1
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Reed KB, Brooks SM, Wells J, Blake KJ, Zhao M, Placido K, d'Oelsnitz S, Trivedi A, Gadhiyar S, Alper HS. A modular and synthetic biosynthesis platform for de novo production of diverse halogenated tryptophan-derived molecules. Nat Commun 2024; 15:3188. [PMID: 38609402 PMCID: PMC11015028 DOI: 10.1038/s41467-024-47387-1] [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: 07/22/2023] [Accepted: 03/31/2024] [Indexed: 04/14/2024] Open
Abstract
Halogen-containing molecules are ubiquitous in modern society and present unique chemical possibilities. As a whole, de novo fermentation and synthetic pathway construction for these molecules remain relatively underexplored and could unlock molecules with exciting new applications in industries ranging from textiles to agrochemicals to pharmaceuticals. Here, we report a mix-and-match co-culture platform to de novo generate a large array of halogenated tryptophan derivatives in Escherichia coli from glucose. First, we engineer E. coli to produce between 300 and 700 mg/L of six different halogenated tryptophan precursors. Second, we harness the native promiscuity of multiple downstream enzymes to access unexplored regions of metabolism. Finally, through modular co-culture fermentations, we demonstrate a plug-and-play bioproduction platform, culminating in the generation of 26 distinct halogenated molecules produced de novo including precursors to prodrugs 4-chloro- and 4-bromo-kynurenine and new-to-nature halogenated beta carbolines.
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Affiliation(s)
- Kevin B Reed
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Sierra M Brooks
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Jordan Wells
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Kristin J Blake
- Mass Spectrometry Facility, Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Austin, TX, USA
| | - Minye Zhao
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Kira Placido
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Simon d'Oelsnitz
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, USA
| | - Adit Trivedi
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Shruti Gadhiyar
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, USA.
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2
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Panaccione DG. Derivation of the multiply-branched ergot alkaloid pathway of fungi. Microb Biotechnol 2023; 16:742-756. [PMID: 36636806 PMCID: PMC10034635 DOI: 10.1111/1751-7915.14214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/16/2022] [Accepted: 01/02/2023] [Indexed: 01/14/2023] Open
Abstract
Ergot alkaloids are a large family of fungal specialized metabolites that are important as toxins in agriculture and as the foundation of powerful pharmaceuticals. Fungi from several lineages and diverse ecological niches produce ergot alkaloids from at least one of several branches of the ergot alkaloid pathway. The biochemical and genetic bases for the different branches have been established and are summarized briefly herein. Several pathway branches overlap among fungal lineages and ecological niches, indicating activities of ergot alkaloids benefit fungi in different environments and conditions. Understanding the functions of the multiple genes in each branch of the pathway allows researchers to parse the abundant genomic sequence data available in public databases in order to assess the ergot alkaloid biosynthesis capacity of previously unexplored fungi. Moreover, the characterization of the genes involved in the various branches provides opportunities and resources for the biotechnological manipulation of ergot alkaloids for experimentation and pharmaceutical development.
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Affiliation(s)
- Daniel G Panaccione
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
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3
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Milne N, Sáez-Sáez J, Nielsen AM, Dyekjaer JD, Rago D, Kristensen M, Wulff T, Borodina I. Engineering Saccharomyces cerevisiae for the de novo Production of Halogenated Tryptophan and Tryptamine Derivatives. ChemistryOpen 2023; 12:e202200266. [PMID: 36929157 PMCID: PMC10068768 DOI: 10.1002/open.202200266] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
The indole scaffold is a recurring structure in multiple bioactive heterocycles and natural products. Substituted indoles like the amino acid tryptophan serve as a precursor for a wide range of natural products with pharmaceutical or agrochemical applications. Inspired by the versatility of these compounds, medicinal chemists have for decades exploited indole as a core structure in the drug discovery process. With the aim of tuning the properties of lead drug candidates, regioselective halogenation of the indole scaffold is a common strategy. However, chemical halogenation is generally expensive, has a poor atom economy, lacks regioselectivity, and generates hazardous waste streams. As an alternative, in this work we engineer the industrial workhorse Saccharomyces cerevisiae for the de novo production of halogenated tryptophan and tryptamine derivatives. Functional expression of bacterial tryptophan halogenases together with a partner flavin reductase and a tryptophan decarboxylase resulted in the production of halogenated tryptophan and tryptamine with chlorine or bromine. Furthermore, by combining tryptophan halogenases, production of di-halogenated molecules was also achieved. Overall, this works paves the road for the production of new-to-nature halogenated natural products in yeast.
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Affiliation(s)
- Nicholas Milne
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.,Octarine Bio ApS, Lersø Parkallé 42, 1. Sal, 2100, Copenhagen, Denmark
| | - Javier Sáez-Sáez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Annette Munch Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.,Octarine Bio ApS, Lersø Parkallé 42, 1. Sal, 2100, Copenhagen, Denmark
| | - Jane Dannow Dyekjaer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Daniela Rago
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Mette Kristensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
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4
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Hu M, Zhou Y, Du S, Zhang X, Tang S, Yang Y, Zhang W, Chen S, Huang X, Lu X. Construction of an efficient Claviceps paspali cell factory for lysergic acid production. Front Bioeng Biotechnol 2023; 10:1093402. [PMID: 36760750 PMCID: PMC9905238 DOI: 10.3389/fbioe.2022.1093402] [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: 11/09/2022] [Accepted: 12/28/2022] [Indexed: 01/27/2023] Open
Abstract
Lysergic acid (LA) is the key precursor of ergot alkaloids, and its derivatives have been used extensively for the treatment of neurological disorders. However, the poor fermentation efficiency limited its industrial application. At the same time, the hardship of genetic manipulation has hindered the metabolic engineering of Claviceps strains to improve the LA titer further. In this study, an efficient genetic manipulation system based on the protoplast-mediated transformation was established in the industrial strain Claviceps paspali. On this basis, the gene lpsB located in the ergot alkaloids biosynthetic gene cluster was deleted to construct the LA-producing cell factory. Plackett-Burman and Box-Behnken designs were used in shaking flasks, achieving an optimal fermentation medium composition. The final titer of LA and iso-lysergic acid (ILA) reached 3.7 g·L-1, which was 4.6 times higher than that in the initial medium. Our work provides an efficient strategy for the biosynthesis of LA and ILA and lays the groundwork for its industrial production.
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Affiliation(s)
- Mingzhe Hu
- College of Life Sciences, Qingdao University, Qingdao, China,Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China,Shandong Energy Institute, Qingdao, China,Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Yu Zhou
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China,Shandong Energy Institute, Qingdao, China,Qingdao New Energy Shandong Laboratory, Qingdao, China,Institute for Smart Materials and Engineering, University of Jinan, Jinan, China
| | - Siyu Du
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China,Shandong Energy Institute, Qingdao, China,Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Xuan Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China,Shandong Energy Institute, Qingdao, China,Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Shen Tang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China,Shandong Energy Institute, Qingdao, China,Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Yong Yang
- Shisenhai (Hangzhou) Biopharmaceutical Co., Ltd., Hangzhou, China
| | - Wei Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China,Shandong Energy Institute, Qingdao, China,Qingdao New Energy Shandong Laboratory, Qingdao, China,University of Chinese Academy of Sciences, Beijing, China
| | - Shaoxin Chen
- State Key Lab of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, Shanghai, China,*Correspondence: Shaoxin Chen, ; Xuenian Huang,
| | - Xuenian Huang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China,Shandong Energy Institute, Qingdao, China,Qingdao New Energy Shandong Laboratory, Qingdao, China,*Correspondence: Shaoxin Chen, ; Xuenian Huang,
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China,Shandong Energy Institute, Qingdao, China,Qingdao New Energy Shandong Laboratory, Qingdao, China,University of Chinese Academy of Sciences, Beijing, China,Marine Biology and Biotechnology Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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5
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Ma Y, Yan J, Yang L, Yao Y, Wang L, Gao SS, Cui C. A hybrid system for the overproduction of complex ergot alkaloid chanoclavine. Front Bioeng Biotechnol 2022; 10:1095464. [PMID: 36619381 PMCID: PMC9811125 DOI: 10.3389/fbioe.2022.1095464] [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: 11/11/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Synthetic biology-based methods (Sbio) and chemical synthesis (Csyn) are two independent approaches that are both widely used for synthesizing biomolecules. In the current study, two systems were combined for the overproduction of chanoclavine (CC), a structurally complex ergot alkaloid. The whole synthetic pathway for CC was split into three sections: enzymatic synthesis of 4-Br-Trp (4-Bromo-trptophan) using cell-lysate catalysis (CLC), chemical synthesis of prechanoclavine (PCC) from 4-Br-Trp, and overproduction CC from PCC using a whole-cell catalysis (WCC) platform. The final titer of the CC is over 3 g/L in this Sbio-Csyn hybrid system, the highest yield reported so far, to the best of our knowledge. The development of such a combined route could potentially avoid the limitations of both Sbio and Csyn systems and boost the overproduction of complex natural products.
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Affiliation(s)
- Yaqing Ma
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,University of Chinese Academy of Sciences, Beijing, China
| | - Juzhang Yan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Lujia Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yongpeng Yao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Luoyi Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,*Correspondence: Luoyi Wang, ; Shu-Shan Gao, ; Chengsen Cui,
| | - Shu-Shan Gao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Technology Innovation Center of Synthetic Biology, Tianjin, China,*Correspondence: Luoyi Wang, ; Shu-Shan Gao, ; Chengsen Cui,
| | - Chengsen Cui
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Technology Innovation Center of Synthetic Biology, Tianjin, China,*Correspondence: Luoyi Wang, ; Shu-Shan Gao, ; Chengsen Cui,
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6
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Yu ZP, An C, Yao Y, Wang CY, Sun Z, Cui C, Liu L, Gao SS. A combined strategy for the overproduction of complex ergot alkaloid agroclavine. Synth Syst Biotechnol 2022; 7:1126-1132. [PMID: 36092273 PMCID: PMC9428804 DOI: 10.1016/j.synbio.2022.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/10/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022] Open
Abstract
Microbial cell factories (MCFs) and cell-free systems (CFSs) are generally considered as two unrelated approaches for the biosynthesis of biomolecules. In the current study, two systems were combined together for the overproduction of agroclavine (AC), a structurally complex ergot alkaloid. The whole biosynthetic pathway for AC was split into the early pathway and the late pathway at the point of the FAD-linked oxidoreductase EasE, which was reconstituted in an MCF (Aspergillus nidulans) and a four-enzyme CFS, respectively. The final titer of AC of this combined system is 1209 mg/L, which is the highest one that has been reported so far, to the best of our knowledge. The development of such a combined route could potentially avoid the limitations of both MCF and CFS systems, and boost the production of complex ergot alkaloids with polycyclic ring systems.
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Affiliation(s)
- Zhi-Pu Yu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, Institute of Evolution & Marine Biodiversity, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, PR China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, PR China
| | - Chunyan An
- Beijing Institute for Drug Control, NMPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing Key Laboratory of Analysis and Evaluation on Chinese Medicine, Beijing, 102206, PR China
| | - Yongpeng Yao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Chang-Yun Wang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, Institute of Evolution & Marine Biodiversity, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, PR China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, PR China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, PR China
| | - Chengsen Cui
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, PR China
| | - Ling Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
- Corresponding author.
| | - Shu-Shan Gao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, PR China
- Corresponding author.
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7
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Eggbauer B, Schrittwieser JH, Kerschbaumer B, Macheroux P, Kroutil W. Regioselective Biocatalytic C4-Prenylation of Unprotected Tryptophan Derivatives. Chembiochem 2022; 23:e202200311. [PMID: 35770709 PMCID: PMC9540666 DOI: 10.1002/cbic.202200311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/23/2022] [Indexed: 11/25/2022]
Abstract
Regioselective carbon−carbon bond formation belongs to the challenging tasks in organic synthesis. In this context, C−C bond formation catalyzed by 4‐dimethylallyltryptophan synthases (4‐DMATSs) represents a possible tool to regioselectively synthesize C4‐prenylated indole derivatives without site‐specific preactivation and circumventing the need of protection groups as used in chemical synthetic approaches. In this study, a toolbox of 4‐DMATSs to produce a set of 4‐dimethylallyl tryptophan and indole derivatives was identified. Using three wild‐type enzymes as well as variants, various C5‐substituted tryptophan derivatives as well as N‐methyl tryptophan were successfully prenylated with conversions up to 90 %. Even truncated tryptophan derivatives like tryptamine and 3‐indole propanoic acid were regioselectively prenylated in position C4. The acceptance of C5‐substituted tryptophan derivatives was improved up to 5‐fold by generating variants (e. g. T108S). The feasibility of semi‐preparative prenylation of selected tryptophan derivatives was successfully demonstrated on 100 mg scale at 15 mM substrate concentration, allowing to reduce the previously published multistep chemical synthetic sequence to just a single step.
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Affiliation(s)
- Bettina Eggbauer
- University of Graz: Karl-Franzens-Universitat Graz, Chemistry, AUSTRIA
| | | | | | | | - Wolfgang Kroutil
- University of Graz: Karl-Franzens-Universitat Graz, Institute of Chemistry, Heinrichstrasse 28, 8010, Graz, AUSTRIA
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8
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Wong G, Lim LR, Tan YQ, Go MK, Bell DJ, Freemont PS, Yew WS. Reconstituting the complete biosynthesis of D-lysergic acid in yeast. Nat Commun 2022; 13:712. [PMID: 35132076 PMCID: PMC8821704 DOI: 10.1038/s41467-022-28386-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/21/2022] [Indexed: 12/18/2022] Open
Abstract
The ergot alkaloids are a class of natural products known for their pharmacologically privileged molecular structure that are used in the treatment of neurological ailments, such as Parkinsonism and dementia. Their synthesis via chemical and biological routes are therefore of industrial relevance, but suffer from several challenges. Current chemical synthesis methods involve long, multi-step reactions with harsh conditions and are not enantioselective; biological methods utilizing ergot fungi, produce an assortment of products that complicate product recovery, and are susceptible to strain degradation. Reconstituting the ergot alkaloid pathway in a strain strongly amenable for liquid fermentation, could potentially resolve these issues. In this work, we report the production of the main ergoline therapeutic precursor, D-lysergic acid, to a titre of 1.7 mg L−1 in a 1 L bioreactor. Our work demonstrates the proof-of-concept for the biological production of ergoline-derived compounds from sugar in an engineered yeast chassis. The ergot alkaloids are a class of natural products known for their pharmacologically privileged molecular structure that are used in the treatment of neurological ailments. Here the authors report on the production of the ergot (fungus)-derived therapeutic precursor, D-lysergic acid (DLA), in baker’s yeast.
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Affiliation(s)
- Garrett Wong
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,Department of Infectious Diseases, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London, SW7 2AZ, UK
| | - Li Rong Lim
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore
| | - Yong Quan Tan
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore
| | - Maybelle Kho Go
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore
| | - David J Bell
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London, SW7 2AZ, UK
| | - Paul S Freemont
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London, SW7 2AZ, UK. .,London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London, W12 0BZ, UK. .,UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
| | - Wen Shan Yew
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore. .,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.
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9
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Yao Y, Wang W, Shi W, Yan R, Zhang J, Wei G, Liu L, Che Y, An C, Gao SS. Overproduction of medicinal ergot alkaloids based on a fungal platform. Metab Eng 2021; 69:198-208. [PMID: 34902590 DOI: 10.1016/j.ymben.2021.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/17/2021] [Accepted: 12/08/2021] [Indexed: 12/21/2022]
Abstract
Privileged ergot alkaloids (EAs) produced by the fungal genus Claviceps are used to treat a wide range of diseases. However, their use and research have been hampered by the challenging genetic engineering of Claviceps. Here we systematically refactored and rationally engineered the EA biosynthetic pathway in heterologous host Aspergillus nidulans by using a Fungal-Yeast-Shuttle-Vector protocol. The obtained strains allowed the production of diverse EAs and related intermediates, including prechanoclavine (PCC, 333.8 mg/L), chanoclavine (CC, 241.0 mg/L), agroclavine (AC, 78.7 mg/L), and festuclavine (FC, 99.2 mg/L), etc. This fungal platform also enabled the access to the methyl-oxidized EAs (MOEAs), including elymoclavine (EC), lysergic acid (LA), dihydroelysergol (DHLG), and dihydrolysergic acid (DHLA), by overexpressing a P450 enzyme CloA. Furthermore, by optimizing the P450 electron transfer (ET) pathway and using multi-copy of cloA, the titers of EC and DHLG have been improved by 17.3- and 9.4-fold, respectively. Beyond our demonstration of A. nidulans as a robust platform for EA overproduction, our study offers a proof of concept for engineering the eukaryotic P450s-contained biosynthetic pathways in a filamentous fungal host.
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Affiliation(s)
- Yongpeng Yao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Wei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Wenyu Shi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Rui Yan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Jun Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Guangzheng Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Ling Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Yongsheng Che
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, PR China
| | - Chunyan An
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.
| | - Shu-Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.
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10
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Abstract
The Pd-catalyzed carbon-carbon bond formation pioneered by Heck in 1969 has dominated medicinal chemistry development for the ensuing fifty years. As the demand for more complex three-dimensional active pharmaceuticals continues to increase, preparative enzyme-mediated assembly, by virtue of its exquisite selectivity and sustainable nature, is poised to provide a practical and affordable alternative for accessing such compounds. In this minireview, we summarize recent state-of-the-art developments in practical enzyme-mediated assembly of carbocycles. When appropriate, background information on the enzymatic transformation is provided and challenges and/or limitations are also highlighted.
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Affiliation(s)
- Weijin Wang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Douglass F Taber
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Hans Renata
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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11
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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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12
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Purdy TN, Kim MC, Cullum R, Fenical W, Moore BS. Discovery and Biosynthesis of Tetrachlorizine Reveals Enzymatic Benzylic Dehydrogenation via an ortho-Quinone Methide. J Am Chem Soc 2021; 143:3682-3686. [PMID: 33656337 DOI: 10.1021/jacs.0c12415] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ortho-quinone methides (o-QMs) are reactive intermediates in biosynthesis that give rise to a variety of intra- and intermolecular cyclization/addition products in bacteria, fungi, and plants. Herein, we report a new metabolic deviation of an o-QM intermediate in a benzylic dehydrogenation reaction that links the newly described marine bacterial natural products dihydrotetrachlorizine and tetrachlorizine. We discovered these novel dichloropyrrole-containing compounds from actinomycete strain AJS-327 that unexpectedly harbors in its genome a biosynthetic gene cluster (BGC) of striking similarity to that of chlorizidine, another marine alkaloid bearing a different carbon skeleton. Heterologous expression of the homologous flavin-dependent oxidoreductase enzymes Tcz9 and Clz9 revealed their native functions in tetrachlorizine and chlorizidine biosynthesis, respectively, supporting divergent oxidative dehydrogenation and pyrrolizine-forming reactions. Swapping these berberine bridge enzyme-like oxidoreductases, we produced cyclized and dehydrogenated analogs of tetrachlorizine and chlorizidine, including a dearomatized chlorizidine analog that stabilizes an o-QM via conjugation with a 3H-pyrrolizine ring.
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13
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Biosynthesis, total synthesis, and biological profiles of Ergot alkaloids. THE ALKALOIDS: CHEMISTRY AND BIOLOGY 2021; 85:1-112. [DOI: 10.1016/bs.alkal.2020.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14
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Bradley SA, Zhang J, Jensen MK. Deploying Microbial Synthesis for Halogenating and Diversifying Medicinal Alkaloid Scaffolds. Front Bioeng Biotechnol 2020; 8:594126. [PMID: 33195162 PMCID: PMC7644825 DOI: 10.3389/fbioe.2020.594126] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/02/2020] [Indexed: 11/13/2022] Open
Abstract
Plants produce some of the most potent therapeutics and have been used for thousands of years to treat human diseases. Today, many medicinal natural products are still extracted from source plants at scale as their complexity precludes total synthesis from bulk chemicals. However, extraction from plants can be an unreliable and low-yielding source for human therapeutics, making the supply chain for some of these life-saving medicines expensive and unstable. There has therefore been significant interest in refactoring these plant pathways in genetically tractable microbes, which grow more reliably and where the plant pathways can be more easily engineered to improve the titer, rate and yield of medicinal natural products. In addition, refactoring plant biosynthetic pathways in microbes also offers the possibility to explore new-to-nature chemistry more systematically, and thereby help expand the chemical space that can be probed for drugs as well as enable the study of pharmacological properties of such new-to-nature chemistry. This perspective will review the recent progress toward heterologous production of plant medicinal alkaloids in microbial systems. In particular, we focus on the refactoring of halogenated alkaloids in yeast, which has created an unprecedented opportunity for biosynthesis of previously inaccessible new-to-nature variants of the natural alkaloid scaffolds.
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Affiliation(s)
- Samuel A Bradley
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - 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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15
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Chen KL, Lai CY, Pham MT, Chein RJ, Tang Y, Lin HC. Enzyme-Catalyzed Azepinoindole Formation in Clavine Alkaloid Biosynthesis. Org Lett 2020; 22:3302-3306. [PMID: 32243182 PMCID: PMC8092377 DOI: 10.1021/acs.orglett.0c01132] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
(-)-Aurantioclavine (1), which contains a characteristic seven-membered ring fused to an indole ring, belongs to the azepinoindole class of fungal clavine alkaloids. Here we show that starting from a 4-dimethylallyl-l-tryptophan precursor, a flavin adenine dinucleotide (FAD)-binding oxidase and a catalase-like heme-containing protein are involved in the biosynthesis of 1. The function of these two enzymes was characterized by heterologous expression, in vitro characterization, and deuterium labeling experiments.
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Affiliation(s)
- Kuan-Lin Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
| | - Chen-Yu Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
| | - Mai-Truc Pham
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan R.O.C
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan R.O.C
| | - Rong-Jie Chein
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan R.O.C
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
| | - Yi Tang
- Departments of Chemical and Biomolecular Engineering and Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Hsiao-Ching Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan R.O.C
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Yao Y, An C, Evans D, Liu W, Wang W, Wei G, Ding N, Houk KN, Gao SS. Catalase Involved in Oxidative Cyclization of the Tetracyclic Ergoline of Fungal Ergot Alkaloids. J Am Chem Soc 2019; 141:17517-17521. [PMID: 31621316 DOI: 10.1021/jacs.9b10217] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A dedicated enzyme for the formation of the central C ring in the tetracyclic ergoline of clinically important ergot alkaloids has never been found. Herein, we report a dual role catalase (EasC), unexpectedly using O2 as the oxidant, that catalyzes the oxidative cyclization of the central C ring from a 1,3-diene intermediate. Our study showcases how nature evolves the common catalase for enantioselective C-C bond construction of complex polycyclic scaffolds.
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Affiliation(s)
- Yongpeng Yao
- State Key Laboratory of Microbial Resources , Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , P. R. China
| | - Chunyan An
- State Key Laboratory of Microbial Resources , Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , P. R. China
| | - Declan Evans
- Department of Chemistry and Biochemistry , University of California , Los Angeles California 90095 , United States
| | - Weiwei Liu
- State Key Laboratory of Microbial Resources , Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , P. R. China
| | - Wei Wang
- State Key Laboratory of Microbial Resources , Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Guangzheng Wei
- State Key Laboratory of Microbial Resources , Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , P. R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Ning Ding
- School of Food Science and Technology , Jiangnan University , Wuxi , Jiangsu 214122 , P. R. China
| | - K N Houk
- Department of Chemistry and Biochemistry , University of California , Los Angeles California 90095 , United States
| | - Shu-Shan Gao
- State Key Laboratory of Microbial Resources , Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101 , P. R. China
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17
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Qiao YM, Yu RL, Zhu P. Advances in targeting and heterologous expression of genes involved in the synthesis of fungal secondary metabolites. RSC Adv 2019; 9:35124-35134. [PMID: 35530690 PMCID: PMC9074735 DOI: 10.1039/c9ra06908a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/18/2019] [Indexed: 01/11/2023] Open
Abstract
Gene targeting involves integration of foreign DNA into the fungal genome by several strategies including Agrobacterium tumefaciens-mediated transformation (ATMT).
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Affiliation(s)
- Yun-Ming Qiao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines
- NHC Key Laboratory of Biosynthesis of Natural Products
- CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
| | - Rui-Lin Yu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines
- NHC Key Laboratory of Biosynthesis of Natural Products
- CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
| | - Ping Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines
- NHC Key Laboratory of Biosynthesis of Natural Products
- CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
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18
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Martín JF, Álvarez-Álvarez R, Liras P. Clavine Alkaloids Gene Clusters of Penicillium and Related Fungi: Evolutionary Combination of Prenyltransferases, Monooxygenases and Dioxygenases. Genes (Basel) 2017; 8:genes8120342. [PMID: 29186777 PMCID: PMC5748660 DOI: 10.3390/genes8120342] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/13/2017] [Accepted: 11/16/2017] [Indexed: 11/22/2022] Open
Abstract
The clavine alkaloids produced by the fungi of the Aspergillaceae and Arthrodermatacea families differ from the ergot alkaloids produced by Claviceps and Neotyphodium. The clavine alkaloids lack the extensive peptide chain modifications that occur in lysergic acid derived ergot alkaloids. Both clavine and ergot alkaloids arise from the condensation of tryptophan and dimethylallylpyrophosphate by the action of the dimethylallyltryptophan synthase. The first five steps of the biosynthetic pathway that convert tryptophan and dimethylallyl-pyrophosphate (DMA-PP) in chanoclavine-1-aldehyde are common to both clavine and ergot alkaloids. The biosynthesis of ergot alkaloids has been extensively studied and is not considered in this article. We focus this review on recent advances in the gene clusters for clavine alkaloids in the species of Penicillium, Aspergillus (Neosartorya), Arthroderma and Trychophyton and the enzymes encoded by them. The final products of the clavine alkaloids pathways derive from the tetracyclic ergoline ring, which is modified by late enzymes, including a reverse type prenyltransferase, P450 monooxygenases and acetyltransferases. In Aspergillus japonicus, a α-ketoglutarate and Fe2+-dependent dioxygenase is involved in the cyclization of a festuclavine-like unknown type intermediate into cycloclavine. Related dioxygenases occur in the biosynthetic gene clusters of ergot alkaloids in Claviceps purpurea and also in the clavine clusters in Penicillium species. The final products of the clavine alkaloid pathway in these fungi differ from each other depending on the late biosynthetic enzymes involved. An important difference between clavine and ergot alkaloid pathways is that clavine producers lack the enzyme CloA, a P450 monooxygenase, involved in one of the steps of the conversion of chanoclavine-1-aldehyde into lysergic acid. Bioinformatic analysis of the sequenced genomes of the Aspergillaceae and Arthrodermataceae fungi showed the presence of clavine gene clusters in Arthroderma species, Penicillium roqueforti, Penicillium commune, Penicillium camemberti, Penicillium expansum, Penicillium steckii and Penicillium griseofulvum. Analysis of the gene clusters in several clavine alkaloid producers indicates that there are gene gains, gene losses and gene rearrangements. These findings may be explained by a divergent evolution of the gene clusters of ergot and clavine alkaloids from a common ancestral progenitor six genes cluster although horizontal gene transfer of some specific genes may have occurred more recently.
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de Benito A, Ibáñez C, Moncho W, Martínez D, Vettorazzi A, de Cerain AL. Database on the taxonomical characterisation and potential toxigenic capacities of microorganisms used for the industrial production of food enzymes and feed additives, which do not have a recommendation for Qualified Presumption of Safety. EFSA SUPPORTING PUBLICATIONS 2017. [PMCID: PMC7163622 DOI: 10.2903/sp.efsa.2017.en-1274] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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20
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The family of berberine bridge enzyme-like enzymes: A treasure-trove of oxidative reactions. Arch Biochem Biophys 2017; 632:88-103. [PMID: 28676375 DOI: 10.1016/j.abb.2017.06.023] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 12/18/2022]
Abstract
Biological oxidations form the basis of life on earth by utilizing organic compounds as electron donors to drive the generation of metabolic energy carriers, such as ATP. Oxidative reactions are also important for the biosynthesis of complex compounds, i.e. natural products such as alkaloids that provide vital benefits for organisms in all kingdoms of life. The vitamin B2-derived cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) enable an astonishingly diverse array of oxidative reactions that is based on the versatility of the redox-active isoalloxazine ring. The family of FAD-linked oxidases can be divided into subgroups depending on specific sequence features in an otherwise very similar structural context. The sub-family of berberine bridge enzyme (BBE)-like enzymes has recently attracted a lot of attention due to the challenging chemistry catalyzed by its members and the unique and unusual bi-covalent attachment of the FAD cofactor. This family is the focus of the present review highlighting recent advancements into the structural and functional aspects of members from bacteria, fungi and plants. In view of the unprecedented reaction catalyzed by the family's namesake, BBE from the California poppy, recent studies have provided further insights into nature's treasure chest of oxidative reactions.
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21
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Ehrenworth AM, Peralta-Yahya P. Accelerating the semisynthesis of alkaloid-based drugs through metabolic engineering. Nat Chem Biol 2017; 13:249-258. [DOI: 10.1038/nchembio.2308] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 12/19/2016] [Indexed: 02/07/2023]
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Abstract
Ergot alkaloids are a class of indole derivatives produced by the genera of Ascomycota includingClaviceps,Aspergillus,Penicillium, andEpichloë.
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Affiliation(s)
- Jing-Jing Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines
- Key Laboratory of Biosynthesis of Natural Products of National Health and Family Planning Commission
- Institute of Materia Medica
- Peking Union Medical College & Chinese Academy of Medical Sciences
- Beijing 100050
| | - Meng-Yao Han
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines
- Key Laboratory of Biosynthesis of Natural Products of National Health and Family Planning Commission
- Institute of Materia Medica
- Peking Union Medical College & Chinese Academy of Medical Sciences
- Beijing 100050
| | - Ting Gong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines
- Key Laboratory of Biosynthesis of Natural Products of National Health and Family Planning Commission
- Institute of Materia Medica
- Peking Union Medical College & Chinese Academy of Medical Sciences
- Beijing 100050
| | - Jin-Ling Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines
- Key Laboratory of Biosynthesis of Natural Products of National Health and Family Planning Commission
- Institute of Materia Medica
- Peking Union Medical College & Chinese Academy of Medical Sciences
- Beijing 100050
| | - Ping Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines
- Key Laboratory of Biosynthesis of Natural Products of National Health and Family Planning Commission
- Institute of Materia Medica
- Peking Union Medical College & Chinese Academy of Medical Sciences
- Beijing 100050
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23
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Schmidt NG, Eger E, Kroutil W. Building Bridges: Biocatalytic C-C-Bond Formation toward Multifunctional Products. ACS Catal 2016; 6:4286-4311. [PMID: 27398261 PMCID: PMC4936090 DOI: 10.1021/acscatal.6b00758] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/13/2016] [Indexed: 12/12/2022]
Abstract
Carbon-carbon bond formation is the key reaction for organic synthesis to construct the carbon framework of organic molecules. The review gives a selection of biocatalytic C-C-bond-forming reactions which have been investigated during the last 5 years and which have already been proven to be applicable for organic synthesis. In most cases, the reactions lead to products functionalized at the site of C-C-bond formation (e.g., α-hydroxy ketones, aminoalcohols, diols, 1,4-diketones, etc.) or allow to decorate aromatic and heteroaromatic molecules. Furthermore, examples for cyclization of (non)natural precursors leading to saturated carbocycles are given as well as the stereoselective cyclopropanation of olefins affording cyclopropanes. Although many tools are already available, recent research also makes it clear that nature provides an even broader set of enzymes to perform specific C-C coupling reactions. The possibilities are without limit; however, a big library of variants for different types of reactions is required to have the specific enzyme for a desired specific (stereoselective) reaction at hand.
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Affiliation(s)
- Nina G. Schmidt
- ACIB
GmbH c/o, Department of Chemistry, University
of Graz, Heinrichstrasse
28, 8010 Graz, Austria
| | - Elisabeth Eger
- Department
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- ACIB
GmbH c/o, Department of Chemistry, University
of Graz, Heinrichstrasse
28, 8010 Graz, Austria
- Department
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, 8010 Graz, Austria
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Banani H, Marcet-Houben M, Ballester AR, Abbruscato P, González-Candelas L, Gabaldón T, Spadaro D. Genome sequencing and secondary metabolism of the postharvest pathogen Penicillium griseofulvum. BMC Genomics 2016; 17:19. [PMID: 26729047 PMCID: PMC4700700 DOI: 10.1186/s12864-015-2347-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/21/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Penicillium griseofulvum is associated in stored apples with blue mould, the most important postharvest disease of pome fruit. This pathogen can simultaneously produce both detrimental and beneficial secondary metabolites (SM). In order to gain insight into SM synthesis in P. griseofulvum in vitro and during disease development on apple, we sequenced the genome of P. griseofulvum strain PG3 and analysed important SM clusters. RESULTS PG3 genome sequence (29.3 Mb) shows that P. griseofulvum branched off after the divergence of P. oxalicum but before the divergence of P. chrysogenum. Genome-wide analysis of P. griseofulvum revealed putative gene clusters for patulin, griseofulvin and roquefortine C biosynthesis. Furthermore, we quantified the SM production in vitro and on apples during the course of infection. The expression kinetics of key genes of SM produced in infected apple were examined. We found additional SM clusters, including those potentially responsible for the synthesis of penicillin, yanuthone D, cyclopiazonic acid and we predicted a cluster putatively responsible for the synthesis of chanoclavine I. CONCLUSIONS These findings provide relevant information to understand the molecular basis of SM biosynthesis in P. griseofulvum, to allow further research directed to the overexpression or blocking the synthesis of specific SM.
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Affiliation(s)
- Houda Banani
- DiSAFA - Dept. Agricultural, Forestry and Food Sciences and AGROINNOVA - Centre of Competence for the Innovation in the Agroenvironmental Sector, University of Torino, Largo Paolo Braccini 2, I-10095 Grugliasco, Torino, Italy.
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Programme. Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
| | - Ana-Rosa Ballester
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Avda. Agustin Escardino 7, Paterna, Valencia, 46980, Spain.
| | - Pamela Abbruscato
- Bioeconomy Unit, Parco Tecnologico Padano, via Einstein, 26900, Lodi, Italy.
| | - Luis González-Candelas
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Avda. Agustin Escardino 7, Paterna, Valencia, 46980, Spain.
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme. Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Davide Spadaro
- DiSAFA - Dept. Agricultural, Forestry and Food Sciences and AGROINNOVA - Centre of Competence for the Innovation in the Agroenvironmental Sector, University of Torino, Largo Paolo Braccini 2, I-10095 Grugliasco, Torino, Italy.
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Rugbjerg P, Myling-Petersen N, Sommer MOA. Flexible metabolic pathway construction using modular and divisible selection gene regulators. Metab Eng 2015; 31:189-97. [PMID: 26303342 DOI: 10.1016/j.ymben.2015.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 08/10/2015] [Accepted: 08/11/2015] [Indexed: 01/09/2023]
Abstract
Genetic selections are important to biological engineering. Although selectable traits are limited, currently each trait only permits simultaneous introduction of a single DNA fragment. Complex pathway and strain construction however depends on rapid, combinatorial introduction of many genes that encode putative pathway candidates and homologs. To triple the utility of existing selection genes, we have developed divisible selection in Saccharomyces cerevisiae. Here, independent DNA fragments can be introduced and selected for simultaneously using a set of split hybrid transcription factors composed of parts from Escherichia coli LexA and Herpes simplex VP16 to regulate one single selectable phenotype of choice. Only when co-expressed, these split hybrid transcription factors promote transcription of a selection gene, causing tight selection of transformants containing all desired DNA fragments. Upon transformation, 94% of the selected colonies resulted strictly from transforming all three modules based on ARS/CEN plasmids. Similarly when used for chromosome integration, 95% of the transformants contained all three modules. The divisible selection system acts dominantly and thus expands selection gene utility from one to three without any genomic pre-modifications of the strain. We demonstrate the approach by introducing the fungal rubrofusarin polyketide pathway at a gene load of 11 kb distributed on three different plasmids, using a single selection trait and one yeast transformation step. By tripling the utility of existing selection genes, the employment of divisible selection improves flexibility and freedom in the strain engineering process.
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Affiliation(s)
- Peter Rugbjerg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, DK-2970 Hørsholm, Denmark.
| | - Nils Myling-Petersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, DK-2970 Hørsholm, Denmark.
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, DK-2970 Hørsholm, Denmark.
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Jakubczyk D, Caputi L, Hatsch A, Nielsen CAF, Diefenbacher M, Klein J, Molt A, Schröder H, Cheng JZ, Naesby M, O'Connor SE. Discovery and reconstitution of the cycloclavine biosynthetic pathway--enzymatic formation of a cyclopropyl group. Angew Chem Int Ed Engl 2015; 54:5117-21. [PMID: 25712404 PMCID: PMC4471609 DOI: 10.1002/anie.201410002] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 01/29/2015] [Indexed: 12/04/2022]
Abstract
The ergot alkaloids, a class of fungal-derived natural products with important biological activities, are derived from a common intermediate, chanoclavine-I, which is elaborated into a set of diverse structures. Herein we report the discovery of the biosynthetic pathway of cycloclavine, a complex ergot alkaloid containing a cyclopropyl moiety. We used a yeast-based expression platform along with in vitro biochemical experiments to identify the enzyme that catalyzes a rearrangement of the chanoclavine-I intermediate to form a cyclopropyl moiety. The resulting compound, cycloclavine, was produced in yeast at titers of >500 mg L(-1) , thus demonstrating the feasibility of the heterologous expression of these complex alkaloids.
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Affiliation(s)
- Dorota Jakubczyk
- Department of Biological Chemistry, John Innes CentreColney Lane, Norwich (UK)
| | - Lorenzo Caputi
- Department of Biological Chemistry, John Innes CentreColney Lane, Norwich (UK)
| | | | | | | | - Jens Klein
- Evolva SADuggingerstrasse 23, Reinach (Switzerland)
| | | | | | - Johnathan Z Cheng
- Department of Biological Chemistry, John Innes CentreColney Lane, Norwich (UK)
| | | | - Sarah E O'Connor
- Department of Biological Chemistry, John Innes CentreColney Lane, Norwich (UK)
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Lin HC, Chiou G, Chooi YH, McMahon TC, Xu W, Garg NK, Tang Y. Elucidation of the concise biosynthetic pathway of the communesin indole alkaloids. Angew Chem Int Ed Engl 2015; 54:3004-7. [PMID: 25571861 PMCID: PMC4409825 DOI: 10.1002/anie.201411297] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Indexed: 11/07/2022]
Abstract
The communesins are a prominent class of indole alkaloids isolated from Penicillium species. Owing to their daunting structural framework and potential as pharmaceuticals, communesins have inspired numerous synthetic studies. However, the genetic and biochemical basis of communesin biosynthesis has remained unexplored. Herein, we report the identification and characterization of the communesin (cns) biosynthetic gene cluster from Penicillium expansum. We confirmed that communesin is biosynthesized by the coupling of tryptamine and aurantioclavine, two building blocks derived from L-tryptophan. The postmodification steps were mapped by targeted-gene-deletion experiments and the structural elucidation of intermediates and new analogues. Our studies set the stage for the biochemical characterization of communesin biosynthesis. This knowledge will aid our understanding of how nature generates remarkable structural complexity from simple precursors.
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Affiliation(s)
- Hsiao-Ching Lin
- Department of Chemical and Biomolecular Engineering Department of Chemistry and Biochemistry University of California, Los Angeles Los Angeles, CA 90095 (USA)
| | - Grace Chiou
- Department of Chemistry and Biochemistry University of California, Los Angeles
| | - Yit-Heng Chooi
- Plant Sciences Division, Research School of Biology, The Australian National University, Australia
| | - Travis C. McMahon
- Department of Chemistry and Biochemistry University of California, Los Angeles
| | - Wei Xu
- Department of Chemical and Biomolecular Engineering Department of Chemistry and Biochemistry University of California, Los Angeles Los Angeles, CA 90095 (USA)
| | - Neil K. Garg
- Department of Chemistry and Biochemistry University of California, Los Angeles
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering Department of Chemistry and Biochemistry University of California, Los Angeles Los Angeles, CA 90095 (USA)
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Jakubczyk D, Caputi L, Hatsch A, Nielsen CAF, Diefenbacher M, Klein J, Molt A, Schröder H, Cheng JZ, Naesby M, O'Connor SE. Discovery and Reconstitution of the Cycloclavine Biosynthetic Pathway-Enzymatic Formation of a Cyclopropyl Group. ACTA ACUST UNITED AC 2015; 127:5206-5210. [PMID: 27546918 PMCID: PMC4974921 DOI: 10.1002/ange.201410002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 01/29/2015] [Indexed: 12/05/2022]
Abstract
The ergot alkaloids, a class of fungal‐derived natural products with important biological activities, are derived from a common intermediate, chanoclavine‐I, which is elaborated into a set of diverse structures. Herein we report the discovery of the biosynthetic pathway of cycloclavine, a complex ergot alkaloid containing a cyclopropyl moiety. We used a yeast‐based expression platform along with in vitro biochemical experiments to identify the enzyme that catalyzes a rearrangement of the chanoclavine‐I intermediate to form a cyclopropyl moiety. The resulting compound, cycloclavine, was produced in yeast at titers of >500 mg L−1, thus demonstrating the feasibility of the heterologous expression of these complex alkaloids.
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Affiliation(s)
- Dorota Jakubczyk
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich (UK)
| | - Lorenzo Caputi
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich (UK)
| | | | | | | | - Jens Klein
- Evolva SA, Duggingerstrasse 23, Reinach (Switzerland)
| | | | | | - Johnathan Z Cheng
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich (UK)
| | | | - Sarah E O'Connor
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich (UK)
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29
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Diversification of ergot alkaloids in natural and modified fungi. Toxins (Basel) 2015; 7:201-18. [PMID: 25609183 PMCID: PMC4303823 DOI: 10.3390/toxins7010201] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/14/2015] [Indexed: 11/16/2022] Open
Abstract
Several fungi in two different families--the Clavicipitaceae and the Trichocomaceae--produce different profiles of ergot alkaloids, many of which are important in agriculture and medicine. All ergot alkaloid producers share early steps before their pathways diverge to produce different end products. EasA, an oxidoreductase of the old yellow enzyme class, has alternate activities in different fungi resulting in branching of the pathway. Enzymes beyond the branch point differ among lineages. In the Clavicipitaceae, diversity is generated by the presence or absence and activities of lysergyl peptide synthetases, which interact to make lysergic acid amides and ergopeptines. The range of ergopeptines in a fungus may be controlled by the presence of multiple peptide synthetases as well as by the specificity of individual peptide synthetase domains. In the Trichocomaceae, diversity is generated by the presence or absence of the prenyl transferase encoded by easL (also called fgaPT1). Moreover, relaxed specificity of EasL appears to contribute to ergot alkaloid diversification. The profile of ergot alkaloids observed within a fungus also is affected by a delayed flux of intermediates through the pathway, which results in an accumulation of intermediates or early pathway byproducts to concentrations comparable to that of the pathway end product.
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30
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Lin HC, Chiou G, Chooi YH, McMahon TC, Xu W, Garg NK, Tang Y. Elucidation of the Concise Biosynthetic Pathway of the Communesin Indole Alkaloids. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411297] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Gerhards N, Neubauer L, Tudzynski P, Li SM. Biosynthetic pathways of ergot alkaloids. Toxins (Basel) 2014; 6:3281-95. [PMID: 25513893 PMCID: PMC4280535 DOI: 10.3390/toxins6123281] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 01/01/2023] Open
Abstract
Ergot alkaloids are nitrogen-containing natural products belonging to indole alkaloids. The best known producers are fungi of the phylum Ascomycota, e.g., Claviceps, Epichloë, Penicillium and Aspergillus species. According to their structures, ergot alkaloids can be divided into three groups: clavines, lysergic acid amides and peptides (ergopeptines). All of them share the first biosynthetic steps, which lead to the formation of the tetracyclic ergoline ring system (except the simplest, tricyclic compound: chanoclavine). Different modifications on the ergoline ring by specific enzymes result in an abundance of bioactive natural products, which are used as pharmaceutical drugs or precursors thereof. From the 1950s through to recent years, most of the biosynthetic pathways have been elucidated. Gene clusters from several ergot alkaloid producers have been identified by genome mining and the functions of many of those genes have been demonstrated by knock-out experiments or biochemical investigations of the overproduced enzymes.
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Affiliation(s)
- Nina Gerhards
- Philipps-Universität Marburg, Institut für Pharmazeutische Biologie und Biotechnologie, Deutschhausstrasse 17A, D-35037 Marburg, Germany.
| | - Lisa Neubauer
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms Universität Münster, Schlossplatz 8, D-48143 Münster, Germany.
| | - Paul Tudzynski
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms Universität Münster, Schlossplatz 8, D-48143 Münster, Germany.
| | - Shu-Ming Li
- Philipps-Universität Marburg, Institut für Pharmazeutische Biologie und Biotechnologie, Deutschhausstrasse 17A, D-35037 Marburg, Germany.
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