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Smit SJ, Ayten S, Radzikowska BA, Hamilton JP, Langer S, Unsworth WP, Larson TR, Buell CR, Lichman BR. The genomic and enzymatic basis for iridoid biosynthesis in cat thyme (Teucrium marum). Plant J 2024. [PMID: 38489316 DOI: 10.1111/tpj.16698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/30/2024] [Accepted: 02/14/2024] [Indexed: 03/17/2024]
Abstract
Iridoids are non-canonical monoterpenoids produced by both insects and plants. An example is the cat-attracting and insect-repelling volatile iridoid nepetalactone, produced by Nepeta sp. (catmint) and aphids. Recently, both nepetalactone biosynthetic pathways were elucidated, showing a remarkable convergent evolution. The iridoid, dolichodial, produced by Teucrium marum (cat thyme) and multiple insect species, has highly similar properties to nepetalactone but its biosynthetic origin remains unknown. We set out to determine the genomic, enzymatic, and evolutionary basis of iridoid biosynthesis in T. marum. First, we generated a de novo chromosome-scale genome assembly for T. marum using Oxford Nanopore Technologies long reads and proximity-by-ligation Hi-C reads. The 610.3 Mb assembly spans 15 pseudomolecules with a 32.9 Mb N50 scaffold size. This enabled identification of iridoid biosynthetic genes, whose roles were verified via activity assays. Phylogenomic analysis revealed that the evolutionary history of T. marum iridoid synthase, the iridoid scaffold-forming enzyme, is not orthologous to typical iridoid synthases but is derived from its conserved paralog. We discovered an enzymatic route from nepetalactol to diverse iridoids through the coupled activity of an iridoid oxidase cytochrome P450 and acetyltransferases, via an inferred acylated intermediate. This work provides a genomic resource for specialized metabolite research in mints and demonstration of the role of acetylation in T. marum iridoid diversity. This work will enable future biocatalytic or biosynthetic production of potent insect repellents, as well as comparative studies into iridoid biosynthesis in insects.
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Affiliation(s)
- Samuel J Smit
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Sefa Ayten
- Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, Georgia, 30602, USA
| | - Barbara A Radzikowska
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | - John P Hamilton
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, 30602, USA
- Department of Crop & Soil Sciences, University of Georgia, Athens, Georgia, 30602, USA
| | - Swen Langer
- Bioscience Technology Facility, Department of Biology, University of York, York, YO10 5DD, UK
| | | | - Tony R Larson
- Bioscience Technology Facility, Department of Biology, University of York, York, YO10 5DD, UK
| | - C Robin Buell
- Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, Georgia, 30602, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, 30602, USA
- Department of Crop & Soil Sciences, University of Georgia, Athens, Georgia, 30602, USA
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
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2
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Liu C, Smit SJ, Dang J, Zhou P, Godden GT, Jiang Z, Liu W, Liu L, Lin W, Duan J, Wu Q, Lichman BR. A chromosome-level genome assembly reveals that a bipartite gene cluster formed via an inverted duplication controls monoterpenoid biosynthesis in Schizonepeta tenuifolia. Mol Plant 2023; 16:533-548. [PMID: 36609143 DOI: 10.1016/j.molp.2023.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/06/2022] [Accepted: 01/04/2023] [Indexed: 06/09/2023]
Abstract
Biosynthetic gene clusters (BGCs) are regions of a genome where genes involved in a biosynthetic pathway are in proximity. The origin and evolution of plant BGCs as well as their role in specialized metabolism remain largely unclear. In this study, we have assembled a chromosome-scale genome of Japanese catnip (Schizonepeta tenuifolia) and discovered a BGC that contains multiple copies of genes involved in four adjacent steps in the biosynthesis of p-menthane monoterpenoids. This BGC has an unprecedented bipartite structure, with mirrored biosynthetic regions separated by 260 kilobases. This bipartite BGC includes identical copies of a gene encoding an old yellow enzyme, a type of flavin-dependent reductase. In vitro assays and virus-induced gene silencing revealed that this gene encodes the missing isopiperitenone reductase. This enzyme evolved from a completely different enzyme family to isopiperitenone reductase from closely related Mentha spp., indicating convergent evolution of this pathway step. Phylogenomic analysis revealed that this bipartite BGC has emerged uniquely in the S. tenuifolia lineage and through insertion of pathway genes into a region rich in monoterpene synthases. The cluster gained its bipartite structure via an inverted duplication. The discovered bipartite BGC for p-menthane biosynthesis in S. tenuifolia has similarities to the recently described duplicated p-menthane biosynthesis gene pairs in the Mentha longifolia genome, providing an example of the convergent evolution of gene order. This work expands our understanding of plant BGCs with respect to both form and evolution, and highlights the power of BGCs for gene discovery in plant biosynthetic pathways.
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Affiliation(s)
- Chanchan Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Samuel J Smit
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Jingjie Dang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Peina Zhou
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Grant T Godden
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Zheng Jiang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wukun Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Licheng Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei Lin
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China; Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jinao Duan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qinan Wu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.
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3
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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: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
Covering: up to 2022Plants produce a wide range of structurally and biosynthetically diverse natural products to interact with their environment. These specialised metabolites typically evolve in limited taxonomic groups presumably in response to specific selective pressures. With the increasing availability of sequencing data, it has become apparent that in many cases the genes encoding biosynthetic enzymes for specialised metabolic pathways are not randomly distributed on the genome. Instead they are physically linked in structures such as arrays, pairs and clusters. The exact function of these clusters is debated. In this review we take a broad view of gene arrangement in plant specialised metabolism, examining types of structures and variation. We discuss the evolution of biosynthetic gene clusters in the wider context of metabolism, populations and epigenetics. Finally, we synthesise our observations to propose a new hypothesis for biosynthetic gene cluster formation in plants.
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Affiliation(s)
- Samuel J Smit
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
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5
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Rodríguez-López CE, Jiang Y, Kamileen MO, Lichman BR, Hong B, Vaillancourt B, Buell CR, O'Connor SE. Phylogeny-aware chemoinformatic analysis of chemical diversity in the Lamiaceae enables iridoid pathway assembly and discovery of aucubin synthase. Mol Biol Evol 2022; 39:6550147. [PMID: 35298643 PMCID: PMC9048965 DOI: 10.1093/molbev/msac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Countless reports describe the isolation and structural characterization of natural products, yet this information remains disconnected and under-utilized. Using a cheminformatics approach, we leverage the reported observations of iridoid glucosides with the known phylogeny of a large iridoid producing plant family (Lamiaceae), to generate a set of biosynthetic pathways that best explain the extant iridoid chemical diversity. We developed a pathway reconstruction algorithm that connects iridoid reports via reactions, and prunes this solution space by considering phylogenetic relationships between genera. We formulate a model that emulates the evolution of iridoid glucosides to create a synthetic dataset, used to select the parameters that would best reconstruct the pathways, and apply them to the iridoid dataset to generate Pathway Hypotheses. These computationally generated pathways were then used as the basis by which to select and screen biosynthetic enzyme candidates. Our model was successfully applied to discover a cytochrome P450 enzyme from Callicarpa americana that catalyzes the oxidation of bartsioside to aucubin, predicted by our model despite neither molecule having been observed in the genus. We also demonstrate aucubin synthase activity in orthologues of Vitex agnus-castus, and the outgroup Paulownia tomentosa, further strengthening the hypothesis, enabled by our model, that the reaction was present in the ancestral biosynthetic pathway. This is the first systematic hypothesis on the epi-iridoid glucosides biosynthesis in 25 years, and sets the stage for streamlined work on the iridoid pathway. This work highlights how curation and computational analysis of widely available structural data can facilitate hypothesis-based gene discovery.
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Affiliation(s)
- Carlos E Rodríguez-López
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany.,Escuela de Ingenieria y Ciencias, Tecnologico de Monterrey, 64849 Monterrey, Mexico
| | - Yindi Jiang
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Mohamed O Kamileen
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Benjamin R Lichman
- Department of Biology, University of York, YO10 5DD York, United Kingdom
| | - Benke Hong
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Brieanne Vaillancourt
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - C Robin Buell
- Department of Crop & Soil Sciences, University of Georgia, Athens, GA 30602, USA
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
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6
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Lichman BR. Ancestral Sequence Reconstruction for Exploring Alkaloid Evolution. Methods Mol Biol 2022; 2505:165-179. [PMID: 35732944 DOI: 10.1007/978-1-0716-2349-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The complex and bioactive monoterpene indole alkaloids (MIAs) found in Catharanthus roseus and related species are the products of many millions of years of evolution through mutation and natural selection. Ancestral sequence reconstruction (ASR) is a method that combines phylogenetic analysis and experimental biochemistry to infer details about past events in protein evolution. Here, I propose that ASR could be leveraged to understand how enzymes catalyzing the formation of complex alkaloids arose over evolutionary time. I discuss the steps of ASR, including sequence selection, multiple sequence alignment, tree inference, and the generation and characterization of inferred ancestral enzymes.
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Affiliation(s)
- Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK.
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7
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Bat-Erdene U, Billingsley JM, Turner WC, Lichman BR, Ippoliti FM, Garg NK, O'Connor SE, Tang Y. Cell-Free Total Biosynthesis of Plant Terpene Natural Products using an Orthogonal Cofactor Regeneration System. ACS Catal 2021; 11:9898-9903. [PMID: 35355836 DOI: 10.1021/acscatal.1c02267] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here we report the one-pot, cell-free enzymatic synthesis of the plant monoterpene nepetalactol starting from the readily available geraniol. A pair of orthogonal cofactor regeneration systems permitted NAD+-dependent geraniol oxidation followed by NADPH-dependent reductive cyclization without isolation of intermediates. The orthogonal cofactor regeneration system maintained a high ratio of NAD+ to NADH and a low ratio of NADP+ to NADPH. The overall reaction contains four biosynthetic enzymes, including a soluble P450; and five accessory and cofactor regeneration enzymes. Furthermore, addition of a NAD+-dependent dehydrogenase to the one-pot mixture led to ~1 g/L of nepetalactone, the active cat- attractant in catnip.
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Affiliation(s)
- Undramaa Bat-Erdene
- 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
| | - William C Turner
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Benjamin R Lichman
- Centre for Agricultural Products, Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Francesca M Ippoliti
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Neil K Garg
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
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8
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Eljounaidi K, Lichman BR. Dreaming of clean bean protein. Nat Plants 2021; 7:860-861. [PMID: 34226691 DOI: 10.1038/s41477-021-00949-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Kaouthar Eljounaidi
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK.
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9
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Roddan R, Sula A, Méndez-Sánchez D, Subrizi F, Lichman BR, Broomfield J, Richter M, Andexer JN, Ward JM, Keep NH, Hailes HC. Single step syntheses of (1S)-aryl-tetrahydroisoquinolines by norcoclaurine synthases. Commun Chem 2020; 3:170. [PMID: 36703392 PMCID: PMC9814250 DOI: 10.1038/s42004-020-00416-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/14/2020] [Indexed: 01/29/2023] Open
Abstract
The 1-aryl-tetrahydroisoquinoline (1-aryl-THIQ) moiety is found in many biologically active molecules. Single enantiomer chemical syntheses are challenging and although some biocatalytic routes have been reported, the substrate scope is limited to certain structural motifs. The enzyme norcoclaurine synthase (NCS), involved in plant alkaloid biosynthesis, has been shown to perform stereoselective Pictet-Spengler reactions between dopamine and several carbonyl substrates. Here, benzaldehydes are explored as substrates and found to be accepted by both wild-type and mutant constructs of NCS. In particular, the variant M97V gives a range of (1 S)-aryl-THIQs in high yields (48-99%) and e.e.s (79-95%). A co-crystallised structure of the M97V variant with an active site reaction intermediate analogue is also obtained with the ligand in a pre-cyclisation conformation, consistent with (1 S)-THIQs formation. Selected THIQs are then used with catechol O-methyltransferases with exceptional regioselectivity. This work demonstrates valuable biocatalytic approaches to a range of (1 S)-THIQs.
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Affiliation(s)
- Rebecca Roddan
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, WC1E 7HX, UK
- Department of Chemistry, Christopher Ingold Building, University College London, London, WC1H 0AJ, UK
| | - Altin Sula
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, WC1E 7HX, UK
| | - Daniel Méndez-Sánchez
- Department of Chemistry, Christopher Ingold Building, University College London, London, WC1H 0AJ, UK
| | - Fabiana Subrizi
- Department of Chemistry, Christopher Ingold Building, University College London, London, WC1H 0AJ, UK
| | - Benjamin R Lichman
- Department of Biochemical Engineering, Bernard Katz Building, University College London, London, WC1E 6BT, UK
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Joseph Broomfield
- Department of Chemistry, Christopher Ingold Building, University College London, London, WC1H 0AJ, UK
| | - Michael Richter
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Schulgasse 11a, 94315, Straubing, Germany
| | - Jennifer N Andexer
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - John M Ward
- Department of Biochemical Engineering, Bernard Katz Building, University College London, London, WC1E 6BT, UK.
| | - Nicholas H Keep
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, WC1E 7HX, UK.
| | - Helen C Hailes
- Department of Chemistry, Christopher Ingold Building, University College London, London, WC1H 0AJ, UK.
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Abstract
Plants produce a diverse array of natural products, many of which have high pharmaceutical value or therapeutic potential. However, these compounds often occur at low concentrations in uncultivated species. Producing phytochemicals in heterologous systems has the potential to address the bioavailability issues related to obtaining these molecules from their natural source. Plants are suitable heterologous systems for the production of valuable phytochemicals as they are autotrophic, derive energy and carbon from photosynthesis, and have similar cellular context to native producer plants. In this review we highlight the methods that are used to elucidate natural product biosynthetic pathways, including the approaches leading to proposing the sequence of enzymatic steps, selecting enzyme candidates and characterizing gene function. We will also discuss the advantages of using plant chasses as production platforms for high value phytochemicals. In addition, through this report we will assess the emerging metabolic engineering strategies that have been developed to enhance and optimize the production of natural and novel bioactive phytochemicals in heterologous plant systems.
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Affiliation(s)
- Kaouthar Eljounaidi
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
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11
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Abstract
Alkaloids from plants are characterised by structural diversity and bioactivity, and maintain a privileged position in both modern and traditional medicines. In recent years, there have been significant advances in elucidating the biosynthetic origins of plant alkaloids. In this review, I will describe the progress made in determining the metabolic origins of the so-called true alkaloids, specialised metabolites derived from amino acids containing a nitrogen heterocycle. By identifying key biosynthetic steps that feature in the majority of pathways, I highlight the key roles played by modifications to primary metabolism, iminium reactivity and spontaneous reactions in the molecular and evolutionary origins of these pathways.
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Affiliation(s)
- Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.
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12
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Nelson A, Phipps RJ, Crane GJ, Venanzi NAE, Lockley WJS, Tredwell M, Buurma NJ, Ballard A, Ahmad HO, Narduolo S, Rosa L, Chand N, Cosgrove DA, Varkonyi P, Asaad N, Tomasi S, Leach AG, Summerhill N, Bloom J, Newby M, Madden S, Roman D, Exner RM, Cortezon-Tamarit F, Ge H, Paisey S, Pascu SI, de Rosales RTM, Hailes HC, Wang Y, Zhao J, Méndez-Sánchez D, Rodan R, Subrizi F, Lichman BR, Keep NH, Ward JM, Harris M, Lamb M, Wilson V, Iafrate P, Bulat F, Néves AA, Hesse F, Hu DE, Aigbirhio F, Leeper FJ, Brindle KM, Rowbotham JS, Urata K, Reeve HA, Vincent KA, Hueting R. Abstracts of the 28 th International Isotope Society (UK group) Symposium: The Synthesis & Applications of Labelled Compounds 2019. J Labelled Comp Radiopharm 2020; 63:608-617. [PMID: 32678462 DOI: 10.1002/jlcr.3867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 04/23/2020] [Indexed: 11/08/2022]
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13
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Lichman BR, Godden GT, Buell CR. Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae. Curr Opin Plant Biol 2020; 55:74-83. [PMID: 32344371 DOI: 10.1016/j.pbi.2020.03.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 02/19/2020] [Accepted: 03/04/2020] [Indexed: 05/28/2023]
Abstract
Plants are reservoirs of extreme chemical diversity, yet biosynthetic pathways remain underexplored in the majority of taxa. Access to improved, inexpensive genomic and computational technologies has recently enhanced our understanding of plant specialized metabolism at the biochemical and evolutionary levels including the elucidation of pathways leading to key metabolites. Furthermore, these approaches have provided insights into the mechanisms of chemical evolution, including neofunctionalization and subfunctionalization, structural variation, and modulation of gene expression. The broader utilization of genomic tools across the plant tree of life, and an expansion of genomic resources from multiple accessions within species or populations, will improve our overall understanding of chemodiversity. These data and knowledge will also lead to greater insight into the selective pressures contributing to and maintaining this diversity, which in turn will enable the development of more accurate predictive models of specialized metabolism in plants.
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Affiliation(s)
- Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Grant T Godden
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Carol Robin Buell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI 48824, USA.
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14
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Lichman BR, Godden GT, Hamilton JP, Palmer L, Kamileen MO, Zhao D, Vaillancourt B, Wood JC, Sun M, Kinser TJ, Henry LK, Rodriguez-Lopez C, Dudareva N, Soltis DE, Soltis PS, Buell CR, O’Connor SE. The evolutionary origins of the cat attractant nepetalactone in catnip. Sci Adv 2020; 6:eaba0721. [PMID: 32426505 PMCID: PMC7220310 DOI: 10.1126/sciadv.aba0721] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/02/2020] [Indexed: 05/07/2023]
Abstract
Catnip or catmint (Nepeta spp.) is a flowering plant in the mint family (Lamiaceae) famed for its ability to attract cats. This phenomenon is caused by the compound nepetalactone, a volatile iridoid that also repels insects. Iridoids are present in many Lamiaceae species but were lost in the ancestor of the Nepetoideae, the subfamily containing Nepeta. Using comparative genomics, ancestral sequence reconstructions, and phylogenetic analyses, we probed the re-emergence of iridoid biosynthesis in Nepeta. The results of these investigations revealed mechanisms for the loss and subsequent re-evolution of iridoid biosynthesis in the Nepeta lineage. We present evidence for a chronology of events that led to the formation of nepetalactone biosynthesis and its metabolic gene cluster. This study provides insights into the interplay between enzyme and genome evolution in the origins, loss, and re-emergence of plant chemical diversity.
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Affiliation(s)
- Benjamin R. Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
- Corresponding author. (B.R.L.); (C.R.B.); (S.E.O.)
| | - Grant T. Godden
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - John P. Hamilton
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Lira Palmer
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Mohamed O. Kamileen
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Dongyan Zhao
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Joshua C. Wood
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Miao Sun
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Taliesin J. Kinser
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Laura K. Henry
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Carlos Rodriguez-Lopez
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - C. Robin Buell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
- MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI 48824, USA
- Corresponding author. (B.R.L.); (C.R.B.); (S.E.O.)
| | - Sarah E. O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany
- Corresponding author. (B.R.L.); (C.R.B.); (S.E.O.)
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15
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Lichman BR, O'Connor SE, Kries H. Frontispiece: Biocatalytic Strategies towards [4+2] Cycloadditions. Chemistry 2019. [DOI: 10.1002/chem.201982862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Benjamin R. Lichman
- Department of Biological ChemistryThe John Innes Centre Colney Lane Norwich UK
- Current address: Department of BiologyUniversity of York York YO10 5YW UK
| | - Sarah E. O'Connor
- Department of Biological ChemistryThe John Innes Centre Colney Lane Norwich UK
| | - Hajo Kries
- Independent Junior Research Group, Biosynthetic Design of Natural ProductsLeibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena) Beutenbergstr. 11a 07745 Jena Germany
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16
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Lichman BR, O'Connor SE, Kries H. Biocatalytic Strategies towards [4+2] Cycloadditions. Chemistry 2019; 25:6864-6877. [DOI: 10.1002/chem.201805412] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/17/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Benjamin R. Lichman
- Department of Biological Chemistry; The John Innes Centre; Colney Lane Norwich UK
- Current address: Department of Biology; University of York; York YO10 5YW UK
| | - Sarah E. O'Connor
- Department of Biological Chemistry; The John Innes Centre; Colney Lane Norwich UK
| | - Hajo Kries
- Independent Junior Research Group, Biosynthetic Design of Natural Products; Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena); Beutenbergstr. 11a 07745 Jena Germany
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17
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Boachon B, Buell CR, Crisovan E, Dudareva N, Garcia N, Godden G, Henry L, Kamileen MO, Kates HR, Kilgore MB, Lichman BR, Mavrodiev EV, Newton L, Rodriguez-Lopez C, O'Connor SE, Soltis D, Soltis P, Vaillancourt B, Wiegert-Rininger K, Zhao D. Phylogenomic Mining of the Mints Reveals Multiple Mechanisms Contributing to the Evolution of Chemical Diversity in Lamiaceae. Mol Plant 2018; 11:1084-1096. [PMID: 29920355 DOI: 10.1016/j.molp.2018.06.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 06/05/2018] [Accepted: 06/10/2018] [Indexed: 05/24/2023]
Abstract
The evolution of chemical complexity has been a major driver of plant diversification, with novel compounds serving as key innovations. The species-rich mint family (Lamiaceae) produces an enormous variety of compounds that act as attractants and defense molecules in nature and are used widely by humans as flavor additives, fragrances, and anti-herbivory agents. To elucidate the mechanisms by which such diversity evolved, we combined leaf transcriptome data from 48 Lamiaceae species and four outgroups with a robust phylogeny and chemical analyses of three terpenoid classes (monoterpenes, sesquiterpenes, and iridoids) that share and compete for precursors. Our integrated chemical-genomic-phylogenetic approach revealed that: (1) gene family expansion rather than increased enzyme promiscuity of terpene synthases is correlated with mono- and sesquiterpene diversity; (2) differential expression of core genes within the iridoid biosynthetic pathway is associated with iridoid presence/absence; (3) generally, production of iridoids and canonical monoterpenes appears to be inversely correlated; and (4) iridoid biosynthesis is significantly associated with expression of geraniol synthase, which diverts metabolic flux away from canonical monoterpenes, suggesting that competition for common precursors can be a central control point in specialized metabolism. These results suggest that multiple mechanisms contributed to the evolution of chemodiversity in this economically important family.
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18
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Zhao J, Lichman BR, Ward JM, Hailes HC. One-pot chemoenzymatic synthesis of trolline and tetrahydroisoquinoline analogues. Chem Commun (Camb) 2018; 54:1323-1326. [PMID: 29345260 PMCID: PMC5804477 DOI: 10.1039/c7cc08024g] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 11/30/2017] [Indexed: 01/21/2023]
Abstract
Chemoenzymatic reaction cascades can provide access to chiral compounds from low-cost starting materials in one pot. Here we describe one-pot asymmetric routes to tetrahydroisoquinoline alkaloids (THIAs) using the Pictet-Spenglerase norcoclaurine synthase (NCS) followed by a cyclisation, to give alkaloids with two new heterocyclic rings. These reactions operated with a high atom economy to generate THIAs in high yields.
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Affiliation(s)
- Jianxiong Zhao
- Department of Chemistry , University College London , Christopher Ingold Building, 20 Gordon Street , London , WC1H 0AJ , UK .
| | - Benjamin R. Lichman
- Department of Biochemical Engineering , University College London , Gower Street , London , WC1E 6BT , UK
| | - John M. Ward
- Department of Biochemical Engineering , University College London , Gower Street , London , WC1E 6BT , UK
| | - Helen C. Hailes
- Department of Chemistry , University College London , Christopher Ingold Building, 20 Gordon Street , London , WC1H 0AJ , UK .
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19
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Wintle BC, Boehm CR, Rhodes C, Molloy JC, Millett P, Adam L, Breitling R, Carlson R, Casagrande R, Dando M, Doubleday R, Drexler E, Edwards B, Ellis T, Evans NG, Hammond R, Haseloff J, Kahl L, Kuiken T, Lichman BR, Matthewman CA, Napier JA, ÓhÉigeartaigh SS, Patron NJ, Perello E, Shapira P, Tait J, Takano E, Sutherland WJ. A transatlantic perspective on 20 emerging issues in biological engineering. eLife 2017; 6:e30247. [PMID: 29132504 PMCID: PMC5685469 DOI: 10.7554/elife.30247] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/26/2017] [Indexed: 01/09/2023] Open
Abstract
Advances in biological engineering are likely to have substantial impacts on global society. To explore these potential impacts we ran a horizon scanning exercise to capture a range of perspectives on the opportunities and risks presented by biological engineering. We first identified 70 potential issues, and then used an iterative process to prioritise 20 issues that we considered to be emerging, to have potential global impact, and to be relatively unknown outside the field of biological engineering. The issues identified may be of interest to researchers, businesses and policy makers in sectors such as health, energy, agriculture and the environment.
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Affiliation(s)
- Bonnie C Wintle
- Centre for the Study of Existential RiskUniversity of CambridgeCambridgeUnited Kingdom
| | - Christian R Boehm
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Centre for the Study of Existential RiskUniversity of CambridgeCambridgeUnited Kingdom
| | - Catherine Rhodes
- Centre for the Study of Existential RiskUniversity of CambridgeCambridgeUnited Kingdom
| | - Jennifer C Molloy
- Department of Plant SciencesUniversity of CambridgeCambridgeUnited Kingdom
| | - Piers Millett
- Future of Humanity InstituteUniversity of OxfordOxfordUnited Kingdom
| | - Laura Adam
- Department of Electrical EngineeringUniversity of WashingtonSeattleUnited States
| | - Rainer Breitling
- Manchester Synthetic Biology Research Centre (SYNBIOCHEM), Manchester Institute of BiotechnologyUniversity of ManchesterManchesterUnited Kingdom
| | | | | | - Malcolm Dando
- Division of Peace Studies and the Bradford Centre for International DevelopmentUniversity of BradfordBradfordUnited Kingdom
| | - Robert Doubleday
- Centre for Science and PolicyUniversity of CambridgeCambridgeUnited Kingdom
| | - Eric Drexler
- Future of Humanity InstituteUniversity of OxfordOxfordUnited Kingdom
| | - Brett Edwards
- Department of Politics, Languages & International StudiesUniversity of BathBathUnited Kingdom
| | - Tom Ellis
- Centre for Synthetic Biology and InnovationImperial College LondonLondonUnited Kingdom
| | - Nicholas G Evans
- Department of PhilosophyUniversity of MassachusettsLowellUnited States
| | | | - Jim Haseloff
- Department of Plant SciencesUniversity of CambridgeCambridgeUnited Kingdom
| | - Linda Kahl
- BioBricks FoundationSan FranciscoUnited States
| | - Todd Kuiken
- Genetic Engineering & Society CenterNorth Carolina State UniversityRaleighUnited States
| | | | | | | | - Seán S ÓhÉigeartaigh
- Centre for the Study of Existential RiskUniversity of CambridgeCambridgeUnited Kingdom
| | | | | | - Philip Shapira
- Manchester Institute of Innovation Research, Alliance Manchester Business SchoolUniversity of ManchesterManchesterUnited Kingdom
- School of Public PolicyGeorgia Institute of TechnologyAtlantaUnited States
| | - Joyce Tait
- Innogen InstituteUniversity of EdinburghEdinburghUnited Kingdom
| | - Eriko Takano
- Manchester Synthetic Biology Research Centre (SYNBIOCHEM), Manchester Institute of BiotechnologyUniversity of ManchesterManchesterUnited Kingdom
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20
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Abstract
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Norcoclaurine
synthase (NCS) is a Pictet-Spenglerase that catalyzes
the first key step in plant benzylisoquinoline alkaloid metabolism,
a compound family that includes bioactive natural products such as
morphine. The enzyme has also shown great potential as a biocatalyst
for the formation of chiral isoquinolines. Here we present new high-resolution
X-ray crystallography data describing Thalictrum flavum NCS bound to a mechanism-inspired ligand. The structure supports
two key features of the NCS “dopamine-first” mechanism:
the binding of dopamine catechol to Lys-122 and the position of the
carbonyl substrate binding site at the active site entrance. The catalytically
vital residue Glu-110 occupies a previously unobserved ligand-bound
conformation that may be catalytically significant. The potential
roles of inhibitory binding and alternative amino acid conformations
in the mechanism have also been revealed. This work significantly
advances our understanding of the NCS mechanism and will aid future
efforts to engineer the substrate scope and catalytic properties of
this useful biocatalyst.
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Affiliation(s)
- Benjamin R Lichman
- Department of Biochemical Engineering, University College London , Gower Street, London WC1E 6BT, U.K
| | - Altin Sula
- Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London , Malet Street, London WC1E 7HX, U.K
| | - Thomas Pesnot
- Department of Chemistry, University College London , Christopher Ingold Building, London WC1H 0AJ, U.K
| | - Helen C Hailes
- Department of Chemistry, University College London , Christopher Ingold Building, London WC1H 0AJ, U.K
| | - John M Ward
- Department of Biochemical Engineering, University College London , Gower Street, London WC1E 6BT, U.K
| | - Nicholas H Keep
- Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London , Malet Street, London WC1E 7HX, U.K
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21
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Erdmann V, Lichman BR, Zhao J, Simon RC, Kroutil W, Ward JM, Hailes HC, Rother D. Enzymatic and Chemoenzymatic Three-Step Cascades for the Synthesis of Stereochemically Complementary Trisubstituted Tetrahydroisoquinolines. Angew Chem Int Ed Engl 2017; 56:12503-12507. [PMID: 28727894 PMCID: PMC5658969 DOI: 10.1002/anie.201705855] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Indexed: 11/19/2022]
Abstract
Chemoenzymatic and enzymatic cascade reactions enable the synthesis of complex stereocomplementary 1,3,4‐trisubstituted tetrahydroisoquinolines (THIQs) with three chiral centers in a step‐efficient and selective manner without intermediate purification. The cascade employs inexpensive substrates (3‐hydroxybenzaldehyde and pyruvate), and involves a carboligation step, a subsequent transamination, and finally a Pictet–Spengler reaction with a carbonyl cosubstrate. Appropriate selection of the carboligase and transaminase enzymes enabled the biocatalytic formation of (1R,2S)‐metaraminol. Subsequent cyclization catalyzed either enzymatically by a norcoclaurine synthase or chemically by phosphate resulted in opposite stereoselectivities in the products at the C1 position, thus providing access to both orientations of the THIQ C1 substituent. This highlights the importance of selecting from both chemo‐ and biocatalysts for optimal results.
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Affiliation(s)
- Vanessa Erdmann
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | | | - Jianxiong Zhao
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
| | - Robert C Simon
- Roche-Diagnostics GmbH, DOZCBE, 82377, Penzberg, Germany
| | - Wolfgang Kroutil
- Department of Chemistry, University of Graz, 8010, Graz, Austria
| | - John M Ward
- Department of Biochemical Engineering, University College London, London, WC1E 6BT, UK
| | - Helen C Hailes
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
| | - Dörte Rother
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
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22
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Erdmann V, Lichman BR, Zhao J, Simon RC, Kroutil W, Ward JM, Hailes HC, Rother D. Enzymatic and Chemoenzymatic Three‐Step Cascades for the Synthesis of Stereochemically Complementary Trisubstituted Tetrahydroisoquinolines. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705855] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Vanessa Erdmann
- IBG-1: Biotechnology Forschungszentrum Jülich GmbH 52425 Jülich Germany
| | | | - Jianxiong Zhao
- Department of Chemistry University College London London WC1H 0AJ UK
| | | | | | - John M. Ward
- Department of Biochemical Engineering University College London London WC1E 6BT UK
| | - Helen C. Hailes
- Department of Chemistry University College London London WC1H 0AJ UK
| | - Dörte Rother
- IBG-1: Biotechnology Forschungszentrum Jülich GmbH 52425 Jülich Germany
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23
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Lichman BR, Zhao J, Hailes HC, Ward JM. Enzyme catalysed Pictet-Spengler formation of chiral 1,1'-disubstituted- and spiro-tetrahydroisoquinolines. Nat Commun 2017; 8:14883. [PMID: 28368003 PMCID: PMC5382262 DOI: 10.1038/ncomms14883] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/08/2017] [Indexed: 01/26/2023] Open
Abstract
The Pictet–Spengler reaction (PSR) involves the condensation and ring closure between a β-arylethylamine and a carbonyl compound. The combination of dopamine and ketones in a PSR leads to the formation of 1,1′-disubstituted tetrahydroisoquinolines (THIQs), structures that are challenging to synthesize and yet are present in a number of bioactive natural products and synthetic pharmaceuticals. Here we have discovered that norcoclaurine synthase from Thalictrum flavum (TfNCS) can catalyse the PSR between dopamine and unactivated ketones, thus facilitating the facile biocatalytic generation of 1,1′-disubstituted THIQs. Variants of TfNCS showing improved conversions have been identified and used to synthesize novel chiral 1,1′-disubstituted and spiro-THIQs. Enzyme catalysed PSRs with unactivated ketones are unprecedented, and, furthermore, there are no equivalent stereoselective chemical methods for these transformations. This discovery advances the utility of enzymes for the generation of diverse THIQs in vitro and in vivo. The Pictet-Spengler condensation of β-arylethylamine and carbonyl compounds is an important step in the synthesis of bioactive alkaloids. Here, the authors report a Pictet-Spengler reaction between dopamine and unactivated ketones catalysed by norcoclaurine synthase and its engineered variants.
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Affiliation(s)
- Benjamin R Lichman
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, UK
| | - Jianxiong Zhao
- Department of Chemistry, University College London, Christopher Ingold Building, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Helen C Hailes
- Department of Chemistry, University College London, Christopher Ingold Building, 20 Gordon Street, London, WC1H 0AJ, UK
| | - John M Ward
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, UK
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24
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Lichman BR, Gershater MC, Lamming ED, Pesnot T, Sula A, Keep NH, Hailes HC, Ward JM. 'Dopamine-first' mechanism enables the rational engineering of the norcoclaurine synthase aldehyde activity profile. FEBS J 2015; 282:1137-51. [PMID: 25620686 PMCID: PMC4413047 DOI: 10.1111/febs.13208] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/09/2015] [Accepted: 01/19/2015] [Indexed: 12/26/2022]
Abstract
Norcoclaurine synthase (NCS) (EC 4.2.1.78) catalyzes the Pictet–Spengler condensation of dopamine and an aldehyde, forming a substituted (S)-tetrahydroisoquinoline, a pharmaceutically important moiety. This unique activity has led to NCS being used for both in vitro biocatalysis and in vivo recombinant metabolism. Future engineering of NCS activity to enable the synthesis of diverse tetrahydroisoquinolines is dependent on an understanding of the NCS mechanism and kinetics. We assess two proposed mechanisms for NCS activity: (a) one based on the holo X-ray crystal structure and (b) the ‘dopamine-first’ mechanism based on computational docking. Thalictrum flavum NCS variant activities support the dopamine-first mechanism. Suppression of the non-enzymatic background reaction reveals novel kinetic parameters for NCS, showing it to act with low catalytic efficiency. This kinetic behaviour can account for the ineffectiveness of recombinant NCS in in vivo systems, and also suggests NCS may have an in planta role as a metabolic gatekeeper. The amino acid substitution L76A, situated in the proposed aldehyde binding site, results in the alteration of the enzyme's aldehyde activity profile. This both verifies the dopamine-first mechanism and demonstrates the potential for the rational engineering of NCS activity.
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25
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Kwa LG, Wensley BG, Alexander CG, Browning SJ, Lichman BR, Clarke J. The folding of a family of three-helix bundle proteins: spectrin R15 has a robust folding nucleus, unlike its homologous neighbours. J Mol Biol 2014; 426:1600-10. [PMID: 24373753 PMCID: PMC3988883 DOI: 10.1016/j.jmb.2013.12.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/13/2013] [Accepted: 12/17/2013] [Indexed: 11/13/2022]
Abstract
Three homologous spectrin domains have remarkably different folding characteristics. We have previously shown that the slow-folding R16 and R17 spectrin domains can be altered to resemble the fast folding R15, in terms of speed of folding (and unfolding), landscape roughness and folding mechanism, simply by substituting five residues in the core. Here we show that, by contrast, R15 cannot be engineered to resemble R16 and R17. It is possible to engineer a slow-folding version of R15, but our analysis shows that this protein neither has a rougher energy landscape nor does change its folding mechanism. Quite remarkably, R15 appears to be a rare example of a protein with a folding nucleus that does not change in position or in size when its folding nucleus is disrupted. Thus, while two members of this protein family are remarkably plastic, the third has apparently a restricted folding landscape.
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Affiliation(s)
- Lee Gyan Kwa
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Beth G Wensley
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Crispin G Alexander
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Stuart J Browning
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Benjamin R Lichman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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