-Rauvolfioideae species hints at a transposon-mediated mechanism behind gene loss. Phylogenetic analysis not only showcases the evolutionary divergence of specialized metabolite biosynthesis within Apocynaceae but also underscores the role of transposable elements in this intricate process. Moreover, we shed light on the low conservation of enzymes involved in the final stages of MIA biosynthesis in the distinct MIA-producing plant families, inferring independent gains of these specialized enzymes along the evolution of these medicinal plant clades. Overall, this study marks a leap forward in understanding the genomic dynamics underpinning the evolution of specialized metabolites biosynthesis in the Apocynaceae family, with transposons emerging as potential architects of genomics restructuring and gene loss.
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Affiliation(s)
- Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Hans J. Jansen
- Future Genomics Technologies, 2333 BE, Leiden, the Netherlands
| | - Cécile Abdallah
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | | | - Caroline Birer Williams
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Mickael Durand
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Audrey Oudin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000, Angers, France
| | | | - Ron P. Dirks
- Future Genomics Technologies, 2333 BE, Leiden, the Netherlands
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Sarah Ellen O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
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4
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López-Vázquez AL, Sepúlveda-García EB, Rubio-Rodríguez E, Ponce-Noyola T, Trejo-Tapia G, Barrera-Cortés J, Cerda-García-Rojas CM, Ramos-Valdivia AC. Induction of Monoterpenoid Oxindole Alkaloids Production and Related Biosynthetic Gene Expression in Response to Signaling Molecules in Hamelia patens Plant Cultures. PLANTS (BASEL, SWITZERLAND) 2024; 13:966. [PMID: 38611495 PMCID: PMC11013434 DOI: 10.3390/plants13070966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024]
Abstract
Hamelia patens (Rubiaceae), known as firebush, is a source of bioactive monoterpenoid oxindole alkaloids (MOAs) derived from monoterpenoid indole alkaloids (MIAs). With the aim of understanding the regulation of the biosynthesis of these specialized metabolites, micropropagated plants were elicited with jasmonic acid (JA) and salicylic acid (SA). The MOA production and MIA biosynthetic-related gene expression were evaluated over time. The production of MOAs was increased compared to the control up to 2-fold (41.3 mg g DW-1) at 72 h in JA-elicited plants and 2.5-fold (42.4 mg g DW-1) at 120 h in plants elicited with SA. The increment concurs with the increase in the expression levels of the genes HpaLAMT, HpaTDC, HpaSTR, HpaNPF2.9, HpaTHAS1, and HpaTHAS2. Interestingly, it was found that HpaSGD was downregulated in both treatments after 24 h but in the SA treatment at 120 h only was upregulated to 8-fold compared to the control. In this work, we present the results of MOA production in H. patens and discuss how JA and SA might be regulating the central biosynthetic steps that involve HpaSGD and HpaTHAS genes.
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Affiliation(s)
- Ana Luisa López-Vázquez
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de Mexico 07360, Mexico; (A.L.L.-V.); (T.P.-N.); (J.B.-C.)
| | - Edgar Baldemar Sepúlveda-García
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, División de Estudios de Posgrado, Universidad del Papaloapan, San Juan de Tuxtepec 68301, Oaxaca, Mexico;
| | - Elizabeth Rubio-Rodríguez
- Departamento de Biotecnología, Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional (CEPROBI-IPN), Yautepec 62730, Morelos, Mexico; (E.R.-R.); (G.T.-T.)
| | - Teresa Ponce-Noyola
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de Mexico 07360, Mexico; (A.L.L.-V.); (T.P.-N.); (J.B.-C.)
| | - Gabriela Trejo-Tapia
- Departamento de Biotecnología, Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional (CEPROBI-IPN), Yautepec 62730, Morelos, Mexico; (E.R.-R.); (G.T.-T.)
| | - Josefina Barrera-Cortés
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de Mexico 07360, Mexico; (A.L.L.-V.); (T.P.-N.); (J.B.-C.)
| | - Carlos M. Cerda-García-Rojas
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de Mexico 07360, Mexico;
| | - Ana C. Ramos-Valdivia
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de Mexico 07360, Mexico; (A.L.L.-V.); (T.P.-N.); (J.B.-C.)
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5
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Roth S, Niese R, Müller M, Hall M. Redox Out of the Box: Catalytic Versatility Across NAD(P)H-Dependent Oxidoreductases. Angew Chem Int Ed Engl 2024; 63:e202314740. [PMID: 37924279 DOI: 10.1002/anie.202314740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/06/2023]
Abstract
The asymmetric reduction of double bonds using NAD(P)H-dependent oxidoreductases has proven to be an efficient tool for the synthesis of important chiral molecules in research and on industrial scale. These enzymes are commercially available in screening kits for the reduction of C=O (ketones), C=C (activated alkenes), or C=N bonds (imines). Recent reports, however, indicate that the ability to accommodate multiple reductase activities on distinct C=X bonds occurs in different enzyme classes, either natively or after mutagenesis. This challenges the common perception of highly selective oxidoreductases for one type of electrophilic substrate. Consideration of this underexplored potential in enzyme screenings and protein engineering campaigns may contribute to the identification of complementary biocatalytic processes for the synthesis of chiral compounds. This review will contribute to a global understanding of the promiscuous behavior of NAD(P)H-dependent oxidoreductases on C=X bond reduction and inspire future discoveries with respect to unconventional biocatalytic routes in asymmetric synthesis.
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Affiliation(s)
- Sebastian Roth
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Richard Niese
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Mélanie Hall
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
- BioHealth, Field of Excellence, University of Graz, 8010, Graz, Austria
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6
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Nitin K, Rajakumara E. Proxy-approach in understanding the bisubstrate activity of strictosidine synthases. Int J Biol Macromol 2024; 262:130091. [PMID: 38354931 DOI: 10.1016/j.ijbiomac.2024.130091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/20/2024] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
Besides tryptamine (1) and secologanin (2), non-cognate substrates also undergo a Pictet-Spengler reaction (PSR) catalyzed by strictosidine synthases (STR) with differing catalytic properties. We characterized the bisubstrate binding aspect of catalysis - order, affinity, and cooperativity - with STR orthologs from Rauvolfia serpentina (RsSTR) and Ophiorrhiza pumila (OpSTR) by an isothermal titration calorimetry (ITC) based 'proxy approach' that employed a non-reactive tryptamine analog (m1) to capture its inert ternary complexes with STRs and (2). ITC studies with OpSTR and (2) revealed 'tryptamine-first' cooperative binding with (1) and a simultaneous cooperative binding with (m1). Binding cooperativity among (m1) and (2) towards OpSTR was higher than RsSTR. Crystallographic study of RsSTR-(m1) complex helped to understand the unreactive binding of (m1) in terms of orientation and interactions in the RsSTR pocket. PSR with (m1) was revealed to be energetically unfeasible by the density functional theory (DFT) scans of the first hydrogen abstraction by RsSTR. The effect of pH on the bisubstrate binding to OpSTR was deciphered by molecular dynamics simulations (MDS), which also provided a molecular basis for the stability of complex of OpSTR with (m1) and (2). Therefore, we investigated STRs from a substrate binding perspective to inform drug-design and rational enzyme engineering efforts.
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Affiliation(s)
- Kulhar Nitin
- Macromolecular Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Hyderabad (IITH), Kandi, Sangareddy 502284, Telangana, India.
| | - Eerappa Rajakumara
- Macromolecular Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Hyderabad (IITH), Kandi, Sangareddy 502284, Telangana, India.
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7
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Liu G, Wang J, Chu J, Jiang T, Qin S, Gao Z, He B. Engineering Substrate Promiscuity of Nucleoside Phosphorylase Via an Insertions-Deletions Strategy. JACS AU 2024; 4:454-464. [PMID: 38425912 PMCID: PMC10900210 DOI: 10.1021/jacsau.3c00581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 03/02/2024]
Abstract
Nucleoside phosphorylases (NPs) are the key enzymes in the nucleoside metabolism pathway and are widely employed for the synthesis of nucleoside analogs, which are difficult to access via conventional synthetic methods. NPs are generally classified as purine nucleoside phosphorylase (PNP) and pyrimidine or uridine nucleoside phosphorylase (PyNP/UP), based on their substrate preference. Here, based on the evolutionary information on the NP-I family, we adopted an insertions-deletions (InDels) strategy to engineer the substrate promiscuity of nucleoside phosphorylase AmPNPΔS2V102 K, which exhibits both PNP and UP activities from a trimeric PNP (AmPNP) of Aneurinibacillus migulanus. Furthermore, the AmPNPΔS2V102 K exerted phosphorylation activities toward arabinose nucleoside, fluorosyl nucleoside, and dideoxyribose, thereby broadening the unnatural-ribose nucleoside substrate spectrum of AmPNP. Finally, six purine nucleoside analogues were successfully synthesized, using the engineered AmPNPΔS2V102 K instead of the traditional "two-enzymes PNP/UP" approach. These results provide deep insights into the catalytic mechanisms of the PNP and demonstrate the benefits of using the InDels strategy to achieve substrate promiscuity in an enzyme, as well as broadening the substrate spectrum of the enzyme.
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Affiliation(s)
- Gaofei Liu
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Jialing Wang
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Jianlin Chu
- School
of Pharmaceutical Sciences, Nanjing Tech
University, Nanjing 211800, China
| | - Tianyue Jiang
- School
of Pharmaceutical Sciences, Nanjing Tech
University, Nanjing 211800, China
| | - Song Qin
- School
of Pharmaceutical Sciences, Nanjing Tech
University, Nanjing 211800, China
| | - Zhen Gao
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Bingfang He
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
- School
of Pharmaceutical Sciences, Nanjing Tech
University, Nanjing 211800, China
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8
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DeMars MD, O’Connor SE. Evolution and diversification of carboxylesterase-like [4+2] cyclases in aspidosperma and iboga alkaloid biosynthesis. Proc Natl Acad Sci U S A 2024; 121:e2318586121. [PMID: 38319969 PMCID: PMC10873640 DOI: 10.1073/pnas.2318586121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
Monoterpene indole alkaloids (MIAs) are a large and diverse class of plant natural products, and their biosynthetic construction has been a subject of intensive study for many years. The enzymatic basis for the production of aspidosperma and iboga alkaloids, which are produced exclusively by members of the Apocynaceae plant family, has recently been discovered. Three carboxylesterase (CXE)-like enzymes from Catharanthus roseus and Tabernanthe iboga catalyze regio- and enantiodivergent [4+2] cycloaddition reactions to generate the aspidosperma (tabersonine synthase, TS) and iboga (coronaridine synthase, CorS; catharanthine synthase, CS) scaffolds from a common biosynthetic intermediate. Here, we use a combined phylogenetic and biochemical approach to investigate the evolution and functional diversification of these cyclase enzymes. Through ancestral sequence reconstruction, we provide evidence for initial evolution of TS from an ancestral CXE followed by emergence of CorS in two separate lineages, leading in turn to CS exclusively in the Catharanthus genus. This progression from aspidosperma to iboga alkaloid biosynthesis is consistent with the chemotaxonomic distribution of these MIAs. We subsequently generate and test a panel of chimeras based on the ancestral cyclases to probe the molecular basis for differential cyclization activity. Finally, we show through partial heterologous reconstitution of tabersonine biosynthesis using non-pathway enzymes how aspidosperma alkaloids could have first appeared as "underground metabolites" via recruitment of promiscuous enzymes from common protein families. Our results provide insight into the evolution of biosynthetic enzymes and how new secondary metabolic pathways can emerge through small but important sequence changes following co-option of preexisting enzymatic functions.
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Affiliation(s)
- Matthew D. DeMars
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena07745, Germany
| | - Sarah E. O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena07745, Germany
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9
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Liu Y, Lyu R, Singleton JJ, Patra B, Pattanaik S, Yuan L. A Cotyledon-based Virus-Induced Gene Silencing (Cotyledon-VIGS) approach to study specialized metabolism in medicinal plants. PLANT METHODS 2024; 20:26. [PMID: 38347628 PMCID: PMC10860238 DOI: 10.1186/s13007-024-01154-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
BACKGROUND Virus-induced gene silencing (VIGS) is widely used in plant functional genomics. However, the efficiency of VIGS in young plantlets varies across plant species. Additionally, VIGS is not optimized for many plant species, especially medicinal plants that produce valuable specialized metabolites. RESULTS We evaluated the efficacy of five-day-old, etiolated seedlings of Catharanthus roseus (periwinkle) for VIGS. The seedlings were vacuum-infiltrated with Agrobacterium tumefaciens GV3101 cells carrying the tobacco rattle virus (TRV) vectors. The protoporphyrin IX magnesium chelatase subunit H (ChlH) gene, a key gene in chlorophyll biosynthesis, was used as the target for VIGS, and we observed yellow cotyledons 6 days after infiltration. As expected, the expression of CrChlH and the chlorophyll contents of the cotyledons were significantly decreased after VIGS. To validate the cotyledon based-VIGS method, we silenced the genes encoding several transcriptional regulators of the terpenoid indole alkaloid (TIA) biosynthesis in C. roseus, including two activators (CrGATA1 and CrMYC2) and two repressors (CrGBF1 and CrGBF2). Silencing CrGATA1 led to downregulation of the vindoline pathway genes (T3O, T3R, and DAT) and decreased vindoline contents in cotyledons. Silencing CrMYC2, followed by elicitation with methyl jasmonate (MeJA), resulted in the downregulation of ORCA2 and ORCA3. We also co-infiltrated C. roseus seedlings with TRV vectors that silence both CrGBF1 and CrGBF2 and overexpress CrMYC2, aiming to simultaneous silencing two repressors while overexpressing an activator. The simultaneous manipulation of repressors and activator resulted in significant upregulation of the TIA pathway genes. To demonstrate the broad application of the cotyledon-based VIGS method, we optimized the method for two other valuable medicinal plants, Glycyrrhiza inflata (licorice) and Artemisia annua (sweet wormwood). When TRV vectors carrying the fragments of the ChlH genes were infiltrated into the seedlings of these plants, we observed yellow cotyledons with decreased chlorophyll contents. CONCLUSIONS The widely applicable cotyledon-based VIGS method is faster, more efficient, and easily accessible to additional treatments than the traditional VIGS method. It can be combined with transient gene overexpression to achieve simultaneous up- and down-regulation of desired genes in non-model plants. This method provides a powerful tool for functional genomics of medicinal plants, facilitating the discovery and production of valuable therapeutic compounds.
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Affiliation(s)
- Yongliang Liu
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Ruiqing Lyu
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Joshua J Singleton
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Barunava Patra
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Sitakanta Pattanaik
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
| | - Ling Yuan
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
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10
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Guo J, Gao D, Lian J, Qu Y. De novo biosynthesis of antiarrhythmic alkaloid ajmaline. Nat Commun 2024; 15:457. [PMID: 38212296 PMCID: PMC10784492 DOI: 10.1038/s41467-024-44797-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024] Open
Abstract
The antiarrhythmic drug ajmaline is a monoterpenoid indole alkaloid (MIA) isolated from the Ayurvedic plant Rauvolfia serpentina (Indian Snakeroot). Research into the biosynthesis of ajmaline and another renowned MIA chemotherapeutic drug vinblastine has yielded pivotal advancements in the fields of plant specialized metabolism and engineering over recent decades. While the majority of vinblastine biosynthesis has been recently elucidated, the quest for comprehending ajmaline biosynthesis remains incomplete, marked by the absence of two critical enzymes. Here, we show the discovery and characterization of these two elusive reductases, alongside the identification of two physiologically relevant esterases that complete the biosynthesis of ajmaline. We show that ajmaline biosynthesis proceeds with vomilenine 1,2(R)-reduction followed by its 19,20(S)-reduction. This process is further modulated by two root-expressing esterases that deacetylate 17-O-acetylnorajmaline. Expanding upon the successful completion of the ajmaline biosynthetic pathway, we engineer the de novo biosynthesis of ajmaline in Baker's yeast.
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Affiliation(s)
- Jun Guo
- Department of Chemistry, University of New Brunswick, Fredericton, NB, Canada
| | - Di Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China.
- Zhejiang Key Laboratory of Smart Biomaterials, Zhejiang University, Hangzhou, China.
| | - Yang Qu
- Department of Chemistry, University of New Brunswick, Fredericton, NB, Canada.
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11
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Guedes JG, Ribeiro R, Carqueijeiro I, Guimarães AL, Bispo C, Archer J, Azevedo H, Fonseca NA, Sottomayor M. The leaf idioblastome of the medicinal plant Catharanthus roseus is associated with stress resistance and alkaloid metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:274-299. [PMID: 37804484 PMCID: PMC10735432 DOI: 10.1093/jxb/erad374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 10/06/2023] [Indexed: 10/09/2023]
Abstract
Catharanthus roseus leaves produce a range of monoterpenoid indole alkaloids (MIAs) that include low levels of the anticancer drugs vinblastine and vincristine. The MIA pathway displays a complex architecture spanning different subcellular and cell type localizations, and is under complex regulation. As a result, the development of strategies to increase the levels of the anticancer MIAs has remained elusive. The pathway involves mesophyll specialized idioblasts where the late unsolved biosynthetic steps are thought to occur. Here, protoplasts of C. roseus leaf idioblasts were isolated by fluorescence-activated cell sorting, and their differential alkaloid and transcriptomic profiles were characterized. This involved the assembly of an improved C. roseus transcriptome from short- and long-read data, IDIO+. It was observed that C. roseus mesophyll idioblasts possess a distinctive transcriptomic profile associated with protection against biotic and abiotic stresses, and indicative that this cell type is a carbon sink, in contrast to surrounding mesophyll cells. Moreover, it is shown that idioblasts are a hotspot of alkaloid accumulation, suggesting that their transcriptome may hold the key to the in-depth understanding of the MIA pathway and the success of strategies leading to higher levels of the anticancer drugs.
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Affiliation(s)
- Joana G Guedes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Programa Doutoral em Biologia Molecular e Celular (MCbiology), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
| | - Rogério Ribeiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Inês Carqueijeiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Ana Luísa Guimarães
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Cláudia Bispo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - John Archer
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Herlander Azevedo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
| | - Nuno A Fonseca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Mariana Sottomayor
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal
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12
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Bradley SA, Lehka BJ, Hansson FG, Adhikari KB, Rago D, Rubaszka P, Haidar AK, Chen L, Hansen LG, Gudich O, Giannakou K, Lengger B, Gill RT, Nakamura Y, de Bernonville TD, Koudounas K, Romero-Suarez D, Ding L, Qiao Y, Frimurer TM, Petersen AA, Besseau S, Kumar S, Gautron N, Melin C, Marc J, Jeanneau R, O'Connor SE, Courdavault V, Keasling JD, Zhang J, Jensen MK. Biosynthesis of natural and halogenated plant monoterpene indole alkaloids in yeast. Nat Chem Biol 2023; 19:1551-1560. [PMID: 37932529 PMCID: PMC10667104 DOI: 10.1038/s41589-023-01430-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/25/2023] [Indexed: 11/08/2023]
Abstract
Monoterpenoid indole alkaloids (MIAs) represent a large class of plant natural products with marketed pharmaceutical activities against a wide range of indications, including cancer, malaria and hypertension. Halogenated MIAs have shown improved pharmaceutical properties; however, synthesis of new-to-nature halogenated MIAs remains a challenge. Here we demonstrate a platform for de novo biosynthesis of two MIAs, serpentine and alstonine, in baker's yeast Saccharomyces cerevisiae and deploy it to systematically explore the biocatalytic potential of refactored MIA pathways for the production of halogenated MIAs. From this, we demonstrate conversion of individual haloindole derivatives to a total of 19 different new-to-nature haloserpentine and haloalstonine analogs. Furthermore, by process optimization and heterologous expression of a modified halogenase in the microbial MIA platform, we document de novo halogenation and biosynthesis of chloroalstonine. Together, this study highlights a microbial platform for enzymatic exploration and production of complex natural and new-to-nature MIAs with therapeutic potential.
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Affiliation(s)
- Samuel A Bradley
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Beata J Lehka
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Frederik G Hansson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Khem B Adhikari
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Daniela Rago
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Paulina Rubaszka
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ahmad K Haidar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ling Chen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lea G Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Olga Gudich
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Konstantina Giannakou
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Bettina Lengger
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ryan T Gill
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Yoko Nakamura
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | | | - David Romero-Suarez
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ling Ding
- Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Yijun Qiao
- Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Thomas M Frimurer
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Anja A Petersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Sébastien Besseau
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Sandeep Kumar
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Nicolas Gautron
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Celine Melin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Jillian Marc
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | | | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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13
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Stander EA, Lehka B, Carqueijeiro I, Cuello C, Hansson FG, Jansen HJ, Dugé De Bernonville T, Birer Williams C, Vergès V, Lezin E, Lorensen MDBB, Dang TT, Oudin A, Lanoue A, Durand M, Giglioli-Guivarc'h N, Janfelt C, Papon N, Dirks RP, O'connor SE, Jensen MK, Besseau S, Courdavault V. The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids. Commun Biol 2023; 6:1197. [PMID: 38001233 PMCID: PMC10673892 DOI: 10.1038/s42003-023-05574-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Monoterpene indole alkaloids (MIAs) are a structurally diverse family of specialized metabolites mainly produced in Gentianales to cope with environmental challenges. Due to their pharmacological properties, the biosynthetic modalities of several MIA types have been elucidated but not that of the yohimbanes. Here, we combine metabolomics, proteomics, transcriptomics and genome sequencing of Rauvolfia tetraphylla with machine learning to discover the unexpected multiple actors of this natural product synthesis. We identify a medium chain dehydrogenase/reductase (MDR) that produces a mixture of four diastereomers of yohimbanes including the well-known yohimbine and rauwolscine. In addition to this multifunctional yohimbane synthase (YOS), an MDR synthesizing mainly heteroyohimbanes and the short chain dehydrogenase vitrosamine synthase also display a yohimbane synthase side activity. Lastly, we establish that the combination of geissoschizine synthase with at least three other MDRs also produces a yohimbane mixture thus shedding light on the complex mechanisms evolved for the synthesis of these plant bioactives.
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Affiliation(s)
- Emily Amor Stander
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Beata Lehka
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Inês Carqueijeiro
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Frederik G Hansson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Hans J Jansen
- Future Genomics Technologies, 2333 BE, Leiden, The Netherlands
| | - Thomas Dugé De Bernonville
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
- Limagrain, Centre de Recherche, Route d'Ennezat, Chappes, France
| | - Caroline Birer Williams
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Valentin Vergès
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Enzo Lezin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | | | - Thu-Thuy Dang
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
| | - Audrey Oudin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Arnaud Lanoue
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | - Mickael Durand
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France
| | | | - Christian Janfelt
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000, Angers, France
| | - Ron P Dirks
- Future Genomics Technologies, 2333 BE, Leiden, The Netherlands
| | - Sarah Ellen O'connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany.
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark.
| | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France.
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200, Tours, France.
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14
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Kim K, Shahsavarani M, Garza-García JJO, Carlisle JE, Guo J, De Luca V, Qu Y. Biosynthesis of kratom opioids. THE NEW PHYTOLOGIST 2023; 240:757-769. [PMID: 37518950 DOI: 10.1111/nph.19162] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/06/2023] [Indexed: 08/01/2023]
Abstract
Mitragynine, an analgesic alkaloid from the plant Mitragyna speciosa (kratom), offers a safer alternative to clinical opioids such as morphine, owing to its more favorable side effect profile. Although kratom has been traditionally used for stimulation and pain management in Southeast Asia, the mitragynine biosynthesis pathway has remained elusive. We embarked on a search for mitragynine biosynthetic genes from the transcriptomes of kratom and other members of the Rubiaceae family. We studied their functions in vitro and in vivo. Our investigations led to the identification of several reductases and an enol methyltransferase that forms a new clade within the SABATH methyltransferase family. Furthermore, we discovered a methyltransferase from Hamelia patens (firebush), which catalyzes the final step. With the tryptamine 4-hydroxylase from the psychedelic mushroom Psilocybe cubensis, we accomplished the four-step biosynthesis for mitragynine and its stereoisomer, speciogynine in both yeast and Escherichia coli when supplied with tryptamine and secologanin. Although we have yet to pinpoint the authentic hydroxylase and methyltransferase in kratom, our discovery completes the mitragynine biosynthesis. Through these breakthroughs, we achieved the microbial biosynthesis of kratom opioids for the first time. The remarkable enzyme promiscuity suggests the possibility of generating derivatives and analogs of kratom opioids in heterologous systems.
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Affiliation(s)
- Kyunghee Kim
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | | | | | - Jack Edward Carlisle
- Department of Chemistry, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada
| | - Jun Guo
- Department of Chemistry, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada
| | - Vincenzo De Luca
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Yang Qu
- Department of Chemistry, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada
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15
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Wu Y, Liu C, Koganitsky A, Gong FL, Li S. Discovering Dynamic Plant Enzyme Complexes in Yeast for Kratom Alkaloid Pathway Identification. Angew Chem Int Ed Engl 2023; 62:e202307995. [PMID: 37549372 PMCID: PMC10530425 DOI: 10.1002/anie.202307995] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
Discovering natural product biosynthetic pathways of medicinal plants is challenging and laborious. Capturing the coregulation patterns of pathway enzymes, particularly transcriptomic regulation, has proven an effective method to accelerate pathway identification. In this study, we developed a yeast-based screening method to capture the protein-protein interactions (PPI) between plant enzymes, which is another useful pattern to complement the prevalent approach. Combining this method with plant multiomics analysis, we discovered four enzyme complexes and their organized pathways from kratom, an alkaloid-producing plant. The four pathway branches involved six enzymes, including a strictosidine synthase, a strictosidine β-D-glucosidase (MsSGD), and four medium-chain dehydrogenase/reductases (MsMDRs). PPI screening selected six MsMDRs interacting with MsSGD from 20 candidates predicted by multiomics analysis. Four of the six MsMDRs were then characterized as functional, indicating the high selectivity of the PPI screening method. This study highlights the opportunity of leveraging post-translational regulation features to discover novel plant natural product biosynthetic pathways.
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Affiliation(s)
- Yinan Wu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Chang Liu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Anna Koganitsky
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Franklin L Gong
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Sijin Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
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16
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Salim V, Jarecki SA, Vick M, Miller R. Advances in Metabolic Engineering of Plant Monoterpene Indole Alkaloids. BIOLOGY 2023; 12:1056. [PMID: 37626942 PMCID: PMC10452178 DOI: 10.3390/biology12081056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023]
Abstract
Monoterpene indole alkaloids (MIAs) encompass a diverse family of over 3000 plant natural products with a wide range of medical applications. Further utilizations of these compounds, however, are hampered due to low levels of abundance in their natural sources, causing difficult isolation and complex multi-steps in uneconomical chemical syntheses. Metabolic engineering of MIA biosynthesis in heterologous hosts is attractive, particularly for increasing the yield of natural products of interest and expanding their chemical diversity. Here, we review recent advances and strategies which have been adopted to engineer microbial and plant systems for the purpose of generating MIAs and discuss the current issues and future developments of manufacturing MIAs by synthetic biology approaches.
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Affiliation(s)
- Vonny Salim
- Department of Biological Sciences, Louisiana State University Shreveport, Shreveport, LA 71115, USA; (S.-A.J.); (M.V.)
| | - Sara-Alexis Jarecki
- Department of Biological Sciences, Louisiana State University Shreveport, Shreveport, LA 71115, USA; (S.-A.J.); (M.V.)
| | - Marshall Vick
- Department of Biological Sciences, Louisiana State University Shreveport, Shreveport, LA 71115, USA; (S.-A.J.); (M.V.)
| | - Ryan Miller
- School of Medicine, Louisiana State University Health New Orleans, New Orleans, LA 70112, USA;
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17
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Li C, Wood JC, Vu AH, Hamilton JP, Rodriguez Lopez CE, Payne RME, Serna Guerrero DA, Gase K, Yamamoto K, Vaillancourt B, Caputi L, O'Connor SE, Robin Buell C. Single-cell multi-omics in the medicinal plant Catharanthus roseus. Nat Chem Biol 2023:10.1038/s41589-023-01327-0. [PMID: 37188960 PMCID: PMC10374443 DOI: 10.1038/s41589-023-01327-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
Advances in omics technologies now permit the generation of highly contiguous genome assemblies, detection of transcripts and metabolites at the level of single cells and high-resolution determination of gene regulatory features. Here, using a complementary, multi-omics approach, we interrogated the monoterpene indole alkaloid (MIA) biosynthetic pathway in Catharanthus roseus, a source of leading anticancer drugs. We identified clusters of genes involved in MIA biosynthesis on the eight C. roseus chromosomes and extensive gene duplication of MIA pathway genes. Clustering was not limited to the linear genome, and through chromatin interaction data, MIA pathway genes were present within the same topologically associated domain, permitting the identification of a secologanin transporter. Single-cell RNA-sequencing revealed sequential cell-type-specific partitioning of the leaf MIA biosynthetic pathway that, when coupled with a single-cell metabolomics approach, permitted the identification of a reductase that yields the bis-indole alkaloid anhydrovinblastine. We also revealed cell-type-specific expression in the root MIA pathway.
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Affiliation(s)
- Chenxin Li
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Joshua C Wood
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Anh Hai Vu
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - John P Hamilton
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | | | - Richard M E Payne
- The John Innes Centre, Department of Biological Chemistry, Norwich Research Park, Norwich, UK
| | | | - Klaus Gase
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Kotaro Yamamoto
- School of Science, Association of International Arts and Science, Yokohama City University, Yokohama, Japan
| | | | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany.
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany.
| | - C Robin Buell
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA.
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA.
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18
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Schotte C, Jiang Y, Grzech D, Dang TTT, Laforest LC, León F, Mottinelli M, Nadakuduti SS, McCurdy CR, O’Connor SE. Directed Biosynthesis of Mitragynine Stereoisomers. J Am Chem Soc 2023; 145:4957-4963. [PMID: 36883326 PMCID: PMC9999412 DOI: 10.1021/jacs.2c13644] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Indexed: 02/24/2023]
Abstract
Mitragyna speciosa ("kratom") is used as a natural remedy for pain and management of opioid dependence. The pharmacological properties of kratom have been linked to a complex mixture of monoterpene indole alkaloids, most notably mitragynine. Here, we report the central biosynthetic steps responsible for the scaffold formation of mitragynine and related corynanthe-type alkaloids. We illuminate the mechanistic basis by which the key stereogenic center of this scaffold is formed. These discoveries were leveraged for the enzymatic production of mitragynine, the C-20 epimer speciogynine, and fluorinated analogues.
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Affiliation(s)
- Carsten Schotte
- Department
of Natural Product Biosynthesis, Max Planck
Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Yindi Jiang
- Department
of Natural Product Biosynthesis, Max Planck
Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Dagny Grzech
- Department
of Natural Product Biosynthesis, Max Planck
Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Thu-Thuy T. Dang
- Department
of Natural Product Biosynthesis, Max Planck
Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Larissa C. Laforest
- Plant
Molecular and Cell Biology Program, University
of Florida, Gainesville, Florida 32606, United States
| | - Francisco León
- Department
of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Marco Mottinelli
- Department
of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Satya Swathi Nadakuduti
- Plant
Molecular and Cell Biology Program, University
of Florida, Gainesville, Florida 32606, United States
- Department
of Environmental Horticulture, University
of Florida, Gainesville, Florida 32606, United
States
| | - Christopher R. McCurdy
- Department
of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Sarah E. O’Connor
- Department
of Natural Product Biosynthesis, Max Planck
Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
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19
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Lemos Cruz P, Carqueijeiro I, Koudounas K, Bomzan DP, Stander EA, Abdallah C, Kulagina N, Oudin A, Lanoue A, Giglioli-Guivarc'h N, Nagegowda DA, Papon N, Besseau S, Clastre M, Courdavault V. Identification of a second 16-hydroxytabersonine-O-methyltransferase suggests an evolutionary relationship between alkaloid and flavonoid metabolisms in Catharanthus roseus. PROTOPLASMA 2023; 260:607-624. [PMID: 35947213 DOI: 10.1007/s00709-022-01801-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
The medicinal plant Catharanthus roseus biosynthesizes many important drugs for human health, including the anticancer monoterpene indole alkaloids (MIAs) vinblastine and vincristine. Over the past decades, the continuous increase in pharmaceutical demand has prompted several research groups to characterize MIA biosynthetic pathways for considering future metabolic engineering processes of supply. In line with previous work suggesting that diversification can potentially occur at various steps along the vindoline branch, we were here interested in investigating the involvement of distinct isoforms of tabersonine-16-O-methyltransferase (16OMT) which plays a pivotal role in the MIA biosynthetic pathway. By combining homology searches based on the previously characterized 16OMT1, phylogenetic analyses, functional assays in yeast, and biochemical and in planta characterizations, we identified a second isoform of 16OMT, referred to as 16OMT2. 16OMT2 appears to be a multifunctional enzyme working on both MIA and flavonoid substrates, suggesting that a constrained evolution of the enzyme for accommodating the MIA substrate has probably occurred to favor the apparition of 16OMT2 from an ancestral specific flavonoid-O-methyltransferase. Since 16OMT1 and 16OMT2 displays a high sequence identity and similar kinetic parameters for 16-hydroxytabersonine, we postulate that 16OMT1 may result from a later 16OMT2 gene duplication accompanied by a continuous neofunctionalization leading to an almost complete loss of flavonoid O-methyltransferase activity. Overall, these results participate in increasing our knowledge on the evolutionary processes that have likely led to enzyme co-optation for MIA synthesis.
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Affiliation(s)
- Pamela Lemos Cruz
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Ines Carqueijeiro
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | | | - Dikki Pedenla Bomzan
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru, 560065, India
| | - Emily Amor Stander
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Cécile Abdallah
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Natalja Kulagina
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Audrey Oudin
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Arnaud Lanoue
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | | | - Dinesh A Nagegowda
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru, 560065, India
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR, ICAT, F-49000, Angers, France
| | - Sébastien Besseau
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Marc Clastre
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France
| | - Vincent Courdavault
- Université de Tours, EA2106 "Biomolécules et Biotechnologies Végétales", Tours, France.
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20
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Wu Y, Liu C, Gong FL, Li S. Discovering dynamic plant enzyme complexes in yeast for novel alkaloid pathway identification from a medicinal plant kratom. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524293. [PMID: 36711573 PMCID: PMC9882157 DOI: 10.1101/2023.01.16.524293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Discovering natural product biosynthetic pathways from medicinal plants is challenging and laborious, largely due to the complexity of the transcriptomics-driven pathway prediction process. Here we developed a novel approach that captures the protein-level connections between enzymes for pathway discovery with improved accuracy. We proved that heterologous protein-protein interaction screening in yeast enabled the efficient discovery of both dynamic plant enzyme complexes and the pathways they organize. This approach discovered complexes and pathways in the monoterpene indole alkaloid metabolism of a medicinal plant, kratom with high success rate. Screening using a strictosidine β-D-glucosidase (MsSGD1) against 19 medium-chain dehydrogenase/reductases (MsMDRs) identified five MsSGD1-MsMDR complexes. Three out of the five interacting MsMDRs were then proven functional, while the remaining 14 non-interacting candidates did not show obvious activities. The work discovered three branched pathways by combining transcriptomics, metabolomics, and heterologous PPI screening and demonstrated a new plant pathway discovery strategy.
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Affiliation(s)
| | | | - Franklin L. Gong
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Sijin Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
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21
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Stander EA, Cuello C, Birer-Williams C, Kulagina N, Jansen HJ, Carqueijeiro I, Méteignier LV, Vergès V, Oudin A, Papon N, Dirks RP, Jensen MK, O’Connor SE, Dugé de Bernonville T, Besseau S, Courdavault V. The Vinca minor genome highlights conserved evolutionary traits in monoterpene indole alkaloid synthesis. G3 (BETHESDA, MD.) 2022; 12:jkac268. [PMID: 36200869 PMCID: PMC9713385 DOI: 10.1093/g3journal/jkac268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 09/28/2022] [Indexed: 11/26/2023]
Abstract
Vinca minor, also known as the lesser periwinkle, is a well-known species from the Apocynaceae, native to central and southern Europe. This plant synthesizes monoterpene indole alkaloids, which are a class of specialized metabolites displaying a wide range of bioactive- and pharmacologically important properties. Within the almost 50 monoterpene indole alkaloids it produces, V. minor mainly accumulates vincamine, which is commercially used as a nootropic. Using a combination of Oxford Nanopore Technologies long read- and Illumina short-read sequencing, a 679,098 Mb V. minor genome was assembled into 296 scaffolds with an N50 scaffold length of 6 Mb, and encoding 29,624 genes. These genes were functionally annotated and used in a comparative genomic analysis to establish gene families and to investigate gene family expansion and contraction across the phylogenetic tree. Furthermore, homology-based monoterpene indole alkaloid gene predictions together with a metabolic analysis across 4 different V. minor tissue types guided the identification of candidate monoterpene indole alkaloid genes. These candidates were finally used to identify monoterpene indole alkaloid gene clusters, which combined with synteny analysis allowed for the discovery of a functionally validated vincadifformine-16-hydroxylase, reinforcing the potential of this dataset for monoterpene indole alkaloids gene discovery. It is expected that access to these resources will facilitate the elucidation of unknown monoterpene indole alkaloid biosynthetic routes with the potential of transferring these pathways to heterologous expression systems for large-scale monoterpene indole alkaloid production.
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Affiliation(s)
- Emily Amor Stander
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Clément Cuello
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | | | - Natalja Kulagina
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Hans J Jansen
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands
| | - Ines Carqueijeiro
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | | | - Valentin Vergès
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Audrey Oudin
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Ron P Dirks
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Sarah Ellen O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | | | - Sébastien Besseau
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, EA2106, Université de Tours, 37200 Tours, France
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22
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Langley C, Tatsis E, Hong B, Nakamura Y, Paetz C, Stevenson CEM, Basquin J, Lawson DM, Caputi L, O'Connor SE. Expansion of the Catalytic Repertoire of Alcohol Dehydrogenases in Plant Metabolism. Angew Chem Int Ed Engl 2022; 61:e202210934. [PMID: 36198083 PMCID: PMC9828224 DOI: 10.1002/anie.202210934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 11/19/2022]
Abstract
Medium-chain alcohol dehydrogenases (ADHs) comprise a highly conserved enzyme family that catalyse the reversible reduction of aldehydes. However, recent discoveries in plant natural product biosynthesis suggest that the catalytic repertoire of ADHs has been expanded. Here we report the crystal structure of dihydroprecondylocarpine acetate synthase (DPAS), an ADH that catalyses the non-canonical 1,4-reduction of an α,β-unsaturated iminium moiety. Comparison with structures of plant-derived ADHs suggest the 1,4-iminium reduction does not require a proton relay or the presence of a catalytic zinc ion in contrast to canonical 1,2-aldehyde reducing ADHs that require the catalytic zinc and a proton relay. Furthermore, ADHs that catalysed 1,2-iminium reduction required the presence of the catalytic zinc and the loss of the proton relay. This suggests how the ADH active site can be modified to perform atypical carbonyl reductions, providing insight into how chemical reactions are diversified in plant metabolism.
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Affiliation(s)
- Chloe Langley
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
| | - Evangelos Tatsis
- Chinese Academy of Sciences Centre for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and Ecology300 Feng Lin RoadShanghai200032China
| | - Benke Hong
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
| | - Yoko Nakamura
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany,Research Group Biosynthesis and NMRMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
| | - Christian Paetz
- Research Group Biosynthesis and NMRMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
| | - Clare E. M. Stevenson
- Department of Biochemistry and MetabolismJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Jerome Basquin
- Department of Structural Cell BiologyMax-Planck Institute for BiochemistryAm Klopferspitz 18, Martinsried82152PlaneggGermany
| | - David M. Lawson
- Department of Biochemistry and MetabolismJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Lorenzo Caputi
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
| | - Sarah E. O'Connor
- Department of Natural Product BiosynthesisMax Planck Institute for Chemical EcologyHans-Knöll Straße 8Jena07745Germany
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23
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Kamileen MO, DeMars MD, Hong B, Nakamura Y, Paetz C, Lichman BR, Sonawane PD, Caputi L, O'Connor SE. Recycling Upstream Redox Enzymes Expands the Regioselectivity of Cycloaddition in Pseudo-Aspidosperma Alkaloid Biosynthesis. J Am Chem Soc 2022; 144:19673-19679. [PMID: 36240425 PMCID: PMC9634793 DOI: 10.1021/jacs.2c08107] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Nature uses cycloaddition reactions to generate complex natural product scaffolds. Dehydrosecodine is a highly reactive biosynthetic intermediate that undergoes cycloaddition to generate several alkaloid scaffolds that are the precursors to pharmacologically important compounds such as vinblastine and ibogaine. Here we report how dehydrosecodine can be subjected to redox chemistry, which in turn allows cycloaddition reactions with alternative regioselectivity. By incubating dehydrosecodine with reductase and oxidase biosynthetic enzymes that act upstream in the pathway, we can access the rare pseudoaspidosperma alkaloids pseudo-tabersonine and pseudo-vincadifformine, both in vitro and by reconstitution in the plant Nicotiana benthamiana from an upstream intermediate. We propose a stepwise mechanism to explain the formation of the pseudo-tabersonine scaffold by structurally characterizing enzyme intermediates and by monitoring the incorporation of deuterium labels. This discovery highlights how plants use redox enzymes to enantioselectively generate new scaffolds from common precursors.
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Affiliation(s)
- Mohamed O Kamileen
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany.,Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, U.K
| | - Matthew D DeMars
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Benke Hong
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Yoko Nakamura
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany.,Research Group Biosynthesis and NMR, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Christian Paetz
- Research Group Biosynthesis and NMR, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, U.K
| | - Prashant D Sonawane
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
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24
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Reconstitution of monoterpene indole alkaloid biosynthesis in genome engineered Nicotiana benthamiana. Commun Biol 2022; 5:949. [PMID: 36088516 PMCID: PMC9464250 DOI: 10.1038/s42003-022-03904-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/25/2022] [Indexed: 12/17/2022] Open
Abstract
Monoterpene indole alkaloids (MIAs) are a diverse class of plant natural products that include a number of medicinally important compounds. We set out to reconstitute the pathway for strictosidine, a key intermediate of all MIAs, from central metabolism in Nicotiana benthamiana. A disadvantage of this host is that its rich background metabolism results in the derivatization of some heterologously produced molecules. Here we use transcriptomic analysis to identify glycosyltransferases that are upregulated in response to biosynthetic intermediates and produce plant lines with targeted mutations in the genes encoding them. Expression of the early MIA pathway in these lines produces a more favorable product profile. Strictosidine biosynthesis was successfully reconstituted, with the best yields obtained by the co-expression of 14 enzymes, of which a major latex protein-like enzyme (MLPL) from Nepeta (catmint) is critical for improving flux through the iridoid pathway. The removal of endogenous glycosyltransferases does not impact the yields of strictosidine, highlighting that the metabolic flux of the pathway enzymes to a stable biosynthetic intermediate minimizes the need to engineer the endogenous metabolism of the host. The production of strictosidine in planta expands the range of MIA products amenable to biological synthesis. The biosynthesis of strictosidine, a key intermediate of monoterpene indole alkaloids, was successfully reconstructed in Nicotiana benthamiana, demonstrating the potential of Nicotiana benthamiana as a bioproduction chassis for small molecules.
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25
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Hong B, Grzech D, Caputi L, Sonawane P, López CER, Kamileen MO, Hernández Lozada NJ, Grabe V, O'Connor SE. Biosynthesis of strychnine. Nature 2022; 607:617-622. [PMID: 35794473 PMCID: PMC9300463 DOI: 10.1038/s41586-022-04950-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/08/2022] [Indexed: 11/08/2022]
Abstract
Strychnine is a natural product that, through isolation, structural elucidation and synthetic efforts, shaped the field of organic chemistry. Currently, strychnine is used as a pesticide to control rodents1 because of its potent neurotoxicity2,3. The polycyclic architecture of strychnine has inspired chemists to develop new synthetic transformations and strategies to access this molecular scaffold4, yet it is still unknown how plants create this complex structure. Here we report the biosynthetic pathway of strychnine, along with the related molecules brucine and diaboline. Moreover, we successfully recapitulate strychnine, brucine and diaboline biosynthesis in Nicotiana benthamiana from an upstream intermediate, thus demonstrating that this complex, pharmacologically active class of compounds can now be harnessed through metabolic engineering approaches.
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Affiliation(s)
- Benke Hong
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Dagny Grzech
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Prashant Sonawane
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Carlos E Rodríguez López
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Mohamed Omar Kamileen
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Néstor J Hernández Lozada
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Veit Grabe
- Microscopic Imaging Service Group, Max-Planck Institute for Chemical Ecology, Jena, Germany
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany.
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26
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Kulagina N, Méteignier LV, Papon N, O'Connor SE, Courdavault V. More than a Catharanthus plant: A multicellular and pluri-organelle alkaloid-producing factory. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102200. [PMID: 35339956 DOI: 10.1016/j.pbi.2022.102200] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/14/2022] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Plants represent a huge reservoir of natural products. A broad series of these compounds now find application for human health. In this respect, the monoterpene indole alkaloids (MIAs), particularly from Madagascar periwinkle, are a prominent example of plant specialized metabolites with an important therapeutic potential. However, the supply of MIA drugs has always been a challenge since the low-yield accumulation in planta. This mainly results from the complex architecture of the MIA biosynthetic pathway that involves several organs, tissue types and subcellular organelles. Here, we describe the most recent advances towards the elucidation of this pathway route as well as its spatial organization in planta. Besides allowing a better understanding of the MIA biosynthetic flux in the whole plant, such knowledge will also probably pave the way for the development of metabolic engineering strategies to sustain the MIA supply.
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Affiliation(s)
- Natalja Kulagina
- Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, Tours, France
| | | | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, F-49000 Angers, France
| | - Sarah Ellen O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany.
| | - Vincent Courdavault
- Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, Tours, France.
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27
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Koudounas K, Guirimand G, Hoyos LFR, Carqueijeiro I, Cruz PL, Stander E, Kulagina N, Perrin J, Oudin A, Besseau S, Lanoue A, Atehortùa L, St-Pierre B, Giglioli-Guivarc'h N, Papon N, O'Connor SE, Courdavault V. Tonoplast and Peroxisome Targeting of γ-tocopherol N-methyltransferase Homologs Involved in the Synthesis of Monoterpene Indole Alkaloids. PLANT & CELL PHYSIOLOGY 2022; 63:200-216. [PMID: 35166361 DOI: 10.1093/pcp/pcab160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 06/14/2023]
Abstract
Many plant species from the Apocynaceae, Loganiaceae and Rubiaceae families evolved a specialized metabolism leading to the synthesis of a broad palette of monoterpene indole alkaloids (MIAs). These compounds are believed to constitute a cornerstone of the plant chemical arsenal but above all several MIAs display pharmacological properties that have been exploited for decades by humans to treat various diseases. It is established that MIAs are produced in planta due to complex biosynthetic pathways engaging a multitude of specialized enzymes but also a complex tissue and subcellular organization. In this context, N-methyltransferases (NMTs) represent an important family of enzymes indispensable for MIA biosynthesis but their characterization has always remained challenging. In particular, little is known about the subcellular localization of NMTs in MIA-producing plants. Here, we performed an extensive analysis on the subcellular localization of NMTs from four distinct medicinal plants but also experimentally validated that two putative NMTs from Catharanthus roseus exhibit NMT activity. Apart from providing unprecedented data regarding the targeting of these enzymes in planta, our results point out an additional layer of complexity to the subcellular organization of the MIA biosynthetic pathway by introducing tonoplast and peroxisome as new actors of the final steps of MIA biosynthesis.
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Affiliation(s)
- Konstantinos Koudounas
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | | | - Luisa Fernanda Rojas Hoyos
- Grupo de Biotransformación-Escuela de Microbiología, Universidad de Antioquia, Calle 70 No 52-21, A.A 1226, Medellín, Colombia
| | - Ines Carqueijeiro
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Pamela Lemos Cruz
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Emily Stander
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Natalja Kulagina
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Jennifer Perrin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Audrey Oudin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Sébastien Besseau
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Arnaud Lanoue
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Lucia Atehortùa
- Laboratorio de Biotecnología, Sede de Investigación Universitaria, Universidad de Antioquia, Medellin 50010, Colombia
| | - Benoit St-Pierre
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | | | - Nicolas Papon
- GEIHP, SFR ICAT, University of Angers, Université de Bretagne Occidentale, 4 rue de Larrey - F49933, Angers 49000, France
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
- Graduate School of Sciences, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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28
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Liu T, Gou Y, Zhang B, Gao R, Dong C, Qi M, Jiang L, Ding X, Li C, Lian J. Construction of Ajmalicine and Sanguinarine
de novo
Biosynthetic Pathways using Stable Integration Sites in Yeast. Biotechnol Bioeng 2022; 119:1314-1326. [DOI: 10.1002/bit.28040] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/22/2021] [Accepted: 01/02/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Tengfei Liu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
| | - Bei Zhang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Rui Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
| | - Chang Dong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
| | - Mingming Qi
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Lihong Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Xuanwei Ding
- 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 100081 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 100081 China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
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29
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Boccia M, Grzech D, Lopes AA, O’Connor SE, Caputi L. Directed Biosynthesis of New to Nature Alkaloids in a Heterologous Nicotiana benthamiana Expression Host. FRONTIERS IN PLANT SCIENCE 2022; 13:919443. [PMID: 35812900 PMCID: PMC9257203 DOI: 10.3389/fpls.2022.919443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/24/2022] [Indexed: 05/17/2023]
Abstract
Plants produce a wide variety of pharmacologically active molecules classified as natural products. Derivatization of these natural products can modulate or improve the bioactivity of the parent compound. Unfortunately, chemical derivatization of natural products is often difficult or impractical. Here we use the newly discovered biosynthetic genes for two monoterpene indole alkaloids, alstonine and stemmadenine acetate, to generate analogs of these compounds. We reconstitute these biosynthetic genes in the heterologous host Nicotiana benthamiana along with an unnatural starting substrate to produce the corresponding new-to-nature alkaloid product.
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Affiliation(s)
- Marianna Boccia
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Dagny Grzech
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Adriana A. Lopes
- Biotechnology Unit, Universidade de Ribeirão Preto (UNAERP), Ribeirão Preto, Brazil
| | - Sarah E. O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
- *Correspondence: Sarah E. O’Connor,
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
- Lorenzo Caputi,
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30
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Singh SK, Patra B, Singleton JJ, Liu Y, Paul P, Sui X, Suttipanta N, Pattanaik S, Yuan L. Identification and Characterization of Transcription Factors Regulating Terpenoid Indole Alkaloid Biosynthesis in Catharanthus roseus. Methods Mol Biol 2022; 2505:203-221. [PMID: 35732947 DOI: 10.1007/978-1-0716-2349-7_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Biosynthesis of the therapeutically valuable terpenoid indole alkaloids (TIAs), in the medicinal plant Catharanthus roseus, is one of the most elaborate and complex metabolic processes. Although genomic and transcriptomic resources have significantly accelerated gene discovery in the TIA pathway, relatively few genes of transcription factors (TFs) have been identified and characterized thus far. Systematic identification of TFs and elucidation of their functions are crucial for understanding TIA pathway regulation. The successful discovery of TFs in the TIA pathway has relied mostly on three different approaches, (1) identification of cis-regulatory motifs (CRMs) present in the pathway gene promoters as they often provide clues on potential TFs that bind to the promoters, (2) co-expression analysis, based on the assumption that TFs regulating a metabolic or developmental pathway exhibit similar spatiotemporal expression as the pathway genes, and (3) isolation of homologs of TFs known to regulate structurally similar or diverse specialized metabolites in different plant species. TFs regulating TIA pathway have been isolated using either an individual or a combination of the three approaches. Here we describe transcriptome-based coexpression analysis and cis-element determination to identify TFs in C. roseus. In addition, we describe the protocols for generation of transgenic hairy roots, Agrobacterium infiltration of flowers, and electrophoretic mobility shift assay (EMSA). The methods described here are useful for the identification and characterization of potential TFs involved in the regulation of special metabolism in other medicinal plants.
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Affiliation(s)
- Sanjay K Singh
- Department of Plant and Soil Sciences, and the Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, USA
| | - Barunava Patra
- Department of Plant and Soil Sciences, and the Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, USA
| | - Joshua J Singleton
- Department of Plant and Soil Sciences, and the Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, USA
| | - Yongliang Liu
- Department of Plant and Soil Sciences, and the Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, USA
| | - Priyanka Paul
- Department of Plant and Soil Sciences, and the Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, USA
| | - Xueyi Sui
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Nitima Suttipanta
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ubon Ratchathani University, Ubonratchathani, Thailand
| | - Sitakanta Pattanaik
- Department of Plant and Soil Sciences, and the Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, USA.
| | - Ling Yuan
- Department of Plant and Soil Sciences, and the Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, USA.
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Farzana M, Shahsavarani M, De Luca V, Qu Y. Studying Iridoid Transport in Catharanthus roseus by Grafting. Methods Mol Biol 2022; 2505:69-77. [PMID: 35732937 DOI: 10.1007/978-1-0716-2349-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The plant Catharanthus roseus is well known for its spatial separation of iridoid and monoterpenoid indole alkaloid (MIA) biosynthesis at both intracellular and intercellular levels, collectively suggested by RNA in situ hybridization, enzymatic and transcriptomic studies using leaf epidermis, and fluorescent protein tagging studies. Although documented in other plant species, the long-distance transport of iridoid glycosides, such as secologanin, has not been known in C. roseus until a recent study suggested that secologanin is transported from root to shoot, by grafting low iridoid/MIA mutant scions onto wild-type stock plants. This chapter describes the in vitro cultivation of C. roseus plants and grafting techniques to enable studies concerning iridoid/MIA transport between organs. The iridoid and MIA analysis methods are also provided.
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Affiliation(s)
- Maisha Farzana
- Department of Chemistry, University of New Brunswick, Fredericton, NB, Canada
| | | | - Vincenzo De Luca
- Department of Biological Sciences, Brock University, St. Catharines, ON, Canada
| | - Yang Qu
- Department of Chemistry, University of New Brunswick, Fredericton, NB, Canada.
- Department of Chemical Engineering, University of New Brunswick, Fredericton, NB, Canada.
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32
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Biosynthesis and Modulation of Terpenoid Indole Alkaloids in Catharanthus roseus: A Review of Targeting Genes and Secondary Metabolites. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.4.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The medicinal plant C. roseus synthesizes biologically active alkaloids via the terpenoid indole alkaloid (TIAs) biosynthetic pathway. Most of these alkaloids have high therapeutic value, such as vinblastine and vincristine. Plant signaling components, plant hormones, precursors, growth hormones, prenylated proteins, and transcriptomic factors regulate the complex networks of TIA biosynthesis. For many years, researchers have been evaluating the scientific value of the TIA biosynthetic pathway and its potential in commercial applications for market opportunities. Metabolic engineering has revealed the major blocks in metabolic pathways regulated at the molecular level, unknown structures, metabolites, genes, enzyme expression, and regulatory genes. Conceptually, this information is necessary to create transgenic plants and microorganisms for the commercial production of high-value dimer alkaloids, such as vinca alkaloids, vinblastine, and vincristine In this review, we present current knowledge of the regulatory mechanisms of these components in the C. roseus TIA pathway, from genes to metabolites.
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Liu Y, Patra B, Singh SK, Paul P, Zhou Y, Li Y, Wang Y, Pattanaik S, Yuan L. Terpenoid indole alkaloid biosynthesis in Catharanthus roseus: effects and prospects of environmental factors in metabolic engineering. Biotechnol Lett 2021; 43:2085-2103. [PMID: 34564757 PMCID: PMC8510960 DOI: 10.1007/s10529-021-03179-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/28/2021] [Indexed: 11/10/2022]
Abstract
Plants synthesize a vast array of specialized metabolites that primarily contribute to their defense and survival under adverse conditions. Many of the specialized metabolites have therapeutic values as drugs. Biosynthesis of specialized metabolites is affected by environmental factors including light, temperature, drought, salinity, and nutrients, as well as pathogens and insects. These environmental factors trigger a myriad of changes in gene expression at the transcriptional and posttranscriptional levels. The dynamic changes in gene expression are mediated by several regulatory proteins that perceive and transduce the signals, leading to up- or down-regulation of the metabolic pathways. Exploring the environmental effects and related signal cascades is a strategy in metabolic engineering to produce valuable specialized metabolites. However, mechanistic studies on environmental factors affecting specialized metabolism are limited. The medicinal plant Catharanthus roseus (Madagascar periwinkle) is an important source of bioactive terpenoid indole alkaloids (TIAs), including the anticancer therapeutics vinblastine and vincristine. The emerging picture shows that various environmental factors significantly alter TIA accumulation by affecting the expression of regulatory and enzyme-encoding genes in the pathway. Compared to our understanding of the TIA pathway in response to the phytohormone jasmonate, the impacts of environmental factors on TIA biosynthesis are insufficiently studied and discussed. This review thus focuses on these aspects and discusses possible strategies for metabolic engineering of TIA biosynthesis. PURPOSE OF WORK: Catharanthus roseus is a rich source of bioactive terpenoid indole alkaloids (TIAs). The objective of this work is to present a comprehensive account of the influence of various biotic and abiotic factors on TIA biosynthesis and to discuss possible strategies to enhance TIA production through metabolic engineering.
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Affiliation(s)
- Yongliang Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Barunava Patra
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Sanjay Kumar Singh
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Priyanka Paul
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Yan Zhou
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Yongqing Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Sitakanta Pattanaik
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Ling Yuan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
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Nguyen TD. Gene discovery in plant metabolism: Listening to the sound of silence, but where? PLANT PHYSIOLOGY 2021; 187:670-672. [PMID: 34608980 PMCID: PMC8491014 DOI: 10.1093/plphys/kiab357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
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
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Yamamoto K, Grzech D, Koudounas K, Stander EA, Caputi L, Mimura T, Courdavault V, O’Connor SE. Improved virus-induced gene silencing allows discovery of a serpentine synthase gene in Catharanthus roseus. PLANT PHYSIOLOGY 2021; 187:846-857. [PMID: 34608956 PMCID: PMC8491018 DOI: 10.1093/plphys/kiab285] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/31/2021] [Indexed: 05/28/2023]
Abstract
Specialized metabolites are chemically complex small molecules with a myriad of biological functions. To investigate plant-specialized metabolite biosynthesis more effectively, we developed an improved method for virus-induced gene silencing (VIGS). We designed a plasmid that incorporates fragments of both the target gene and knockdown marker gene (phytoene desaturase, PDS), which identifies tissues that have been successfully silenced in planta. To demonstrate the utility of this method, we used the terpenoid indole alkaloid (TIA) pathway in Madagascar periwinkle (Catharanthus roseus) as a model system. Catharanthus roseus is a medicinal plant well known for producing many bioactive compounds, such as vinblastine and vincristine. Our VIGS method enabled the discovery of a previously unknown biosynthetic enzyme, serpentine synthase (SS). This enzyme is a cytochrome P450 (CYP) that produces the β-carboline alkaloids serpentine and alstonine, compounds with strong blue autofluorescence and potential pharmacological activity. The discovery of this enzyme highlights the complexity of TIA biosynthesis and demonstrates the utility of this improved VIGS method for discovering unidentified metabolic enzymes in plants.
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Affiliation(s)
- Kotaro Yamamoto
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan
| | - Dagny Grzech
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Konstantinos Koudounas
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, Tours 37200, France
| | - Emily Amor Stander
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, Tours 37200, France
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Tetsuro Mimura
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Vincent Courdavault
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, Tours 37200, France
| | - Sarah E. O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
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Jamieson CS, Misa J, Tang Y, Billingsley JM. Biosynthesis and synthetic biology of psychoactive natural products. Chem Soc Rev 2021; 50:6950-7008. [PMID: 33908526 PMCID: PMC8217322 DOI: 10.1039/d1cs00065a] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Psychoactive natural products play an integral role in the modern world. The tremendous structural complexity displayed by such molecules confers diverse biological activities of significant medicinal value and sociocultural impact. Accordingly, in the last two centuries, immense effort has been devoted towards establishing how plants, animals, and fungi synthesize complex natural products from simple metabolic precursors. The recent explosion of genomics data and molecular biology tools has enabled the identification of genes encoding proteins that catalyze individual biosynthetic steps. Once fully elucidated, the "biosynthetic pathways" are often comparable to organic syntheses in elegance and yield. Additionally, the discovery of biosynthetic enzymes provides powerful catalysts which may be repurposed for synthetic biology applications, or implemented with chemoenzymatic synthetic approaches. In this review, we discuss the progress that has been made toward biosynthetic pathway elucidation amongst four classes of psychoactive natural products: hallucinogens, stimulants, cannabinoids, and opioids. Compounds of diverse biosynthetic origin - terpene, amino acid, polyketide - are identified, and notable mechanisms of key scaffold transforming steps are highlighted. We also provide a description of subsequent applications of the biosynthetic machinery, with an emphasis placed on the synthetic biology and metabolic engineering strategies enabling heterologous production.
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Affiliation(s)
- Cooper S Jamieson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Joshua Misa
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Yi Tang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA. and Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - John M Billingsley
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA. and Invizyne Technologies, Inc., Monrovia, CA, USA
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Abstract
Intrinsic fluorescence of nonaromatic amino acids is a puzzling phenomenon with an enormous potential in biophotonic applications. The physical origins of this effect, however, remain elusive. Herein, we demonstrate how specific hydrogen bond networks can modulate fluorescence. We highlight the key role played by short hydrogen bonds, present in the protein structure, on the ensuing fluorescence. We provide detailed experimental and molecular evidence to explain these unusual nonaromatic optical properties. Our findings should benefit the design of novel optically active biomaterials for applications in biosensing and imaging. Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, by employing a combined experimental and computational approach, we show that specific hydrogen bond networks can significantly affect fluorescence. In particular, we reveal that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared with L-glutamine itself. Ab initio molecular dynamics simulations highlight that these short hydrogen bonds prevent the appearance of a conical intersection between the excited and the ground states and thereby significantly decrease nonradiative transition probabilities. Our findings open the door to the design of new photoactive materials with biophotonic applications.
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Colinas M, Pollier J, Vaneechoutte D, Malat DG, Schweizer F, De Milde L, De Clercq R, Guedes JG, Martínez-Cortés T, Molina-Hidalgo FJ, Sottomayor M, Vandepoele K, Goossens A. Subfunctionalization of Paralog Transcription Factors Contributes to Regulation of Alkaloid Pathway Branch Choice in Catharanthus roseus. FRONTIERS IN PLANT SCIENCE 2021; 12:687406. [PMID: 34113373 PMCID: PMC8186833 DOI: 10.3389/fpls.2021.687406] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Catharanthus roseus produces a diverse range of specialized metabolites of the monoterpenoid indole alkaloid (MIA) class in a heavily branched pathway. Recent great progress in identification of MIA biosynthesis genes revealed that the different pathway branch genes are expressed in a highly cell type- and organ-specific and stress-dependent manner. This implies a complex control by specific transcription factors (TFs), only partly revealed today. We generated and mined a comprehensive compendium of publicly available C. roseus transcriptome data for MIA pathway branch-specific TFs. Functional analysis was performed through extensive comparative gene expression analysis and profiling of over 40 MIA metabolites in the C. roseus flower petal expression system. We identified additional members of the known BIS and ORCA regulators. Further detailed study of the ORCA TFs suggests subfunctionalization of ORCA paralogs in terms of target gene-specific regulation and synergistic activity with the central jasmonate response regulator MYC2. Moreover, we identified specific amino acid residues within the ORCA DNA-binding domains that contribute to the differential regulation of some MIA pathway branches. Our results advance our understanding of TF paralog specificity for which, despite the common occurrence of closely related paralogs in many species, comparative studies are scarce.
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Affiliation(s)
- Maite Colinas
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jacob Pollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Dries Vaneechoutte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Deniz G. Malat
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Fabian Schweizer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Liesbeth De Milde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Rebecca De Clercq
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Joana G. Guedes
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairaão, Portugal
- I3S-Instituto de Investigação e Inovação em Saúde, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Teresa Martínez-Cortés
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairaão, Portugal
| | - Francisco J. Molina-Hidalgo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Mariana Sottomayor
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairaão, Portugal
- Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Carqueijeiro I, Koudounas K, Dugé de Bernonville T, Sepúlveda LJ, Mosquera A, Bomzan DP, Oudin A, Lanoue A, Besseau S, Lemos Cruz P, Kulagina N, Stander EA, Eymieux S, Burlaud-Gaillard J, Blanchard E, Clastre M, Atehortùa L, St-Pierre B, Giglioli-Guivarc’h N, Papon N, Nagegowda DA, O’Connor SE, Courdavault V. Alternative splicing creates a pseudo-strictosidine β-d-glucosidase modulating alkaloid synthesis in Catharanthus roseus. PLANT PHYSIOLOGY 2021; 185:836-856. [PMID: 33793899 PMCID: PMC8133614 DOI: 10.1093/plphys/kiaa075] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/24/2020] [Indexed: 05/08/2023]
Abstract
Deglycosylation is a key step in the activation of specialized metabolites involved in plant defense mechanisms. This reaction is notably catalyzed by β-glucosidases of the glycosyl hydrolase 1 (GH1) family such as strictosidine β-d-glucosidase (SGD) from Catharanthus roseus. SGD catalyzes the deglycosylation of strictosidine, forming a highly reactive aglycone involved in the synthesis of cytotoxic monoterpene indole alkaloids (MIAs) and in the crosslinking of aggressor proteins. By exploring C. roseus transcriptomic resources, we identified an alternative splicing event of the SGD gene leading to the formation of a shorter isoform of this enzyme (shSGD) that lacks the last 71-residues and whose transcript ratio with SGD ranges from 1.7% up to 42.8%, depending on organs and conditions. Whereas it completely lacks β-glucosidase activity, shSGD interacts with SGD and causes the disruption of SGD multimers. Such disorganization drastically inhibits SGD activity and impacts downstream MIA synthesis. In addition, shSGD disrupts the metabolic channeling of downstream biosynthetic steps by hampering the recruitment of tetrahydroalstonine synthase in cell nuclei. shSGD thus corresponds to a pseudo-enzyme acting as a regulator of MIA biosynthesis. These data shed light on a peculiar control mechanism of β-glucosidase multimerization, an organization common to many defensive GH1 members.
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Affiliation(s)
- Inês Carqueijeiro
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Konstantinos Koudounas
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | | | - Liuda Johana Sepúlveda
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
- Laboratorio de Biotecnología, Universidad de Antioquia, Sede de Investigación Universitaria, 50010 Medellin, Colombia
| | - Angela Mosquera
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
- Laboratorio de Biotecnología, Universidad de Antioquia, Sede de Investigación Universitaria, 50010 Medellin, Colombia
| | - Dikki Pedenla Bomzan
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India
| | - Audrey Oudin
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Arnaud Lanoue
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Sébastien Besseau
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Pamela Lemos Cruz
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Natalja Kulagina
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Emily A Stander
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Sébastien Eymieux
- INSERM U1259, Plateforme IBiSA de Microscopie Electronique, Université de Tours, 37200 Tours, France
| | - Julien Burlaud-Gaillard
- INSERM U1259, Plateforme IBiSA de Microscopie Electronique, Université de Tours, 37200 Tours, France
| | - Emmanuelle Blanchard
- INSERM U1259, Plateforme IBiSA de Microscopie Electronique, Université de Tours, 37200 Tours, France
- Centre Hospitalier Régional de Tours, 37170 Tours, France
| | - Marc Clastre
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | - Lucia Atehortùa
- Laboratorio de Biotecnología, Universidad de Antioquia, Sede de Investigación Universitaria, 50010 Medellin, Colombia
| | - Benoit St-Pierre
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
| | | | - Nicolas Papon
- EA3142 “Groupe d'Etude des Interactions Hôte-Pathogène,” Université d’Angers, 49035 Angers, France
| | - Dinesh A Nagegowda
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India
| | - Sarah E O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Vincent Courdavault
- EA2106 “Biomolécules et Biotechnologies Végétales,” Université de Tours, 37200 Tours, France
- Author for communication:
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40
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Qiu F, Yan Y, Zeng J, Huang JP, Zeng L, Zhong W, Lan X, Chen M, Huang SX, Liao Z. Biochemical and Metabolic Insights into Hyoscyamine Dehydrogenase. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04667] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fei Qiu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Yijun Yan
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Junlan Zeng
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jian-Ping Huang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Lingjiang Zeng
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Wei Zhong
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiaozhong Lan
- TAAHC-SWU Medicinal Plant Joint R&D Centre, Tibetan Collaborative Innovation Centre of Agricultural and Animal Husbandry Resources, Xizang Agricultural and Animal Husbandry College, Nyingchi of Tibet 860000, China
| | - Min Chen
- College of Pharmaceutical Sciences, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Ministry of Education), Southwest University, Chongqing 400715, China
| | - Sheng-Xiong Huang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Zhihua Liao
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing 400715, China
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Stander EA, Sepúlveda LJ, Dugé de Bernonville T, Carqueijeiro I, Koudounas K, Lemos Cruz P, Besseau S, Lanoue A, Papon N, Giglioli-Guivarc’h N, Dirks R, O’Connor SE, Atehortùa L, Oudin A, Courdavault V. Identifying Genes Involved in alkaloid Biosynthesis in Vinca minor Through Transcriptomics and Gene Co-Expression Analysis. Biomolecules 2020; 10:biom10121595. [PMID: 33255314 PMCID: PMC7761029 DOI: 10.3390/biom10121595] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 12/19/2022] Open
Abstract
The lesser periwinkle Vinca minor accumulates numerous monoterpene indole alkaloids (MIAs) including the vasodilator vincamine. While the biosynthetic pathway of MIAs has been largely elucidated in other Apocynaceae such as Catharanthus roseus, the counterpart in V. minor remains mostly unknown, especially for reactions leading to MIAs specific to this plant. As a consequence, we generated a comprehensive V. minor transcriptome elaborated from eight distinct samples including roots, old and young leaves exposed to low or high light exposure conditions. This optimized resource exhibits an improved completeness compared to already published ones. Through homology-based searches using C. roseus genes as bait, we predicted candidate genes for all common steps of the MIA pathway as illustrated by the cloning of a tabersonine/vincadifformine 16-O-methyltransferase (Vm16OMT) isoform. The functional validation of this enzyme revealed its capacity of methylating 16-hydroxylated derivatives of tabersonine, vincadifformine and lochnericine with a Km 0.94 ± 0.06 µM for 16-hydroxytabersonine. Furthermore, by combining expression of fusions with yellow fluorescent proteins and interaction assays, we established that Vm16OMT is located in the cytosol and forms homodimers. Finally, a gene co-expression network was performed to identify candidate genes of the missing V. minor biosynthetic steps to guide MIA pathway elucidation.
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Affiliation(s)
- Emily Amor Stander
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Liuda Johana Sepúlveda
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
- Laboratorio de Biotecnología, Sede de Investigación Universitaria, Universidad de Antioquia, Antioquia Medellin 050021, Colombia;
| | - Thomas Dugé de Bernonville
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Inês Carqueijeiro
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Konstantinos Koudounas
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Pamela Lemos Cruz
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Sébastien Besseau
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Arnaud Lanoue
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Nicolas Papon
- Host-Pathogen Interaction Study Group (GEIHP, EA 3142), UNIV Angers, UNIV Brest, 49933 Angers, France;
| | - Nathalie Giglioli-Guivarc’h
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
| | - Ron Dirks
- Future Genomics Technologies, 2333 BE Leiden, The Netherlands;
| | - Sarah Ellen O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany;
| | - Lucia Atehortùa
- Laboratorio de Biotecnología, Sede de Investigación Universitaria, Universidad de Antioquia, Antioquia Medellin 050021, Colombia;
| | - Audrey Oudin
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
- Correspondence: (A.O.); (V.C.)
| | - Vincent Courdavault
- EA2106 “Biomolécules et Biotechnologies Végétales”, Université de Tours, 37200 Tours, France; (E.A.S.); (L.J.S.); (T.D.d.B.); (I.C.); (K.K.); (P.L.C.); (S.B.); (A.L.); (N.G.-G.)
- Correspondence: (A.O.); (V.C.)
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Jarret M, Tap A, Turpin V, Denizot N, Kouklovsky C, Poupon E, Evanno L, Vincent G. Bioinspired Divergent Oxidative Cyclizations of Geissoschizine: Total Synthesis of (–)‐17‐nor‐Excelsinidine, (+)‐16‐
epi
‐Pleiocarpamine, (+)‐16‐Hydroxymethyl‐Pleiocarpamine and (+)‐Taberdivarine H. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000962] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Maxime Jarret
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) Université Paris‐Saclay, CNRS 91405 Orsay France
| | - Aurélien Tap
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) Université Paris‐Saclay, CNRS 91405 Orsay France
| | - Victor Turpin
- Biomolécules: Conception, Isolement et Synthèse (BioCIS) Université Paris‐Saclay, CNRS, BioCIS 92290 Châtenay‐Malabry France
| | - Natacha Denizot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) Université Paris‐Saclay, CNRS 91405 Orsay France
| | - Cyrille Kouklovsky
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) Université Paris‐Saclay, CNRS 91405 Orsay France
| | - Erwan Poupon
- Biomolécules: Conception, Isolement et Synthèse (BioCIS) Université Paris‐Saclay, CNRS, BioCIS 92290 Châtenay‐Malabry France
| | - Laurent Evanno
- Biomolécules: Conception, Isolement et Synthèse (BioCIS) Université Paris‐Saclay, CNRS, BioCIS 92290 Châtenay‐Malabry France
| | - Guillaume Vincent
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) Université Paris‐Saclay, CNRS 91405 Orsay France
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Sandholu AS, Mujawar SP, Ramakrishnan K, Thulasiram HV, Kulkarni K. Structural studies on 10-hydroxygeraniol dehydrogenase: A novel linear substrate-specific dehydrogenase from Catharanthus roseus. Proteins 2020; 88:1197-1206. [PMID: 32181958 DOI: 10.1002/prot.25891] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 02/26/2020] [Accepted: 03/07/2020] [Indexed: 11/07/2022]
Abstract
Conversion of 10-hydroxygeraniol to 10-oxogeranial is a crucial step in iridoid biosynthesis. This reaction is catalyzed by a zinc-dependent alcohol dehydrogenase, 10-hydroxygeraniol dehydrogenase, belonging to the family of medium-chain dehydrogenase/reductase (MDR). Here, we report the crystal structures of a novel 10-hydroxygeraniol dehydrogenase from Catharanthus roseus in its apo and nicotinamide adenine dinucleotide phosphate (NADP+ ) bound forms. Structural analysis and docking studies reveal how subtle conformational differences of loops L1, L2, L3, and helix α9' at the orifice of the catalytic site confer differential activity of the enzyme toward various substrates, by modulating the binding pocket shape and volume. The present study, first of its kind, provides insights into the structural basis of substrate specificity of MDRs specific to linear substrates. Furthermore, comparison of apo and NADP+ bound structures suggests that the enzyme adopts open and closed states to facilitate cofactor binding.
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Affiliation(s)
- Anand S Sandholu
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Sharmila P Mujawar
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Krithika Ramakrishnan
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory, Pune, Maharashtra, India
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Hirekodathakallu V Thulasiram
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory, Pune, Maharashtra, India
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Kiran Kulkarni
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory, Pune, Maharashtra, India
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Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins. Proc Natl Acad Sci U S A 2020; 117:10806-10817. [PMID: 32371491 DOI: 10.1073/pnas.1920097117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Radiation of the plant pyridoxal 5'-phosphate (PLP)-dependent aromatic l-amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic l-amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. Here, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.
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Ambrin G, Ahmad M, Alqarawi AA, Hashem A, Abd Allah EF, Ahmad A. Conversion of Cytochrome P450 2D6 of Human Into a FRET-Based Tool for Real-Time Monitoring of Ajmalicine in Living Cells. Front Bioeng Biotechnol 2019; 7:375. [PMID: 31828069 PMCID: PMC6890717 DOI: 10.3389/fbioe.2019.00375] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/14/2019] [Indexed: 11/13/2022] Open
Abstract
Ajmalicine is naturally present in the root bark of Catharanthus roseus L. and Rauvolfia serpentina (L.) Benth ex.Kurz. It has been extensively utilized in the treatment of hypertension across the world. The increased demand, overconsumption, and low content of the alkaloid in the plants have raised the issue of the depletion of natural sources. The metabolic engineering approach has not been successful in improving the content of the ajmalicine because the metabolic regulation of this metabolite is not known. The regulation of a metabolite in the metabolic pathway requires a tool that can carry out real-time measurement of the flux of the metabolite in living system. Given this, the present study was conducted to develop a genetically encoded FRET-based nanosensor by engineering human Cytochrome P450-2D6, an ajmalicine binding protein. The Cytochrome P450-2D6 was sandwiched between two FRET fluorophores. The design of the nanosensor brings two fluorescent proteins in conjunction with the ajmalicine binding protein, such that it undergoes FRET (Fluorescence Resonance Energy Transfer) upon binding of the ligand. The nanosensor, named as FLIP-Ajn (Fluorescence Indicator Protein for Ajmalicine), was pH stable and ajmalicine specific. The affinity of the FLIP-Ajn was 582 μM. The FLIP-Ajn successfully performed real-time measurement of ajmalicine in prokaryotic (bacteria) and eukaryotic systems (yeast, animal cell line, and plant suspension culture), thereby, establishing its biocompatibility in monitoring of ajmalicine in living cells. Besides, several affinity mutants of the nanosensor were generated through mutations in the ajmalicine binding protein to increase the detection range of the nanosensor at varying physiological scales. The non-invasiveness and high spatial and temporal resolution of the tool holds a great significance in the bio-imaging of a highly compartmentalized metabolic pathway. The flux study of ajmalicine will help in identifying the regulatory steps involved in the synthesis of the alkaloids and, hence, will improve the production rate of ajmalicine from its natural sources.
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Affiliation(s)
- Ghazala Ambrin
- Department of Botany, Faculty of Life Science, Aligarh Muslim University, Aligarh, India
| | - Mohammad Ahmad
- Department of Physics, Syracuse University, New York, NY, United States
| | - Abdulaziz A Alqarawi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia.,Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Gaza, Egypt
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Altaf Ahmad
- Department of Botany, Faculty of Life Science, Aligarh Muslim University, Aligarh, India
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Akhgari A, Laakso I, Maaheimo H, Choi YH, Seppänen-Laakso T, Oksman-Caldentey KM, Rischer H. Methyljasmonate Elicitation Increases Terpenoid Indole Alkaloid Accumulation in Rhazya stricta Hairy Root Cultures. PLANTS (BASEL, SWITZERLAND) 2019; 8:E534. [PMID: 31766620 PMCID: PMC6963348 DOI: 10.3390/plants8120534] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/14/2019] [Accepted: 11/19/2019] [Indexed: 01/08/2023]
Abstract
Methyl jasmonate is capable of initiating or improving the biosynthesis of secondary metabolites in plants and therefore has opened up a concept for the biosynthesis of valuable constituents. In this study, the effect of different doses of methyl jasmonate (MeJA) elicitation on the accumulation of terpenoid indole alkaloids (TIAs) in the hairy root cultures of the medicinal plant, Rhazya stricta throughout a time course (one-seven days) was investigated. Gas chromatography-mass spectrometry (GC-MS) analyses were carried out for targeted ten major non-polar alkaloids. Furthermore, overall alterations in metabolite contents in elicited and control cultures were investigated applying proton nuclear magnetic resonance (1H NMR) spectroscopy. Methyl jasmonate caused dosage- and time course-dependent significant rise in the accumulation of TIAs as determined by GC-MS. The contents of seven alkaloids including eburenine, quebrachamine, fluorocarpamine, pleiocarpamine, tubotaiwine, tetrahydroalstonine, and ajmalicine increased compared to non-elicited cultures. However, MeJA-elicitation did not induce the accumulation of vincanine, yohimbine (isomer II), and vallesiachotamine. Furthermore, principal component analysis (PCA) of 1H NMR metabolic profiles revealed a discrimination between elicited hairy roots and control cultures with significant increase in total vindoline-type alkaloid content and elevated levels of organic and amino acids. In addition, elicited and control samples had different sugar and fatty acid profiles, suggesting that MeJA also influences the primary metabolism of R. stricta hairy roots. It is evident that methyl jasmonate is applicable for elevating alkaloid accumulation in "hairy root" organ cultures of R. strica.
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Affiliation(s)
- Amir Akhgari
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, Espoo 02044, Finland; (H.M.); (T.S.-L.); (K.-M.O.-C.)
- Department of Biochemistry, University of Turku, Turku 20014, Finland
| | - Into Laakso
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, P.O. Box 56, University of Helsinki, Helsinki, 00014, Finland;
| | - Hannu Maaheimo
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, Espoo 02044, Finland; (H.M.); (T.S.-L.); (K.-M.O.-C.)
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg BE, Leiden 72, 2333, The Netherlands;
| | - Tuulikki Seppänen-Laakso
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, Espoo 02044, Finland; (H.M.); (T.S.-L.); (K.-M.O.-C.)
| | - Kirsi-Marja Oksman-Caldentey
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, Espoo 02044, Finland; (H.M.); (T.S.-L.); (K.-M.O.-C.)
| | - Heiko Rischer
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, Espoo 02044, Finland; (H.M.); (T.S.-L.); (K.-M.O.-C.)
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Matzel P, Wenske S, Merdivan S, Günther S, Höhne M. Synthesis of β‐Chiral Amines by Dynamic Kinetic Resolution of α‐Branched Aldehydes Applying Imine Reductases. ChemCatChem 2019. [DOI: 10.1002/cctc.201900806] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Philipp Matzel
- Institute of BiochemistryUniversity Greifswald Greifswald 17487 Germany
| | - Sebastian Wenske
- Institute of BiochemistryUniversity Greifswald Greifswald 17487 Germany
| | - Simon Merdivan
- Institut of PharmacyUniversity of Greifswald Greifswald 17489 Germany
| | - Sebastian Günther
- Institut of PharmacyUniversity of Greifswald Greifswald 17489 Germany
| | - Matthias Höhne
- Institute of BiochemistryUniversity Greifswald Greifswald 17487 Germany
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Norwood VM, Huigens RW. Harnessing the Chemistry of the Indole Heterocycle to Drive Discoveries in Biology and Medicine. Chembiochem 2019; 20:2273-2297. [DOI: 10.1002/cbic.201800768] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Verrill M. Norwood
- Department of Medicinal ChemistryCenter for Natural Products Drug Discovery and Development (CNPD3)University of Florida 1345 Center Drive Gainesville FL 32610 USA
| | - Robert W. Huigens
- Department of Medicinal ChemistryCenter for Natural Products Drug Discovery and Development (CNPD3)University of Florida 1345 Center Drive Gainesville FL 32610 USA
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Liu XY, Qin Y. Indole Alkaloid Synthesis Facilitated by Photoredox Catalytic Radical Cascade Reactions. Acc Chem Res 2019; 52:1877-1891. [PMID: 31264824 DOI: 10.1021/acs.accounts.9b00246] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The monoterpene indole alkaloids, containing over 3000 known members and more than 40 structural types, represent one of the largest natural product families that have proven to be an important drug source. Their complex chemical structures and significant biological activities have rendered these alkaloids attractive targets in the synthetic community for decades. While chemists have developed many synthetic methodologies and tactics toward this end, general strategies allowing divergent access to a large variety of structural types and members of monoterpene indole alkaloids are still limited and highly desirable. Photoredox catalysis has emerged in recent years as a powerful tool to realize chemical transformations via single electron transfer (SET) processes that would otherwise be inaccessible. In particular, when the radical species generated by the visible light photoinduced approach is involved in well-designed cascade reactions, the formation of multiple chemical bonds and the assembly of structurally complex molecules would be secured in a green and economic manner. This protocol might serve to remodel the way of thinking for the preparation of useful pharmaceuticals and complex natural products. Due to a long-standing interest in the synthesis of diverse indole alkaloids, our group previously developed a cyclopropanation strategy ( Qin , Y. Acc. Chem. Res. 2011 , 44 , 447 ) that was versatile to access several intriguing indole alkaloid molecules. With an idea of developing more general synthetic approaches to as many members of various indole alkaloids as possible, we recently disclosed new radical cascade reactions enabled by photoredox catalysis, leading to the collective asymmetric total synthesis of 42 monoterpene indole alkaloids belonging to 7 structural types. Several important discoveries deserve to be highlighted. First, the use of photocatalytic technology allowed us to achieve an unusual reaction pathway that reversed the conventional reactivity between two nucleophilic amine and enamine groups. Second, a crucial nitrogen-centered radical, directly generated from a sulfonamide N-H bond, triggered three types of cascade reactions to deliver indole alkaloid cores with manifold functionalities and controllable diastereoselectivities. Moreover, expansion of this catalytic, scalable, and general methodology permitted the total synthesis of a large collection of indole alkaloids. In this Account, we wish to provide a complete picture of our studies concerning the original synthetic design, method development, and applications in total synthesis. It is anticipated that the visible-light-driven cascade strategy will find further utility in the realm of natural product synthesis.
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Affiliation(s)
- Xiao-Yu Liu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Yong Qin
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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50
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Zhou S, Wang L. Unraveling the structural and chemical features of biological short hydrogen bonds. Chem Sci 2019; 10:7734-7745. [PMID: 31588321 PMCID: PMC6764281 DOI: 10.1039/c9sc01496a] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/30/2019] [Indexed: 02/06/2023] Open
Abstract
Short hydrogen bonds are ubiquitous in biological macromolecules and exhibit distinctive proton potential energy surfaces and proton sharing properties.
The three-dimensional architecture of biomolecules often creates specialized structural elements, notably short hydrogen bonds that have donor–acceptor separations below 2.7 Å. In this work, we statistically analyze 1663 high-resolution biomolecular structures from the Protein Data Bank and demonstrate that short hydrogen bonds are prevalent in proteins, protein–ligand complexes and nucleic acids. From these biological macromolecules, we characterize the preferred location, connectivity and amino acid composition in short hydrogen bonds and hydrogen bond networks, and assess their possible functional importance. Using electronic structure calculations, we further uncover how the interplay of the structural and chemical features determines the proton potential energy surfaces and proton sharing conditions in biological short hydrogen bonds.
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Affiliation(s)
- Shengmin Zhou
- Department of Chemistry and Chemical Biology , Institute for Quantitative Biomedicine , Rutgers University , Piscataway , NJ 08854 , USA .
| | - Lu Wang
- Department of Chemistry and Chemical Biology , Institute for Quantitative Biomedicine , Rutgers University , Piscataway , NJ 08854 , USA .
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