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Gou Y, Li T, Wang Y. Active-Site Oxygen Accessibility and Catalytic Loop Dynamics of Plant Aromatic Amino Acid Decarboxylases from Molecular Simulations. Biochemistry 2024; 63:1980-1990. [PMID: 39008055 PMCID: PMC11308512 DOI: 10.1021/acs.biochem.4c00144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 07/05/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024]
Abstract
Aromatic amino acid decarboxylases (AAADs) are pyridoxal-5'-phosphate (PLP)-dependent enzymes that catalyze the decarboxylation of aromatic amino acid l-amino acids. In plants, apart from canonical AAADs that catalyze the straightforward decarboxylation reaction, other members of the AAAD family function as aromatic acetaldehyde synthases (AASs) and catalyze more complex decarboxylation-dependent oxidative deamination. The interconversion between a canonical AAAD and an AAS can be achieved by a single tyrosine-phenylalanine mutation in the large catalytic loop of the enzymes. In this work, we report implicit ligand sampling (ILS) calculations of the canonical l-tyrosine decarboxylase from Papaver somniferum (PsTyDC) that catalyzes l-tyrosine decarboxylation and its Y350F mutant that instead catalyzes the decarboxylation-dependent oxidative deamination of the same substrate. Through comparative analysis of the resulting three-dimensional (3D) O2 free energy profiles, we evaluate the impact of the key tyrosine/phenylalanine mutation on oxygen accessibility to both the wild type and Y350F mutant of PsTyDC. Additionally, using molecular dynamics (MD) simulations of the l-tryptophan decarboxylase from Catharanthus roseus (CrTDC), we further investigate the dynamics of a large catalytic loop known to be indispensable to all AAADs. Results of our ILS and MD calculations shed new light on how key structural elements and loop conformational dynamics underlie the enzymatic functions of different members of the plant AAAD family.
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Affiliation(s)
- Yitao Gou
- Department of Physics, The
Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Tianjie Li
- Department of Physics, The
Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yi Wang
- Department of Physics, The
Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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2
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Ferreira S, Balola A, Sveshnikova A, Hatzimanikatis V, Vilaça P, Maia P, Carreira R, Stoney R, Carbonell P, Souza CS, Correia J, Lousa D, Soares CM, Rocha I. Computer-aided design and implementation of efficient biosynthetic pathways to produce high added-value products derived from tyrosine in Escherichia coli. Front Bioeng Biotechnol 2024; 12:1360740. [PMID: 38978715 PMCID: PMC11228882 DOI: 10.3389/fbioe.2024.1360740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 06/03/2024] [Indexed: 07/10/2024] Open
Abstract
Developing efficient bioprocesses requires selecting the best biosynthetic pathways, which can be challenging and time-consuming due to the vast amount of data available in databases and literature. The extension of the shikimate pathway for the biosynthesis of commercially attractive molecules often involves promiscuous enzymes or lacks well-established routes. To address these challenges, we developed a computational workflow integrating enumeration/retrosynthesis algorithms, a toolbox for pathway analysis, enzyme selection tools, and a gene discovery pipeline, supported by manual curation and literature review. Our focus has been on implementing biosynthetic pathways for tyrosine-derived compounds, specifically L-3,4-dihydroxyphenylalanine (L-DOPA) and dopamine, with significant applications in health and nutrition. We selected one pathway to produce L-DOPA and two different pathways for dopamine-one already described in the literature and a novel pathway. Our goal was either to identify the most suitable gene candidates for expression in Escherichia coli for the known pathways or to discover innovative pathways. Although not all implemented pathways resulted in the accumulation of target compounds, in our shake-flask experiments we achieved a maximum L-DOPA titer of 0.71 g/L and dopamine titers of 0.29 and 0.21 g/L for known and novel pathways, respectively. In the case of L-DOPA, we utilized, for the first time, a mutant version of tyrosinase from Ralstonia solanacearum. Production of dopamine via the known biosynthesis route was accomplished by coupling the L-DOPA pathway with the expression of DOPA decarboxylase from Pseudomonas putida, resulting in a unique biosynthetic pathway never reported in literature before. In the context of the novel pathway, dopamine was produced using tyramine as the intermediate compound. To achieve this, tyrosine was initially converted into tyramine by expressing TDC from Levilactobacillus brevis, which, in turn, was converted into dopamine through the action of the enzyme encoded by ppoMP from Mucuna pruriens. This marks the first time that an alternative biosynthetic pathway for dopamine has been validated in microbes. These findings underscore the effectiveness of our computational workflow in facilitating pathway enumeration and selection, offering the potential to uncover novel biosynthetic routes, thus paving the way for other target compounds of biotechnological interest.
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Affiliation(s)
- Sofia Ferreira
- Systems and Synthetic Biology Laboratory, ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Alexandra Balola
- Systems and Synthetic Biology Laboratory, ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Anastasia Sveshnikova
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Paulo Vilaça
- SilicoLife-Computational Biology Solutions for the Life Sciences, Braga, Portugal
| | - Paulo Maia
- SilicoLife-Computational Biology Solutions for the Life Sciences, Braga, Portugal
| | - Rafael Carreira
- SilicoLife-Computational Biology Solutions for the Life Sciences, Braga, Portugal
| | - Ruth Stoney
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
| | - Pablo Carbonell
- Institute of Industrial Control Systems and Computing (AI2), Universitat Politècnica de València (UPV), Valencia, Spain
- Institute for Integrative Systems Biology I2SysBio, Universitat de València-CSIC: Consejo Superior de Investigaciones Científicas, Paterna, Spain
| | - Caio Silva Souza
- Protein Modelling Laboratory, ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - João Correia
- Protein Modelling Laboratory, ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Diana Lousa
- Protein Modelling Laboratory, ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Cláudio M Soares
- Protein Modelling Laboratory, ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Isabel Rocha
- Systems and Synthetic Biology Laboratory, ITQB Nova-Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
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3
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Gou Y, Li D, Zhao M, Li M, Zhang J, Zhou Y, Xiao F, Liu G, Ding H, Sun C, Ye C, Dong C, Gao J, Gao D, Bao Z, Huang L, Xu Z, Lian J. Intein-mediated temperature control for complete biosynthesis of sanguinarine and its halogenated derivatives in yeast. Nat Commun 2024; 15:5238. [PMID: 38898098 PMCID: PMC11186835 DOI: 10.1038/s41467-024-49554-w] [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: 01/01/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
While sanguinarine has gained recognition for antimicrobial and antineoplastic activities, its complex conjugated structure and low abundance in plants impede broad applications. Here, we demonstrate the complete biosynthesis of sanguinarine and halogenated derivatives using highly engineered yeast strains. To overcome sanguinarine cytotoxicity, we establish a splicing intein-mediated temperature-responsive gene expression system (SIMTeGES), a simple strategy that decouples cell growth from product synthesis without sacrificing protein activity. To debottleneck sanguinarine biosynthesis, we identify two reticuline oxidases and facilitated functional expression of flavoproteins and cytochrome P450 enzymes via protein molecular engineering. After comprehensive metabolic engineering, we report the production of sanguinarine at a titer of 448.64 mg L-1. Additionally, our engineered strain enables the biosynthesis of fluorinated sanguinarine, showcasing the biotransformation of halogenated derivatives through more than 15 biocatalytic steps. This work serves as a blueprint for utilizing yeast as a scalable platform for biomanufacturing diverse benzylisoquinoline alkaloids and derivatives.
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Affiliation(s)
- Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Dongfang Li
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Minghui Zhao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Mengxin Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiaojiao Zhang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Yilian Zhou
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Feng Xiao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Gaofei Liu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Haote Ding
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Chenfan Sun
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Chang Dong
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Jucan Gao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Di Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Zehua Bao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China.
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4
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Li W, Chen Y, Yang R, Hu Z, Wei S, Hu S, Xiong X, Wang M, Lubeiny A, Li X, Feng M, Dong S, Xie X, Nie C, Zhang J, Luo Y, Zhou Y, Liu R, Pan J, Kong DX, Hu X. A terpenoids database with the chemical content as a novel agronomic trait. Database (Oxford) 2024; 2024:baae027. [PMID: 38776380 PMCID: PMC11110934 DOI: 10.1093/database/baae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/02/2023] [Accepted: 05/18/2024] [Indexed: 05/25/2024]
Abstract
Natural products play a pivotal role in drug discovery, and the richness of natural products, albeit significantly influenced by various environmental factors, is predominantly determined by intrinsic genetics of a series of enzymatic reactions and produced as secondary metabolites of organisms. Heretofore, few natural product-related databases take the chemical content into consideration as a prominent property. To gain unique insights into the quantitative diversity of natural products, we have developed the first TerPenoids database embedded with Content information (TPCN) with features such as compound browsing, structural search, scaffold analysis, similarity analysis and data download. This database can be accessed through a web-based computational toolkit available at http://www.tpcn.pro/. By conducting meticulous manual searches and analyzing over 10 000 reference papers, the TPCN database has successfully integrated 6383 terpenoids obtained from 1254 distinct plant species. The database encompasses exhaustive details including isolation parts, comprehensive molecule structures, chemical abstracts service registry number (CAS number) and 7508 content descriptions. The TPCN database accentuates both the qualitative and quantitative dimensions as invaluable phenotypic characteristics of natural products that have undergone genetic evolution. By acting as an indispensable criterion, the TPCN database facilitates the discovery of drug alternatives with high content and the selection of high-yield medicinal plant species or phylogenetic alternatives, thereby fostering sustainable, cost-effective and environmentally friendly drug discovery in pharmaceutical farming. Database URL: http://www.tpcn.pro/.
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Affiliation(s)
- Wenqian Li
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Yinliang Chen
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruofei Yang
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Zilong Hu
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shaozhong Wei
- Colorectal cancer clinical research center of HuBei Province,Colorectal cancer clinical research center of Wuhan, Hubei Cancer Hospital,Tongji Medical College, Huazhong University of Science and Technology,, Wuhan, Hubei 430069, China
| | - Sheng Hu
- Colorectal cancer clinical research center of HuBei Province,Colorectal cancer clinical research center of Wuhan, Hubei Cancer Hospital,Tongji Medical College, Huazhong University of Science and Technology,, Wuhan, Hubei 430069, China
| | - Xinjun Xiong
- Research Center for Rural Revitalization, Power China Kunming Engineering Corporation Limited, Kunming 650051, China
| | - Meijuan Wang
- Shennongjia Academy of Forestry, Shennongjia, Hubei 442400 China
| | | | - Xiaohua Li
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Minglei Feng
- Research Center for Rural Revitalization, Power China Kunming Engineering Corporation Limited, Kunming 650051, China
| | - Shuang Dong
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinlu Xie
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao Nie
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingyi Zhang
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunhao Luo
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Yichen Zhou
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruodi Liu
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinhai Pan
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - De-Xin Kong
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuebo Hu
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
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Seibold PS, Dörner S, Fricke J, Schäfer T, Beemelmanns C, Hoffmeister D. Genetic regulation of L-tryptophan metabolism in Psilocybe mexicana supports psilocybin biosynthesis. Fungal Biol Biotechnol 2024; 11:4. [PMID: 38664850 PMCID: PMC11046786 DOI: 10.1186/s40694-024-00173-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Although Basidiomycota produce pharmaceutically and ecologically relevant natural products, knowledge of how they coordinate their primary and secondary metabolism is virtually non-existent. Upon transition from vegetative mycelium to carpophore formation, mushrooms of the genus Psilocybe use L-tryptophan to supply the biosynthesis of the psychedelic tryptamine alkaloid psilocybin with the scaffold, leading to a strongly increased demand for this particular amino acid as this alkaloid may account for up to 2% of the dry mass. Using Psilocybe mexicana as our model and relying on genetic, transcriptomic, and biochemical methods, this study investigated if L-tryptophan biosynthesis and degradation in P. mexicana correlate with natural product formation. RESULTS A comparative transcriptomic approach of gene expression in P. mexicana psilocybin non-producing vegetative mycelium versus producing carpophores identified the upregulation of L-tryptophan biosynthesis genes. The shikimate pathway genes trpE1, trpD, and trpB (encoding anthranilate synthase, anthranilate phosphoribosyltransferase, and L-tryptophan synthase, respectively) were upregulated in carpophores. In contrast, genes idoA and iasA, encoding indole-2,3-dioxygenase and indole-3-acetaldehyde synthase, i.e., gateway enzymes for L-tryptophan-consuming pathways, were massively downregulated. Subsequently, IasA was heterologously produced in Escherichia coli and biochemically characterized in vitro. This enzyme represents the first characterized microbial L-tryptophan-preferring acetaldehyde synthase. A comparison of transcriptomic data collected in this study with prior data of Psilocybe cubensis showed species-specific differences in how L-tryptophan metabolism genes are regulated, despite the close taxonomic relationship. CONCLUSIONS The upregulated L-tryptophan biosynthesis genes and, oppositely, the concomitant downregulated genes encoding L-tryptophan-consuming enzymes reflect a well-adjusted cellular system to route this amino acid toward psilocybin production. Our study has pilot character beyond the genus Psilocybe and provides, for the first time, insight in the coordination of mushroom primary and secondary metabolism.
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Affiliation(s)
- Paula Sophie Seibold
- Institute for Pharmacy, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, 07745, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Neugasse 23, 07743, Jena, Germany
| | - Sebastian Dörner
- Institute for Pharmacy, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Janis Fricke
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Neugasse 23, 07743, Jena, Germany
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Tim Schäfer
- Institute for Pharmacy, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Christine Beemelmanns
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Neugasse 23, 07743, Jena, Germany
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, 07745, Jena, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
- Saarland University, 66123, Saarbrücken, Germany
| | - Dirk Hoffmeister
- Institute for Pharmacy, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany.
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, 07745, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Neugasse 23, 07743, Jena, Germany.
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6
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Cui Q, Liu Q, Fan Y, Wang C, Li Y, Li S, Zhang J, Rao G. Functional differentiation of olive PLP_deC genes: insights into metabolite biosynthesis and genetic improvement at the whole-genome level. PLANT CELL REPORTS 2024; 43:127. [PMID: 38652203 DOI: 10.1007/s00299-024-03212-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/01/2024] [Indexed: 04/25/2024]
Abstract
KEY MESSAGE This study identified 16 pyridoxal phosphate-dependent decarboxylases in olive at the whole-genome level, conducted analyses on their physicochemical properties, evolutionary relationships and characterized their activity. Group II pyridoxal phosphate-dependent decarboxylases (PLP_deC II) mediate the biosynthesis of characteristic olive metabolites, such as oleuropein and hydroxytyrosol. However, there have been no report on the functional differentiation of this gene family at the whole-genome level. This study conducted an exploration of the family members of PLP_deC II at the whole-genome level, identified 16 PLP_deC II genes, and analyzed their gene structure, physicochemical properties, cis-acting elements, phylogenetic evolution, and gene expression patterns. Prokaryotic expression and enzyme activity assays revealed that OeAAD2 and OeAAD4 could catalyze the decarboxylation reaction of tyrosine and dopa, resulting in the formation of their respective amine compounds, but it did not catalyze phenylalanine and tryptophan. Which is an important step in the synthetic pathway of hydroxytyrosol and oleuropein. This finding established the foundational data at the molecular level for studying the functional aspects of the olive PLP_deC II gene family and provided essential gene information for genetic improvement of olive.
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Affiliation(s)
- Qizhen Cui
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Qingqing Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yutong Fan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Chenhe Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yufei Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Shuyuan Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Guodong Rao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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7
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Hiura T, Yoshida H, Miyata U, Asami T, Suzuki Y. Conferring High IAA Productivity on Low-IAA-Producing Organisms with PonAAS2, an Aromatic Aldehyde Synthase of a Galling Sawfly, and Identification of Its Inhibitor. INSECTS 2023; 14:598. [PMID: 37504604 PMCID: PMC10380194 DOI: 10.3390/insects14070598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023]
Abstract
Gall-inducing insects often contain high concentrations of phytohormones, such as auxin and cytokinin, which are suggested to be involved in gall induction, but no conclusive evidence has yet been obtained. There are two possible approaches to investigating the importance of phytohormones in gall induction: demonstrating either that high phytohormone productivity can induce gall-inducing ability in non-gall-inducing insects or that the gall-inducing ability is inhibited when phytohormone productivity in galling insects is suppressed. In this study, we show that the overexpression of PonAAS2, which encodes an aromatic aldehyde synthase (AAS) responsible for the rate-limiting step in indoleacetic acid (IAA) biosynthesis in a galling sawfly (Pontania sp.) that contains high levels of endogenous IAA, conferred high IAA productivity on Caenorhabditis elegans, as the model system. This result strongly suggests that PonAAS2 can also confer high IAA productivity on low-IAA-producing insects. We also successfully identified an inhibitor of PonAAS2 in a chemical library. This highly selective inhibitor showed stronger inhibitory activity against AAS than against aromatic amino acid decarboxylase, which belongs to the same superfamily as AAS. We also confirm that this inhibitor clearly inhibited IAA productivity in the high-IAA-producing C. elegans engineered here.
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Affiliation(s)
- Takeshi Hiura
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-0054, Japan
- Department of Food and Life Sciences, College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami-machi, Inashiki-gun, Ibaraki 300-0393, Japan
| | - Hibiki Yoshida
- Department of Food and Life Sciences, College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami-machi, Inashiki-gun, Ibaraki 300-0393, Japan
| | - Umi Miyata
- Department of Food and Life Sciences, College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami-machi, Inashiki-gun, Ibaraki 300-0393, Japan
| | - Tadao Asami
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yoshihito Suzuki
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-0054, Japan
- Department of Food and Life Sciences, College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami-machi, Inashiki-gun, Ibaraki 300-0393, Japan
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8
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Wang Y, Chen Y, Zhang A, Chen K, Ouyang P. Advances in the microbial synthesis of the neurotransmitter serotonin. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12584-3. [PMID: 37326681 DOI: 10.1007/s00253-023-12584-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 06/17/2023]
Abstract
Serotonin, as a monoamine neurotransmitter, modulates the activity of the nervous system. Due to its importance in the coordination of movement and regulation of mood, impairments in the synthesis and homeostasis of serotonin are involved in numerous disorders, including depression, Parkinson's disease, and anxiety. Currently, serotonin is primarily obtained via natural extraction. But this method is time-consuming and low yield, as well as unstable supply of raw materials. With the development of synthetic biology, researchers have established the method of microbial synthesis of serotonin. Compared with natural extraction, microbial synthesis has the advantages of short production cycle, continuous production, not limited by season and source, and environment-friendly; hence, it has garnered considerable research attention. However, the yield of serotonin is still too low to industrialization. Therefore, this review provides the latest progress and examples that illustrate the synthesis pathways of serotonin as well as proposes strategies for increasing the production of serotonin. KEY POINTS: • Two biosynthesis pathways of serotonin are introduced. • L-tryptophan hydroxylation is the rate-limiting step in serotonin biosynthesis. • Effective strategies are proposed to improve serotonin production.
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Affiliation(s)
- Yingying Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
| | - Yan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
| | - Alei Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China.
| | - Pingkai Ouyang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
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9
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Yu H, Gao D, Khashi u Rahman M, Chen S, Wu F. L-phenylalanine in potato onion ( Allium cepa var. aggregatum G. Don) root exudates mediates neighbor detection and trigger physio-morphological root responses of tomato. FRONTIERS IN PLANT SCIENCE 2023; 14:1056629. [PMID: 36875620 PMCID: PMC9981155 DOI: 10.3389/fpls.2023.1056629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
INTERACTION Despite numerous recent insights into neighbor detection and belowground plant communication mediated by root exudates, less is known about the specificity and nature of substances within root exudates and the mechanism by which they may act belowground in root-root interactions. METHODS Here, we used a coculture experiment to study the root length density (RLD) of tomato (Solanum lycopersicum L.) grown with potato onion (Allium cepa var. aggregatum G. Don) cultivars with growth-promoting (S-potato onion) or no growth-promoting (N-potato onion) effects. RESULTS AND DISCUSSION Tomato plants grown with growth-promoting potato onion or its root exudates increased root distribution and length density oppositely and grew their roots away as compared to when grown with potato onion of no growth-promoting potential, its root exudates, and control (tomato monoculture/distilled water treatment). Root exudates profiling of two potato onion cultivars by UPLC-Q-TOF/MS showed that L-phenylalanine was only found in root exudates of S-potato onion. The role of L-phenylalanine was further confirmed in a box experiment in which it altered tomato root distribution and forced the roots grow away. In vitro trial revealed that tomato seedlings root exposed to L-phenylalanine changed the auxin distribution, decreased the concentration of amyloplasts in columella cells of roots, and changed the root deviation angle to grow away from the addition side. These results suggest that L-phenylalanine in S-potato onion root exudates may act as an "active compound" and trigger physio-morphological changes in neighboring tomato roots.
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Affiliation(s)
- Hongjie Yu
- Institute of Agricultural Economy and Scientific Information, Fujian Academy of Agricultural Sciences, Fuzhou, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Area Vegetable Biology, Northeast Agricultural University, Harbin, China
| | - Danmei Gao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Area Vegetable Biology, Northeast Agricultural University, Harbin, China
| | - Muhammad Khashi u Rahman
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Area Vegetable Biology, Northeast Agricultural University, Harbin, China
| | - Shaocan Chen
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Area Vegetable Biology, Northeast Agricultural University, Harbin, China
| | - Fengzhi Wu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Cold Area Vegetable Biology, Northeast Agricultural University, Harbin, China
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10
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Bienzymatic Cascade Combining a Peroxygenase with an Oxidase for the Synthesis of Aromatic Aldehydes from Benzyl Alcohols. Catalysts 2023. [DOI: 10.3390/catal13010145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Aromatic aldehydes are important aromatic compounds for the flavour and fragrance industry. In this study, a parallel cascade combining aryl alcohol oxidase from Pleurotus eryngii (PeAAOx) and unspecific peroxygenase from the basidiomycete Agrocybe aegerita (AaeUPO) to convert aromatic primary alcohols into high-value aromatic aldehydes is proposed. Key influencing factors in the process of enzyme cascade catalysis, such as enzyme dosage, pH and temperature, were investigated. The universality of PeAAOx coupled with AaeUPO cascade catalysis for the synthesis of aromatic aldehyde flavour compounds from aromatic primary alcohols was evaluated. In a partially optimised system (comprising 30 μM PeAAOx, 2 μM AaeUPO at pH 7 and 40 °C) up to 84% conversion of 50 mM veratryl alcohol into veratryl aldehyde was achieved in a self-sufficient aerobic reaction. Promising turnover numbers of 2800 and 21,000 for PeAAOx and AaeUPO, respectively, point towards practical applicability.
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11
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Elucidation of the 1-phenethylisoquinoline pathway from an endemic conifer Cephalotaxus hainanensis. Proc Natl Acad Sci U S A 2023; 120:e2209339120. [PMID: 36577068 PMCID: PMC9910586 DOI: 10.1073/pnas.2209339120] [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] [Indexed: 12/29/2022] Open
Abstract
Cephalotaxines harbor great medical potential, but their natural source, the endemic conifer Cephalotaxus is highly endangered, creating a conflict between biotechnological valorization and preservation of biodiversity. Here, we construct the whole biosynthetic pathway to the 1-phenethylisoquinoline scaffold, as first committed compound for phenylethylisoquinoline alkaloids (PIAs), combining metabolic modeling, and transcriptome mining of Cephalotaxus hainanensis to infer the biosynthesis for PIA precursor. We identify a novel protein, ChPSS, driving the Pictet-Spengler condensation and show that this enzyme represents the branching point where PIA biosynthesis diverges from the concurrent benzylisoquinoline-alkaloids pathway. We also pinpoint ChDBR as crucial step to form 4-hydroxydihydrocinnamaldehyde diverging from lignin biosynthesis. The elucidation of the early PIA pathway represents an important step toward microbe-based production of these pharmaceutically important alkaloids resolving the conflict between biotechnology and preservation of biodiversity.
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12
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Exploring the mechanism of compromised thermostability of aromatic L-amino acid decarboxylase from Bacillus atrophaeus through comparative molecular dynamics simulations. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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13
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Qiao C, Chen F, Liu Z, Huang T, Li W, Zhang G, Luo Y. Functional characterization of a catalytically promiscuous tryptophan decarboxylase from camptothecin-producing Camptotheca acuminata. FRONTIERS IN PLANT SCIENCE 2022; 13:987348. [PMID: 36061783 PMCID: PMC9433702 DOI: 10.3389/fpls.2022.987348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Tryptophan decarboxylases (TDCs) are a group of pyridoxal 5'-phosphate-dependent enzymes involved in the enzymatic conversion of tryptophan into tryptamine, a critical biogenic amine. We herein mined and cloned a TDC-encoding gene, CaTDC3, from camptothecin-producing plant Camptotheca acuminata. The intact CaTDC3 was heterologously overexpressed in Escherichia coli and the recombinant CaTDC3 was purified to homogeneity. High-performance liquid chromatography (HPLC)-diode array detector (DAD) and high resolution mass spectrometry (HRMS) data analyses of the CaTDC3-catalyzed reaction mixture confirmed the catalytically decarboxylative activity of CaTDC3. CaTDC3 shows strict stereoselectivity for L-tryptophan. Homology modeling and molecular docking implied CaTDC3's recognition of L-tryptophan derivatives and analogs. Substrate scope investigations revealed that the appropriate substituent groups on the indole ring, i.e., hydroxylated and halogenated L-tryptophans, could be recognized by CaTDC3 and the decarboxylation reactions generated the corresponding tryptamines. The Cβ -methyl-L-tryptophans were decarboxylated by CaTDC3 efficiently. 1-Thio-L-tryptophan, the NH group of the indole ring replaced by an S atom, could be decarboxylated by CaTDC3. CaTDC3 catalyzed the decarboxylation of 7-aza-L-tryptophan, an N displacement of the C on the aromatic ring, to afford 7-aza-tryptamine. L-Kynurenine, an L-tryptophan degradation product, could be decarboxylated by CaTDC3. The present works uncover a catalytically promiscuous TDC and the TDC is a versatile decarboxylase in synthetic biology for specialized pharmaceutically important substances.
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Affiliation(s)
- Chong Qiao
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Chen
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhan Liu
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianfang Huang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Wei Li
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guolin Zhang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yinggang Luo
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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14
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Commisso M, Negri S, Gecchele E, Fazion E, Pontoriero C, Avesani L, Guzzo F. Indolamine accumulation and TDC/ T5H expression profiles reveal the complex and dynamic regulation of serotonin biosynthesis in tomato ( Solanum lycopersicum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:975434. [PMID: 36035661 PMCID: PMC9405198 DOI: 10.3389/fpls.2022.975434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Tryptamine and serotonin are indolamines that fulfill diverse biological functions in all kingdoms of life. Plants convert l-tryptophan into tryptamine and then serotonin via consecutive decarboxylation and hydroxylation reactions catalyzed by the enzymes tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H). Tryptamine and serotonin accumulate to high levels in the edible fruits and seeds of many plant species, but their biological roles in reproductive organs remain unclear and the metabolic pathways have not been characterized in detail. We identified three TDC genes and a single T5H gene in tomato (Solanum lycopersicum L.) by homology-based screening and confirmed their activity by heterologous expression in Nicotiana benthamiana. The co-analysis of targeted metabolomics and gene expression data revealed complex spatiotemporal gene expression and metabolite accumulation patterns that suggest the involvement of the serotonin pathway in multiple biological processes. Our data support a model in which SlTDC1 allows tryptamine to accumulate in fruits, SlTDC2 causes serotonin to accumulate in aerial vegetative organs, and SlTDC3 works with SlT5H to convert tryptamine into serotonin in the roots and fruits.
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15
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Schenck CA, Busta L. Using interdisciplinary, phylogeny-guided approaches to understand the evolution of plant metabolism. PLANT MOLECULAR BIOLOGY 2022; 109:355-367. [PMID: 34816350 DOI: 10.1007/s11103-021-01220-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
To cope with relentless environmental pressures, plants produce an arsenal of structurally diverse chemicals, often called specialized metabolites. These lineage-specific compounds are derived from the simple building blocks made by ubiquitous core metabolic pathways. Although the structures of many specialized metabolites are known, the underlying metabolic pathways and the evolutionary events that have shaped the plant chemical diversity landscape are only beginning to be understood. However, with the advent of multi-omics data sets and the relative ease of studying pathways in previously intractable non-model species, plant specialized metabolic pathways are now being systematically identified. These large datasets also provide a foundation for comparative, phylogeny-guided studies of plant metabolism. Comparisons of metabolic traits and features like chemical abundances, enzyme activities, or gene sequences from phylogenetically diverse plants provide insights into how metabolic pathways evolved. This review highlights the power of studying evolution through the lens of comparative biochemistry, particularly how placing metabolism into a phylogenetic context can help a researcher identify the metabolic innovations enabling the evolution of structurally diverse plant metabolites.
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Affiliation(s)
- Craig A Schenck
- Department of Biochemistry, University of Missouri, Columbia, MO, USA.
| | - Lucas Busta
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, USA
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16
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Han SW, Shin JS. Aromatic L-amino acid decarboxylases: mechanistic features and microbial applications. Appl Microbiol Biotechnol 2022; 106:4445-4458. [DOI: 10.1007/s00253-022-12028-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/04/2022] [Accepted: 06/10/2022] [Indexed: 11/02/2022]
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17
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Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes. Curr Opin Microbiol 2022; 68:102172. [PMID: 35717707 DOI: 10.1016/j.mib.2022.102172] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/14/2022] [Accepted: 05/16/2022] [Indexed: 11/23/2022]
Abstract
Plants benefit from symbiotic relationships with their microbiomes. Modifying these microbiomes to further promote plant growth and improve stress tolerance in crops is a promising strategy. However, such efforts have had limited success, perhaps because the original microbiomes quickly re-establish. Since the complex biological networks involved are little understood, progress through conventional means is time-consuming. Synthetic biology, with its practical successes in multiple industries, could speed up this research considerably. Some fascinating candidates for production by synthetic microbiomes are organic nitrogen metabolites and related pyridoxal-5'-phosphate-dependent enzymes, which have pivotal roles in microbe-microbe and plant-microbe interactions. This review summarizes recent studies of these metabolites and enzymes and discusses prospective synthetic biology platforms for sustainable agriculture.
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18
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Maoz I, Lewinsohn E, Gonda I. Amino acids metabolism as a source for aroma volatiles biosynthesis. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102221. [PMID: 35533493 DOI: 10.1016/j.pbi.2022.102221] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/22/2022] [Accepted: 03/26/2022] [Indexed: 06/14/2023]
Abstract
Aroma volatiles are essential for plant ecological fitness and reproduction. Plants produce and use volatiles to attract pollinators and seed dispersers, repel herbivores and recruit their natural enemies, and communicate with other plants. Amino acids and their biosynthetic intermediates play key roles as precursors for the biosynthesis of plant volatiles. Different plants utilize different strategies and biosynthetic pathways to meet their specific biological needs. This review focuses on the different biosynthetic pathways that plants utilize to form amino acid-derived aroma volatiles, emphasizing their common and unique aspects and stressing the importance of the limiting enzymes residing in the primary-specialized metabolism interface. We also briefly review how biotechnology has used this interface and point to promising future directions for improving the quality of agricultural produce and the production of key volatiles.
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Affiliation(s)
- Itay Maoz
- Department of Postharvest Science, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel.
| | - Efraim Lewinsohn
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Volcani Institute, Ramat Yishay, Israel.
| | - Itay Gonda
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Volcani Institute, Ramat Yishay, Israel.
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19
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Bisello G, Kusmierska K, Verbeek MM, Sykut-Cegielska J, Willemsen MAAP, Wevers RA, Szymańska K, Poznanski J, Drozak J, Wertheim-Tysarowska K, Rygiel AM, Bertoldi M. The novel P330L pathogenic variant of aromatic amino acid decarboxylase maps on the catalytic flexible loop underlying its crucial role. Cell Mol Life Sci 2022; 79:305. [PMID: 35593933 PMCID: PMC9121088 DOI: 10.1007/s00018-022-04343-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/13/2022] [Accepted: 05/01/2022] [Indexed: 12/14/2022]
Abstract
Aromatic amino acid decarboxylase (AADC) deficiency is a rare monogenic disease, often fatal in the first decade, causing severe intellectual disability, movement disorders and autonomic dysfunction. It is due to mutations in the gene coding for the AADC enzyme responsible for the synthesis of dopamine and serotonin. Using whole exome sequencing, we have identified a novel homozygous c.989C > T (p.Pro330Leu) variant of AADC causing AADC deficiency. Pro330 is part of an essential structural and functional element: the flexible catalytic loop suggested to cover the active site as a lid and properly position the catalytic residues. Our investigations provide evidence that Pro330 concurs in the achievement of an optimal catalytic competence. Through a combination of bioinformatic approaches, dynamic light scattering measurements, limited proteolysis experiments, spectroscopic and in solution analyses, we demonstrate that the substitution of Pro330 with Leu, although not determining gross conformational changes, results in an enzymatic species that is highly affected in catalysis with a decarboxylase catalytic efficiency decreased by 674- and 194-fold for the two aromatic substrates. This defect does not lead to active site structural disassembling, nor to the inability to bind the pyridoxal 5’-phosphate (PLP) cofactor. The molecular basis for the pathogenic effect of this variant is rather due to a mispositioning of the catalytically competent external aldimine intermediate, as corroborated by spectroscopic analyses and pH dependence of the kinetic parameters. Altogether, we determined the structural basis for the severity of the manifestation of AADC deficiency in this patient and discussed the rationale for a precision therapy.
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Affiliation(s)
- Giovanni Bisello
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Strada Le Grazie 8, 37134, Verona, Italy
| | - Katarzyna Kusmierska
- Department of Screening and Metabolic Diagnostics, Institute of Mother and Child, Warsaw, Poland
| | - Marcel M Verbeek
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Cente, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Jolanta Sykut-Cegielska
- Department of Inborn Errors of Metabolism and Paediatrics, Institute of Mother and Child, Warsaw, Poland
| | - Michèl A A P Willemsen
- Department of Pediatric Neurology, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Ron A Wevers
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Cente, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Krystyna Szymańska
- Department of Child and Adolescent Psychiatry, Medical University of Warsaw, Warsaw, Poland
| | - Jarosław Poznanski
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jakub Drozak
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | | | - Mariarita Bertoldi
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Strada Le Grazie 8, 37134, Verona, Italy.
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20
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Han SW, Choi Y, Jang Y, Kim JS, Shin JS. One-pot biosynthesis of aromatic D-amino acids and neuroactive monoamines via enantioselective decarboxylation under in situ product removal using ion exchange resin. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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21
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Colinas M, Fitzpatrick TB. Coenzymes and the primary and specialized metabolism interface. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102170. [PMID: 35063913 DOI: 10.1016/j.pbi.2021.102170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
In plants, primary and specialized metabolism have classically been distinguished as either essential for growth or required for survival in a particular environment. Coenzymes (organic cofactors) are essential for growth but their importance to specialized metabolism is often not considered. In line with the recent proposal of viewing primary and specialized metabolism as an integrated whole rather than segregated lots with a defined interface, we highlight here the importance of collating information on the regulation of coenzyme supply with metabolic demands using examples of vitamin B derived coenzymes. We emphasize that coenzymes can have enormous influence on the outcome of metabolic as well as engineered pathways and should be taken into account in the era of synthetic biology.
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Affiliation(s)
- Maite Colinas
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 80, D-07745 Jena, Germany.
| | - Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland.
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22
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Wang Y, Chen X, Chen Q, Zhou N, Wang X, Zhang A, Chen K, Ouyang P. Construction of cell factory capable of efficiently converting L-tryptophan into 5-hydroxytryptamine. Microb Cell Fact 2022; 21:47. [PMID: 35331215 PMCID: PMC8944007 DOI: 10.1186/s12934-022-01745-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 01/21/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND L-Tryptophan (L-Trp) derivatives such as 5-hydroxytryptophan (5-HTP) and 5-hydroxytryptamine (5-HT), N-Acetyl-5-hydroxytryptamine and melatonin are important molecules with pharmaceutical interest. Among, 5-HT is an inhibitory neurotransmitter with proven benefits for treating the symptoms of depression. At present, 5-HT depends on plant extraction and chemical synthesis, which limits its mass production and causes environmental problems. Therefore, it is necessary to develop an efficient, green and sustainable biosynthesis method to produce 5-HT. RESULTS Here we propose a one-pot production of 5-HT from L-Trp via two enzyme cascades for the first time. First, a chassis cell that can convert L-Trp into 5-HTP was constructed by heterologous expression of tryptophan hydroxylase from Schistosoma mansoni (SmTPH) and an artificial endogenous tetrahydrobiopterin (BH4) module. Then, dopa decarboxylase from Harminia axyridis (HaDDC), which can specifically catalyse 5-HTP to 5-HT, was used for 5-HT production. The cell factory, E. coli BL21(DE3)△tnaA/BH4/HaDDC-SmTPH, which contains SmTPH and HaDDC, was constructed for 5-HT synthesis. The highest concentration of 5-HT reached 414.5 ± 1.6 mg/L (with conversion rate of 25.9 mol%) at the optimal conditions (substrate concentration,2 g/L; induced temperature, 25℃; IPTG concentration, 0.5 mM; catalysis temperature, 30℃; catalysis time, 72 h). CONCLUSIONS This protocol provided an efficient one-pot method for converting. L-Trp into 5-HT production, which opens up possibilities for the practical biosynthesis of natural 5-HT at an industrial scale.
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Affiliation(s)
- Yingying Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Xueman Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Qiaoyu Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Ning Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Alei Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China. .,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China.
| | - Pingkai Ouyang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
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23
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Kerbs A, Burgardt A, Veldmann KH, Schäffer T, Lee JH, Wendisch VF. Fermentative production of halogenated tryptophan derivatives with Corynebacterium glutamicum overexpressing tryptophanase or decarboxylase genes. Chembiochem 2022; 23:e202200007. [PMID: 35224830 PMCID: PMC9315010 DOI: 10.1002/cbic.202200007] [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: 02/08/2022] [Revised: 02/25/2022] [Indexed: 11/24/2022]
Abstract
The aromatic amino acid l‐tryptophan serves as a precursor for many valuable compounds such as neuromodulators, indoleamines and indole alkaloids. In this work, tryptophan biosynthesis was extended by halogenation followed by decarboxylation to the respective tryptamines or cleavage to the respective indoles. Either the tryptophanase genes tnaAs from E. coli and Proteus vulgaris or the aromatic amino acid decarboxylase genes AADCs from Bacillus atrophaeus, Clostridium sporogenes, and Ruminococcus gnavus were expressed in Corynebacterium glutamicum strains producing (halogenated) tryptophan. Regarding indoles, final titers of 16 mg L−1 7‐Cl‐indole and 23 mg L−1 7‐Br‐indole were attained. Tryptamine production led to a much higher titer of 2.26 g L−1 upon expression of AADC from B. atrophaeus. AADC enzymes were shown to be active with halogenated tryptophan in vitro and in vivo and supported production of 0.36 g L−1 7‐Br‐tryptamine with a volumetric productivity of 8.3 mg L−1 h−1 in a fed‐batch fermentation.
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Affiliation(s)
- Anastasia Kerbs
- Bielefeld University: Universitat Bielefeld, Genetics of Prokaryotes, GERMANY
| | - Arthur Burgardt
- Bielefeld University: Universitat Bielefeld, Genetics of Prokaryotes, GERMANY
| | - Kareen H Veldmann
- Bielefeld University: Universitat Bielefeld, Genetisc of Prokaryotes, GERMANY
| | - Thomas Schäffer
- Bielefeld University: Universitat Bielefeld, Fermentation Technology, GERMANY
| | - Jin-Ho Lee
- Kyungsung University, Food Science and Biotechnology, KOREA, REPUBLIC OF
| | - Volker F Wendisch
- Bielefeld University: Universitat Bielefeld, Genetics of Prokaryotes, Universitätsstr. 25, 33615, Bielefeld, GERMANY
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24
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Liu T, Gou Y, Zhang B, Gao R, Dong C, Qi M, Jiang L, Ding X, Li C, Lian J. Construction of Ajmalicine and Sanguinarine
de novo
Biosynthetic Pathways using Stable Integration Sites in Yeast. Biotechnol Bioeng 2022; 119:1314-1326. [DOI: 10.1002/bit.28040] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/22/2021] [Accepted: 01/02/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Tengfei Liu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
| | - Bei Zhang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Rui Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
| | - Chang Dong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
| | - Mingming Qi
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Lihong Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Xuanwei Ding
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 100081 China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 100081 China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
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25
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Dubs NM, Davis BR, de Brito V, Colebrook KC, Tiefel IJ, Nakayama MB, Huang R, Ledvina AE, Hack SJ, Inkelaar B, Martins TR, Aartila SM, Albritton KS, Almuhanna S, Arnoldi RJ, Austin CK, Battle AC, Begeman GR, Bickings CM, Bradfield JT, Branch EC, Conti EP, Cooley B, Dotson NM, Evans CJ, Fries AS, Gilbert IG, Hillier WD, Huang P, Hyde KW, Jevtovic F, Johnson MC, Keeler JL, Lam A, Leach KM, Livsey JD, Lo JT, Loney KR, Martin NW, Mazahem AS, Mokris AN, Nichols DM, Ojha R, Okorafor NN, Paris JR, Reboucas TF, Sant'Anna PB, Seitz MR, Seymour NR, Slaski LK, Stemaly SO, Ulrich BR, Van Meter EN, Young ML, Barkman TJ. A collaborative classroom investigation of the evolution of SABATH methyltransferase substrate preference shifts over 120 million years of flowering plant history. Mol Biol Evol 2022; 39:6503504. [PMID: 35021222 PMCID: PMC8890502 DOI: 10.1093/molbev/msac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Next-generation sequencing has resulted in an explosion of available data, much of which remains unstudied in terms of biochemical function; yet, experimental characterization of these sequences has the potential to provide unprecedented insight into the evolution of enzyme activity. One way to make inroads into the experimental study of the voluminous data available is to engage students by integrating teaching and research in a college classroom such that eventually hundreds or thousands of enzymes may be characterized. In this study, we capitalize on this potential to focus on SABATH methyltransferase enzymes that have been shown to methylate the important plant hormone, salicylic acid (SA), to form methyl salicylate. We analyze data from 76 enzymes of flowering plant species in 23 orders and 41 families to investigate how widely conserved substrate preference is for SA methyltransferase orthologs. We find a high degree of conservation of substrate preference for SA over the structurally similar metabolite, benzoic acid, with recent switches that appear to be associated with gene duplication and at least three cases of functional compensation by paralogous enzymes. The presence of Met in active site position 150 is a useful predictor of SA methylation preference in SABATH methyltransferases but enzymes with other residues in the homologous position show the same substrate preference. Although our dense and systematic sampling of SABATH enzymes across angiosperms has revealed novel insights, this is merely the “tip of the iceberg” since thousands of sequences remain uncharacterized in this enzyme family alone.
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Affiliation(s)
- Nicole M Dubs
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Breck R Davis
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Victor de Brito
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Kate C Colebrook
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Ian J Tiefel
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Madison B Nakayama
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Ruiqi Huang
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Audrey E Ledvina
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Samantha J Hack
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Brent Inkelaar
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Talline R Martins
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Sarah M Aartila
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Kelli S Albritton
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Sarah Almuhanna
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Ryan J Arnoldi
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Clara K Austin
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Amber C Battle
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Gregory R Begeman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Caitlin M Bickings
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Jonathon T Bradfield
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Eric C Branch
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Eric P Conti
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Breana Cooley
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Nicole M Dotson
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Cheyone J Evans
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Amber S Fries
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Ivan G Gilbert
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Weston D Hillier
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Pornkamol Huang
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Kaitlin W Hyde
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Filip Jevtovic
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Mark C Johnson
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Julie L Keeler
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Albert Lam
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Kyle M Leach
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Jeremy D Livsey
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Jonathan T Lo
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Kevin R Loney
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Nich W Martin
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Amber S Mazahem
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Aurora N Mokris
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Destiny M Nichols
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Ruchi Ojha
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Nnanna N Okorafor
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Joshua R Paris
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | | | | | - Mathew R Seitz
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Nathan R Seymour
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Lila K Slaski
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Stephen O Stemaly
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Benjamin R Ulrich
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Emile N Van Meter
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Meghan L Young
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
| | - Todd J Barkman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008
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26
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Wong A, Hu N, Tian X, Yang Y, Gehring C. Nitric oxide sensing revisited. TRENDS IN PLANT SCIENCE 2021; 26:885-897. [PMID: 33867269 DOI: 10.1016/j.tplants.2021.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/10/2021] [Accepted: 03/17/2021] [Indexed: 05/22/2023]
Abstract
Nitric oxide (NO) sensing is an ancient trait enabled by hemoproteins harboring a highly conserved Heme-Nitric oxide/OXygen (H-NOX) domain that operates throughout bacteria, fungi, and animal kingdoms including in humans, but that has long thought to be absent in plants. Recently, H-NOX-containing plant hemoproteins mediating crucial NO-dependent responses such as stomatal closure and pollen tube guidance have been reported. There are indications that the detection method that led to these discoveries will uncover many more heme-based NO sensors that operate as regulatory sites in complex proteins. Their characterizations will in turn offer a much more complete picture of plant NO responses at both the molecular and systems level.
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Affiliation(s)
- Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China; Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province 325060, China.
| | - Ningxin Hu
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Xuechen Tian
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Yixin Yang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China; Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Christoph Gehring
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, I-06121 Perugia, Italy
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27
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Negri S, Commisso M, Avesani L, Guzzo F. The case of tryptamine and serotonin in plants: a mysterious precursor for an illustrious metabolite. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5336-5355. [PMID: 34009335 DOI: 10.1093/jxb/erab220] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
Indolamines are tryptophan-derived specialized metabolites belonging to the huge and ubiquitous indole alkaloids group. Serotonin and melatonin are the best-characterized members of this family, given their many hormonal and physiological roles in animals. Following their discovery in plants, the study of plant indolamines has flourished and their involvement in important processes, including stress responses, growth and development, and reproduction, has been proposed, leading to their classification as a new category of phytohormones. However, the complex indolamine puzzle is far from resolved, particularly the biological roles of tryptamine, the early serotonin precursor representing the central hub of many downstream indole alkaloids. Tryptophan decarboxylase, which catalyzes the synthesis of tryptamine, strictly regulates the flux of carbon and nitrogen from the tryptophan pool into the indolamine pathway. Furthermore, tryptamine accumulates to high levels in the reproductive organs of many plant species and therefore cannot be classed as a mere intermediate but rather as an end product with potentially important functions in fruits and seeds. This review summarizes current knowledge on the role of tryptamine and its close relative serotonin, emphasizing the need for a clear understanding of the functions of, and mutual relations between, these indolamines and their biosynthesis pathways in plants.
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Affiliation(s)
- Stefano Negri
- Department of Biotechnology, University of Verona, Strada Le Grazie, Verona, Italy
| | - Mauro Commisso
- Department of Biotechnology, University of Verona, Strada Le Grazie, Verona, Italy
| | - Linda Avesani
- Department of Biotechnology, University of Verona, Strada Le Grazie, Verona, Italy
| | - Flavia Guzzo
- Department of Biotechnology, University of Verona, Strada Le Grazie, Verona, Italy
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28
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Torrens-Spence MP, Glinkerman CM, Günther J, Weng JK. Imine chemistry in plant metabolism. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:101999. [PMID: 33450608 DOI: 10.1016/j.pbi.2020.101999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/25/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
Imine chemistry represents an important category of chemical reactions involved in the biosynthesis of plant natural products, ranging from the newly discovered mobile defense hormone N-hydroxy-pipecolic acid to the red-to-yellow tyrosine-derived betalain pigments. Spontaneous imine formation reactions have also served as the basis for the evolution of numerous plant metabolic enzymes, such as specialized Pictet-Spenglerases that produce the backbone structures of benzylisoquinoline and monoterpene indole alkaloids and pyridoxal 5'-phosphate-dependent enzymes of diverse functions. Here, we review occurrences of imine chemistry in plant metabolism and their chemical and biochemical mechanisms. A better understanding of plant imine chemistry will ultimately facilitate synthetic biology approaches to further expand the scope of imine natural product biosynthesis for broad biotechnological applications.
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Affiliation(s)
| | | | - Jan Günther
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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29
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Gayathri SC, Manoj N. Crystallographic Snapshots of the Dunathan and Quinonoid Intermediates provide Insights into the Reaction Mechanism of Group II Decarboxylases. J Mol Biol 2020; 432:166692. [PMID: 33122004 DOI: 10.1016/j.jmb.2020.10.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 01/01/2023]
Abstract
PLP-dependent enzymes catalyze a plethora of chemical reactions affecting diverse physiological functions. Here we report the structural determinants of the reaction mechanism in a Group II PLP-dependent decarboxylase by assigning two early intermediates. The in-crystallo complexes of the PLP bound form, and the Dunathan and quinonoid intermediates, allowed direct observation of the active site interactions. The structures reveal that a subtle rearrangement of a conserved Arg residue in concert with a water-mediated interaction with the carboxylate of the Dunathan intermediate, appears to directly stabilize the alignment and facilitate the release of CO2 to yield the quinonoid. Modeling indicates that the conformational change of a dynamic catalytic loop to a closed form controls a conserved network of hydrogen bond interactions between catalytic residues to protonate the quinonoid. Our results provide a structural framework to elucidate mechanistic roles of residues that govern reaction specificity and catalysis in PLP-dependent decarboxylation.
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Affiliation(s)
- Subash Chellam Gayathri
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
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30
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Zhang P, Berardini TZ, Ebert D, Li Q, Mi H, Muruganujan A, Prithvi T, Reiser L, Sawant S, Thomas PD, Huala E. PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference. PLANT DIRECT 2020; 4:e00293. [PMID: 33392435 PMCID: PMC7773024 DOI: 10.1002/pld3.293] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 05/22/2023]
Abstract
We aim to enable the accurate and efficient transfer of knowledge about gene function gained from Arabidopsis thaliana and other model organisms to other plant species. This knowledge transfer is frequently challenging in plants due to duplications of individual genes and whole genomes in plant lineages. Such duplications result in complex evolutionary relationships between related genes, which may have similar sequences but highly divergent functions. In such cases, functional inference requires more than a simple sequence similarity calculation. We have developed an online resource, PhyloGenes (phylogenes.org), that displays precomputed phylogenetic trees for plant gene families along with experimentally validated function information for individual genes within the families. A total of 40 plant genomes and 10 non-plant model organisms are represented in over 8,000 gene families. Evolutionary events such as speciation and duplication are clearly labeled on gene trees to distinguish orthologs from paralogs. Nearly 6,000 families have at least one member with an experimentally supported annotation to a Gene Ontology (GO) molecular function or biological process term. By displaying experimentally validated gene functions associated to individual genes within a tree, PhyloGenes enables functional inference for genes of uncharacterized function, based on their evolutionary relationships to experimentally studied genes, in a visually traceable manner. For the many families containing genes that have evolved to perform different functions, PhyloGenes facilitates the use of evolutionary history to determine the most likely function of genes that have not been experimentally characterized. Future work will enrich the resource by incorporating additional gene function datasets such as plant gene expression atlas data.
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Affiliation(s)
| | | | - Dustin Ebert
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Qian Li
- Phoenix BioinformaticsFremontCAUSA
| | - Huaiyu Mi
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Anushya Muruganujan
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | | | | | | | - Paul D. Thomas
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
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Mahootchi E, Raasakka A, Luan W, Muruganandam G, Loris R, Haavik J, Kursula P. Structure and substrate specificity determinants of the taurine biosynthetic enzyme cysteine sulphinic acid decarboxylase. J Struct Biol 2020; 213:107674. [PMID: 33253877 DOI: 10.1016/j.jsb.2020.107674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/13/2020] [Accepted: 11/21/2020] [Indexed: 02/03/2023]
Abstract
Pyridoxal 5́-phosphate (PLP) is an important cofactor for amino acid decarboxylases with many biological functions, including the synthesis of signalling molecules, such as serotonin, dopamine, histamine, γ-aminobutyric acid, and taurine. Taurine is an abundant amino acid with multiple physiological functions, including osmoregulation, pH regulation, antioxidative protection, and neuromodulation. In mammalian tissues, taurine is mainly produced by decarboxylation of cysteine sulphinic acid to hypotaurine, catalysed by the PLP-dependent cysteine sulphinic acid decarboxylase (CSAD), followed by oxidation of the product to taurine. We determined the crystal structure of mouse CSAD and compared it to other PLP-dependent decarboxylases in order to identify determinants of substrate specificity and catalytic activity. Recognition of the substrate involves distinct side chains forming the substrate-binding cavity. In addition, the backbone conformation of a buried active-site loop appears to be a critical determinant for substrate side chain binding in PLP-dependent decarboxylases. Phe94 was predicted to affect substrate specificity, and its mutation to serine altered both the catalytic properties of CSAD and its stability. Using small-angle X-ray scattering, we further showed that CSAD presents open/close motions in solution. The structure of apo-CSAD indicates that the active site gets more ordered upon internal aldimine formation. Taken together, the results highlight details of substrate recognition in PLP-dependent decarboxylases and provide starting points for structure-based inhibitor design with the aim of affecting the biosynthesis of taurine and other abundant amino acid metabolites.
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Affiliation(s)
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Weisha Luan
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Gopinath Muruganandam
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium; Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Remy Loris
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium; Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jan Haavik
- Department of Biomedicine, University of Bergen, Bergen, Norway; Bergen Center of Brain Plasticity, Division of Psychiatry, Haukeland University Hospital, Bergen, Norway.
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway; Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland.
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Oxygen reactivity with pyridoxal 5'-phosphate enzymes: biochemical implications and functional relevance. Amino Acids 2020; 52:1089-1105. [PMID: 32844248 PMCID: PMC7497351 DOI: 10.1007/s00726-020-02885-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/18/2020] [Indexed: 12/29/2022]
Abstract
The versatility of reactions catalyzed by pyridoxal 5'-phosphate (PLP) enzymes is largely due to the chemistry of their extraordinary catalyst. PLP is necessary for many reactions involving amino acids. Reaction specificity is controlled by the orientation of the external aldimine intermediate that is formed upon addition of the amino acidic substrate to the coenzyme. The breakage of a specific bond of the external aldimine gives rise to a carbanionic intermediate. From this point, the different reaction pathways diverge leading to multiple activities: transamination, decarboxylation, racemization, elimination, and synthesis. A significant novelty appeared approximately 30 years ago when it was reported that some PLP-dependent decarboxylases are able to consume molecular oxygen transforming an amino acid into a carbonyl compound. These side paracatalytic reactions could be particularly relevant for human health, also considering that some of these enzymes are responsible for the synthesis of important neurotransmitters such as γ-aminobutyric acid, dopamine, and serotonin, whose dysregulation under oxidative conditions could have important implications in neurodegenerative states. However, the reactivity of PLP enzymes with dioxygen is not confined to mammals/animals. In fact, some plant PLP decarboxylases have been reported to catalyze oxidative reactions producing carbonyl compounds. Moreover, other recent reports revealed the existence of new oxidase activities catalyzed by new PLP enzymes, MppP, RohP, Ind4, CcbF, PvdN, Cap15, and CuaB. These PLP enzymes belong to the bacterial and fungal kingdoms and are present in organisms synthesizing bioactive compounds. These new PLP activities are not paracatalytic and could only scratch the surface on a wider and unexpected catalytic capability of PLP enzymes.
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Lichman BR. The scaffold-forming steps of plant alkaloid biosynthesis. Nat Prod Rep 2020; 38:103-129. [PMID: 32745157 DOI: 10.1039/d0np00031k] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Alkaloids from plants are characterised by structural diversity and bioactivity, and maintain a privileged position in both modern and traditional medicines. In recent years, there have been significant advances in elucidating the biosynthetic origins of plant alkaloids. In this review, I will describe the progress made in determining the metabolic origins of the so-called true alkaloids, specialised metabolites derived from amino acids containing a nitrogen heterocycle. By identifying key biosynthetic steps that feature in the majority of pathways, I highlight the key roles played by modifications to primary metabolism, iminium reactivity and spontaneous reactions in the molecular and evolutionary origins of these pathways.
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Affiliation(s)
- Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.
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