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Li W, Yan X, Xia W, Zhao L, Pei J. Enzymatic properties and immobilization of a thermostable prenyltransferase from Aspergillus fumigatiaffinis for the production of prenylated naringenin. Bioorg Chem 2024; 145:107183. [PMID: 38340474 DOI: 10.1016/j.bioorg.2024.107183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/24/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Prenyltransferases catalyze the synthesis of prenylated flavonoids, providing these with greater lipid solubility, biological activity, and availability. In this study, a thermostable prenyltransferase (AfPT) from Aspergillus fumigatiaffinis was cloned and expressed in Escherichia coli. By optimizing induction conditions, the expression level of AfPT reached 39.3 mU/mL, which was approximately 200 % of that before optimization. Additionally, we determined the enzymatic properties of AfPT. Subsequently, AfPT was immobilized on carboxymethyl cellulose magnetic nanoparticles (CMN) at a maximum load of 0.6 mg/mg. Optimal activity of CMN-AfPT was achieved at pH 8.0 and 55 °C. Thermostability assays showed that the residual activity of CMN-AfPT was greater than 50 % after incubation at 55 °C for 4 h. Km and Vmax of CMN-AfPT for naringenin were 0.082 mM and 5.57 nmol/min/mg, respectively. The Kcat/Km ratio of CMN-AfPT was higher than that of AfPT. Residual prenyltransferase activity of CMN-AfPT remained higher than 70 % even after 30 days of storage. Further, CMN-AfPT retained 68 % of its original activity after 10 cycles of reuse. Compared with free AfPT, CMN-AfPT showed higher catalytic efficiency, thermostability, metal ion tolerance, substrate affinity, storage stability, and reusability. Our study presents a thermostable prenyltransferase and its immobilized form for the production of prenylated flavonoids in vitro.
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Affiliation(s)
- Wenbo Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Xin Yan
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Wenli Xia
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Linguo Zhao
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China.
| | - Jianjun Pei
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China.
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2
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Spitzer S, Wloka J, Pietruszka J, Kayser O. Generation of Cannabigerolic Acid Derivatives and Their Precursors by Using the Promiscuity of the Aromatic Prenyltransferase NphB. Chembiochem 2023; 24:e202300441. [PMID: 37690998 DOI: 10.1002/cbic.202300441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
NphB is an aromatic prenyltransferase with high promiscuity for phenolics including flavonoids, isoflavonoids, and plant polyketides. It has been demonstrated that cannabigerolic acid is successfully formed by the reaction catalysed by NphB using geranyl diphosphate and olivetolic acid as substrates. In this study, the substrate specificity of NphB was further determined by using olivetolic acid derivatives as potential substrates for the formation of new synthetic cannabinoids. The derivatives differ in the hydrocarbon chain attached to C6 of the core structure. We performed in silico experiments, including docking of olivetolic acid derivatives, to identify differences in their binding modes. Substrate acceptance was predicted. Based on these results, a library of olivetolic acid derivatives was constructed and synthesized by using different organic synthetic routes. Conversion was monitored in in vitro assays with purified NphB versions. For the substrates leading to a high conversion olivetolic acid-C8, olivetolic acid-C2 and 2-benzyl-4,6-dihydroxybenzoic acid, the products were further elucidated and identified as cannbigerolic acid derivatives. Therefore, these substrates show potential to be adapted in cannabinoid biosynthesis.
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Affiliation(s)
- Saskia Spitzer
- Technical Biochemistry Laboratory, Technical University Dortmund, 44227, Dortmund, Germany
| | - Jasmin Wloka
- Institute of Bioorganic Chemistry, Heinrich-Heine University Düsseldorf, 52426, Jülich, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich-Heine University Düsseldorf, 52426, Jülich, Germany
| | - Oliver Kayser
- Technical Biochemistry Laboratory, Technical University Dortmund, 44227, Dortmund, Germany
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3
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Sands LB, Haiden SR, Ma Y, Berkowitz GA. Hormonal control of promoter activities of Cannabis sativa prenyltransferase 1 and 4 and salicylic acid mediated regulation of cannabinoid biosynthesis. Sci Rep 2023; 13:8620. [PMID: 37244890 DOI: 10.1038/s41598-023-35303-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/16/2023] [Indexed: 05/29/2023] Open
Abstract
Cannabis sativa aromatic prenyltransferase 4 (CsPT4) and 1 (CsPT1) have been shown to catalyze cannabigerolic acid (CBGA) biosynthesis, a step that rate-limits the cannabinoid biosynthetic pathway; both genes are highly expressed in flowers. CsPT4 and CsPT1 promoter driven β-glucuronidase (GUS) activities were detected in leaves of cannabis seedlings, and strong CsPT4 promoter activities were associated with glandular trichomes. Hormonal regulation of cannabinoid biosynthetic genes is poorly understood. An in silico analysis of the promoters identified putative hormone responsive elements. Our work examines hormone-responsive elements in the promoters of CsPT4 and CsPT1 in the context of physiological responses of the pathway to the hormone in planta. Dual luciferase assays confirmed the regulation of promoter activities by the hormones. Further studies with salicylic acid (SA) demonstrated that SA pretreatment increased the expression of genes located downstream of the cannabinoid biosynthetic pathway. The results from all aspects of this study demonstrated an interaction between certain hormones and cannabinoid synthesis. The work provides information relevant to plant biology, as we present evidence demonstrating correlations between molecular mechanisms that regulate gene expression and influence plant chemotypes.
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Affiliation(s)
- Lauren B Sands
- Department of Plant Science and Landscape Architecture, Agricultural Biotechnology Laboratory, University of Connecticut, Storrs, CT, 06269-4163, USA
- SafeTiva Labs, Westfield, MA, 01085, USA
| | - Samuel R Haiden
- Department of Plant Science and Landscape Architecture, Agricultural Biotechnology Laboratory, University of Connecticut, Storrs, CT, 06269-4163, USA
| | - Yi Ma
- Department of Plant Science and Landscape Architecture, Agricultural Biotechnology Laboratory, University of Connecticut, Storrs, CT, 06269-4163, USA.
| | - Gerald A Berkowitz
- Department of Plant Science and Landscape Architecture, Agricultural Biotechnology Laboratory, University of Connecticut, Storrs, CT, 06269-4163, USA.
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4
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Ni W, Wang Z, Zheng A, Zhao Y. Preparation and self-cleavage of fusion soluble farnesyl diphosphate synthase in E. coli. Prep Biochem Biotechnol 2023; 53:988-994. [PMID: 36639146 DOI: 10.1080/10826068.2022.2164591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Farnesyl diphosphate synthase (FPPS) is a crucial protein in terpenoid production. However, its industrial application is limited owing to its low solubility in Escherichia coli. In this study, we focused on ispA encoding FPPS and designed a fusion expression system to reduce inclusion body (IB) formation. Among the chosen fusion tags, the GB1-domain (GB1) exhibited the highest ability to solubilize the recombinant protein. Increased rare tRNA abundance not only improved the GB1-FPPS yield but also increased its soluble level. A "one-step" method for the acquisition of soluble FPPS was also considered. By combining GB1-FPPS expression and Tobacco Etch Virus protease (TEVp) cleavage in vivo, a controllable GB1-FPPS "self-cleavage" system was constructed. Overall, this study provides an efficient approach for obtaining soluble forms of FPPS, which show great potential for use in the soluble expression of other homologous diphosphate synthase.
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Affiliation(s)
- Wenfeng Ni
- The Province Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui Province, Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Sciences, Anqing Normal University, Anqing, Anhui, China
| | - Zixuan Wang
- The Province Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui Province, Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Sciences, Anqing Normal University, Anqing, Anhui, China
| | - Aifang Zheng
- The Province Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui Province, Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Sciences, Anqing Normal University, Anqing, Anhui, China
| | - Ying Zhao
- The Province Key Laboratory of the Biodiversity Study and Ecology Conservation in Southwest Anhui Province, Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Sciences, Anqing Normal University, Anqing, Anhui, China
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5
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LIU S, YU B, DAI J, CHEN R. Targeting the biological activity and biosynthesis of hyperforin: a mini-review. Chin J Nat Med 2022; 20:721-728. [DOI: 10.1016/s1875-5364(22)60189-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Indexed: 11/03/2022]
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6
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LimF is a versatile prenyltransferase for histidine-C-geranylation on diverse non-natural substrates. Nat Catal 2022. [DOI: 10.1038/s41929-022-00822-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Eggbauer B, Schrittwieser JH, Kerschbaumer B, Macheroux P, Kroutil W. Regioselective Biocatalytic C4-Prenylation of Unprotected Tryptophan Derivatives. Chembiochem 2022; 23:e202200311. [PMID: 35770709 PMCID: PMC9540666 DOI: 10.1002/cbic.202200311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/23/2022] [Indexed: 11/25/2022]
Abstract
Regioselective carbon−carbon bond formation belongs to the challenging tasks in organic synthesis. In this context, C−C bond formation catalyzed by 4‐dimethylallyltryptophan synthases (4‐DMATSs) represents a possible tool to regioselectively synthesize C4‐prenylated indole derivatives without site‐specific preactivation and circumventing the need of protection groups as used in chemical synthetic approaches. In this study, a toolbox of 4‐DMATSs to produce a set of 4‐dimethylallyl tryptophan and indole derivatives was identified. Using three wild‐type enzymes as well as variants, various C5‐substituted tryptophan derivatives as well as N‐methyl tryptophan were successfully prenylated with conversions up to 90 %. Even truncated tryptophan derivatives like tryptamine and 3‐indole propanoic acid were regioselectively prenylated in position C4. The acceptance of C5‐substituted tryptophan derivatives was improved up to 5‐fold by generating variants (e. g. T108S). The feasibility of semi‐preparative prenylation of selected tryptophan derivatives was successfully demonstrated on 100 mg scale at 15 mM substrate concentration, allowing to reduce the previously published multistep chemical synthetic sequence to just a single step.
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Affiliation(s)
- Bettina Eggbauer
- University of Graz: Karl-Franzens-Universitat Graz, Chemistry, AUSTRIA
| | | | | | | | - Wolfgang Kroutil
- University of Graz: Karl-Franzens-Universitat Graz, Institute of Chemistry, Heinrichstrasse 28, 8010, Graz, AUSTRIA
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8
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Couillaud J, Duquesne K, Iacazio G. Extension of the Terpene Chemical Space: the Very First Biosynthetic Steps. Chembiochem 2021; 23:e202100642. [PMID: 34905641 DOI: 10.1002/cbic.202100642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/14/2021] [Indexed: 11/06/2022]
Abstract
The structural diversity of terpenes is particularly notable and many studies are carried out to increase it further. In the terpene biosynthetic pathway this diversity is accessible from only two common precursors, i. e. isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Methods recently developed (e. g. the Terpene Mini Path) have allowed DMAPP and IPP to be obtained from a two-step enzymatic conversion of industrially available isopentenol (IOH) and dimethylallyl alcohol (DMAOH) into their corresponding diphosphates. Easily available IOH and DMAOH analogues then offer quick access to modified terpenoids thus avoiding the tedious chemical synthesis of unnatural diphosphates. The aim of this minireview is to cover the literature devoted to the use of these analogues for widening the accessible terpene chemical space.
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Affiliation(s)
- Julie Couillaud
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2 Marseille, CNRS UMR 7313, Av. Escadrille Normandie-Niemen, 13013, Marseille, France.,Actual address: Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Katia Duquesne
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2 Marseille, CNRS UMR 7313, Av. Escadrille Normandie-Niemen, 13013, Marseille, France
| | - Gilles Iacazio
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2 Marseille, CNRS UMR 7313, Av. Escadrille Normandie-Niemen, 13013, Marseille, France
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9
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Qiu C, Liu Y, Wu Y, Zhao L, Pei J. Biochemical Characterization of a Novel Prenyltransferase from Streptomyces sp. NT11 and Development of a Recombinant Strain for the Production of 6-Prenylnaringenin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14231-14240. [PMID: 34793146 DOI: 10.1021/acs.jafc.1c06094] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Prenyl groups increase the lipophilicity of flavonoids, endowing them with a special activity, selectivity, and pharmacological properties by prenylation. Herein, a novel prenyltransferase (ShFPT) gene from Streptomyces sp. NT11 was expressed in Escherichia coli, and its biochemical characteristics were determined. ShFPT exhibited high selectivity to prenylate naringenin at C-6 to generate 6-prenylnaringenin. The optimal activity was observed at pH 6.0 and 55 °C. The Kcat and Km for naringenin were 0.0095 s-1 and 0.20 mM, respectively. Several promiscuous kinase and isopentenyl phosphate kinase genes were screened to develop the most efficient dimethylallyl diphosphate (DMAPP) synthesis pathway for 6-prenylnaringenin synthesis in E. coli. The 6-prenylnaringenin production was improved by changing the induction strategies and optimizing the bioconversion conditions. Finally, 6-prenylnaringenin production reached the highest yield of 69.9 mg/L with average productivity of 4.0 mg/L/h after 16 h incubation, which is the highest yield for any prenylated flavonoid reported to date in E. coli. Therefore, this study provides an efficient method for 6-prenylnaringenin production and reveals the DMAPP synthesis pathway.
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Affiliation(s)
- Cong Qiu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Yang Liu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Yangbao Wu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Linguo Zhao
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
| | - Jianjun Pei
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing 210037, China
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Rudrapal M, Khan J, Dukhyil AAB, Alarousy RMII, Attah EI, Sharma T, Khairnar SJ, Bendale AR. Chalcone Scaffolds, Bioprecursors of Flavonoids: Chemistry, Bioactivities, and Pharmacokinetics. Molecules 2021; 26:7177. [PMID: 34885754 PMCID: PMC8659147 DOI: 10.3390/molecules26237177] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 01/20/2023] Open
Abstract
Chalcones are secondary metabolites belonging to the flavonoid (C6-C3-C6 system) family that are ubiquitous in edible and medicinal plants, and they are bioprecursors of plant flavonoids. Chalcones and their natural derivatives are important intermediates of the flavonoid biosynthetic pathway. Plants containing chalcones have been used in traditional medicines since antiquity. Chalcones are basically α,β-unsaturated ketones that exert great diversity in pharmacological activities such as antioxidant, anticancer, antimicrobial, antiviral, antitubercular, antiplasmodial, antileishmanial, immunosuppressive, anti-inflammatory, and so on. This review provides an insight into the chemistry, biosynthesis, and occurrence of chalcones from natural sources, particularly dietary and medicinal plants. Furthermore, the pharmacological, pharmacokinetics, and toxicological aspects of naturally occurring chalcone derivatives are also discussed herein. In view of having tremendous pharmacological potential, chalcone scaffolds/chalcone derivatives and bioflavonoids after subtle chemical modification could serve as a reliable platform for natural products-based drug discovery toward promising drug lead molecules/drug candidates.
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Affiliation(s)
- Mithun Rudrapal
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education & Research, Pune 411019, India
| | - Johra Khan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia; (J.K.); (R.M.I.I.A.)
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia
| | - Abdul Aziz Bin Dukhyil
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia; (J.K.); (R.M.I.I.A.)
| | - Randa Mohammed Ibrahim Ismail Alarousy
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia; (J.K.); (R.M.I.I.A.)
- Department of Microbiology and Immunology, Division of Veterinary Researches, National Research Center, Giza 12622, Egypt
| | - Emmanuel Ifeanyi Attah
- Department of Pharmaceutical and Medicinal Chemistry, University of Nigeria, Nsukka 410001, Nigeria;
| | - Tripti Sharma
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar 751003, India;
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Abstract
Covering: up to mid-2020 Terpenoids, also called isoprenoids, are the largest and most structurally diverse family of natural products. Found in all domains of life, there are over 80 000 known compounds. The majority of characterized terpenoids, which include some of the most well known, pharmaceutically relevant, and commercially valuable natural products, are produced by plants and fungi. Comparatively, terpenoids of bacterial origin are rare. This is counter-intuitive to the fact that recent microbial genomics revealed that almost all bacteria have the biosynthetic potential to create the C5 building blocks necessary for terpenoid biosynthesis. In this review, we catalogue terpenoids produced by bacteria. We collected 1062 natural products, consisting of both primary and secondary metabolites, and classified them into two major families and 55 distinct subfamilies. To highlight the structural and chemical space of bacterial terpenoids, we discuss their structures, biosynthesis, and biological activities. Although the bacterial terpenome is relatively small, it presents a fascinating dichotomy for future research. Similarities between bacterial and non-bacterial terpenoids and their biosynthetic pathways provides alternative model systems for detailed characterization while the abundance of novel skeletons, biosynthetic pathways, and bioactivies presents new opportunities for drug discovery, genome mining, and enzymology.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Tyler A Alsup
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Baofu Xu
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Zining Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
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12
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Xu B, Li Z, Alsup TA, Ehrenberger MA, Rudolf JD. Bacterial diterpene synthases prenylate small molecules. ACS Catal 2021; 11:5906-5915. [PMID: 34796043 PMCID: PMC8594881 DOI: 10.1021/acscatal.1c01113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The biosynthesis of terpenoid natural products begins with a carbocation-based cyclization or prenylation reaction. While these reactions are mechanistically similar, there are several families of enzymes, namely terpene synthases and prenyltransferases, that have evolved to specifically catalyze terpene cyclization or prenylation reactions. Here, we report that bacterial diterpene synthases, enzymes that are traditionally considered to be specific for cyclization, are capable of efficiently catalyzing both diterpene cyclization and the prenylation of small molecules. We investigated this unique dual reactivity of terpene synthases through a series of kinetic, biocatalytic, structural, and bioinformatics studies. Overall, this study unveils the ability of terpene synthases to catalyze C-, N-, O-, and S-prenylation on small molecules, proposes a substrate decoy mechanism for prenylation by terpene synthases, supports the physiological relevance of terpene synthase-catalyzed prenylation in vivo, and addresses questions regarding the evolution of prenylation function and its potential role in natural products biosynthesis.
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Affiliation(s)
- Baofu Xu
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Zining Li
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Tyler A. Alsup
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | | | - Jeffrey D. Rudolf
- Department of Chemistry, University of Florida, Gainesville, FL, USA
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Ren FC, Liu L, Lv YF, Bai X, Kang QJ, Hu XJ, Zhuang HD, Yang L, Hu JM, Zhou J. Antibacterial Prenylated p-Hydroxybenzoic Acid Derivatives from Oberonia myosurus and Identification of Putative Prenyltransferases. JOURNAL OF NATURAL PRODUCTS 2021; 84:417-426. [PMID: 33492131 DOI: 10.1021/acs.jnatprod.0c01101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Twelve hitherto unknown tandem prenylated p-hydroxybenzoic acid derivatives, namely, oberoniamyosurusins A-L, together with five known derivatives, were isolated from an EtOH extract of the whole parts of the plant Oberonia myosurus. Compounds 10, 13, and 17 exhibited moderate inhibitory activity against Staphylococcus aureus subsp. aureus ATCC29213 with MIC50 values ranging from 7.6 to 23 μg/mL. To determine the biosynthetic pathway of this class of tandem prenyl-substituted compounds, the full-length transcriptome of O. myosurus was sequenced, yielding 19.09 Gb of clean data and 10 949 nonredundant sequences. Two isoforms of p-hydroxybenzoic acid prenyltransferases were annotated and functionally characterized as the enzymes that might be involved in the biosynthesis of nervogenic acid (13) in Pichia pastoris.
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Affiliation(s)
- Fu-Cai Ren
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Li Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yong-Feng Lv
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xue Bai
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Qian-Jin Kang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Xiao-Jing Hu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Hong-Dan Zhuang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Liu Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Jiang-Miao Hu
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Jun Zhou
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
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14
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Discovery of a Dual Function Cytochrome P450 that Catalyzes Enyne Formation in Cyclohexanoid Terpenoid Biosynthesis. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Chen Y, Naresh A, Liang S, Lin C, Chein R, Lin H. Discovery of a Dual Function Cytochrome P450 that Catalyzes Enyne Formation in Cyclohexanoid Terpenoid Biosynthesis. Angew Chem Int Ed Engl 2020; 59:13537-13541. [DOI: 10.1002/anie.202004435] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Indexed: 11/12/2022]
Affiliation(s)
- Yu‐Rong Chen
- Institute of Biological Chemistry Academia Sinica Taipei 115 Taiwan R.O.C
| | | | - Suh‐Yuen Liang
- Institute of Biological Chemistry Academia Sinica Taipei 115 Taiwan R.O.C
| | - Chun‐Hung Lin
- Institute of Biological Chemistry Academia Sinica Taipei 115 Taiwan R.O.C
| | - Rong‐Jie Chein
- Institute of Chemistry Academia Sinica Taipei 115 Taiwan R.O.C
| | - Hsiao‐Ching Lin
- Institute of Biological Chemistry Academia Sinica Taipei 115 Taiwan R.O.C
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16
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Lv J, Gao Y, Zhao H, Awakawa T, Liu L, Chen G, Yao X, Hu D, Abe I, Gao H. Biosynthesis of Biscognienyne B Involving a Cytochrome P450‐Dependent Alkynylation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004364] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jian‐Ming Lv
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
- Integrated Chinese and Western Medicine Postdoctoral Research Station Jinan University Guangzhou 510632 P. R. China
| | - Yao‐Hui Gao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Huan Zhao
- College of Traditional Chinese Medicine Jinan University Guangzhou 510632 P. R. China
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Ling Liu
- State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 P. R. China
| | - Guo‐Dong Chen
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Xin‐Sheng Yao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Hao Gao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
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17
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Lv J, Gao Y, Zhao H, Awakawa T, Liu L, Chen G, Yao X, Hu D, Abe I, Gao H. Biosynthesis of Biscognienyne B Involving a Cytochrome P450‐Dependent Alkynylation. Angew Chem Int Ed Engl 2020; 59:13531-13536. [DOI: 10.1002/anie.202004364] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Jian‐Ming Lv
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
- Integrated Chinese and Western Medicine Postdoctoral Research Station Jinan University Guangzhou 510632 P. R. China
| | - Yao‐Hui Gao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Huan Zhao
- College of Traditional Chinese Medicine Jinan University Guangzhou 510632 P. R. China
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Ling Liu
- State Key Laboratory of Mycology Institute of Microbiology Chinese Academy of Sciences Beijing 100101 P. R. China
| | - Guo‐Dong Chen
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Xin‐Sheng Yao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Hao Gao
- Institute of Traditional Chinese Medicine and Natural Products College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research Jinan University Guangzhou 510632 P. R. China
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18
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Johnson BP, Scull EM, Dimas DA, Bavineni T, Bandari C, Batchev AL, Gardner ED, Nimmo SL, Singh S. Acceptor substrate determines donor specificity of an aromatic prenyltransferase: expanding the biocatalytic potential of NphB. Appl Microbiol Biotechnol 2020; 104:4383-4395. [PMID: 32189045 PMCID: PMC7190591 DOI: 10.1007/s00253-020-10529-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/26/2020] [Accepted: 03/05/2020] [Indexed: 12/11/2022]
Abstract
Abstract Aromatic prenyltransferases are known for their extensive promiscuity toward aromatic acceptor substrates and their ability to form various carbon-carbon and carbon-heteroatom bonds. Of particular interest among the prenyltransferases is NphB, whose ability to geranylate cannabinoid precursors has been utilized in several in vivo and in vitro systems. It has therefore been established that prenyltransferases can be utilized as biocatalysts for the generation of useful compounds. However, recent observations of non-native alkyl-donor promiscuity among prenyltransferases indicate the role of NphB in biocatalysis could be expanded beyond geranylation reactions. Therefore, the goal of this study was to elucidate the donor promiscuity of NphB using different acceptor substrates. Herein, we report distinct donor profiles between NphB-catalyzed reactions involving the known substrate 1,6-dihydroxynaphthalene and an FDA-approved drug molecule sulfabenzamide. Furthermore, we report the first instance of regiospecific, NphB-catalyzed N-alkylation of sulfabenzamide using a library of non-native alkyl-donors, indicating the biocatalytic potential of NphB as a late-stage diversification tool. Key Points • NphB can utilize the antibacterial drug sulfabenzamide as an acceptor. • The donor profile of NphB changes dramatically with the choice of acceptor. • NphB performs a previously unknown regiospecific N-alkylation on sulfabenzamide. • Prenyltransferases like NphB can be utilized as drug-alkylating biocatalysts. Electronic supplementary material The online version of this article (10.1007/s00253-020-10529-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bryce P Johnson
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Erin M Scull
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Dustin A Dimas
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Tejaswi Bavineni
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Chandrasekhar Bandari
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Andrea L Batchev
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Eric D Gardner
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Susan L Nimmo
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Shanteri Singh
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
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19
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Abstract
Aromatic prenyltransferases (PTases), including ABBA-type and dimethylallyl tryptophan synthase (DMATS)-type enzymes from bacteria and fungi, play important role for diversification of the natural products and improvement of the biological activities. For a decade, the characterization of enzymes and enzymatic synthesis of prenylated compounds by using ABBA-type and DMATS-type PTases have been demonstrated. Here, I introduce several examples of the studies on chemoenzymatic synthesis of unnatural prenylated compounds and the enzyme engineering of ABBA-type and DMATS-type PTases.
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20
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Combining mutagenesis on Glu281 of prenyltransferase NovQ and metabolic engineering strategies for the increased prenylated activity towards menadione. Appl Microbiol Biotechnol 2020; 104:4371-4382. [PMID: 32125480 DOI: 10.1007/s00253-020-10470-w] [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: 09/16/2019] [Revised: 12/04/2019] [Accepted: 02/13/2020] [Indexed: 12/20/2022]
Abstract
Prenyltransferase NovQ is a vital class involved in the biosynthesis of secondary metabolites such as clorobiocin and novobiocin. To investigate the relationship between structure and catalytic properties of NovQ, here, we have analyzed the substrate-binding site, namely PT barrel, and revealed that menadione hydroquinol formed intermolecular interactions with the residue Glu281 near the center of the active pocket. In this study, Glu281 was substituted with 9 diverse amino acids and catalytic properties of mutants were observed in vitro. Among them, E281Q showed 2.05-fold activities towards the aromatic substrate and prenyl donor, while others obtained catalytic efficiency between 8.4 and 88.6% of that of wild-type NovQ. Furthermore, the effects of catalytic conditions and substrate status on the activity of NovQ and its mutants were considered to obtain the optimized prenylated reaction. When the evolutionary NovQ variant E281Q was overexpressed in the host constructed to synthesize dimethylallyl diphosphate through the engineered mevalonate (MVA) pathway, we harvested up to 4.7 mg/L prenylated menadione at C-3 position by exogenously supplying the aromatic substrate. The construction of the microbial platform based on NovQ opens a new orientation to further biosynthesize various vitamin K2 with other ABBA prenyltransferases in E. coli.
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21
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Ni W, Zheng Z, Liu H, Wang P, Wang L, Wang H, Sun X, Yang Q, Tang H, Zhao G. Synthesis of the carboxymethyl cellulose magnetic nanoparticles for efficient immobilization of prenyltransferase NovQ. Carbohydr Polym 2020; 235:115955. [PMID: 32122491 DOI: 10.1016/j.carbpol.2020.115955] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/20/2020] [Accepted: 02/03/2020] [Indexed: 11/30/2022]
Abstract
Prenyltransferase NovQ immobilized carboxymethyl cellulose magnetic nanoparticles (NCMNs) were successfully synthesized via a valuable approach integrated from nanocomposite preparation, and applied for the production of vitamin K2 using menadione hydroquinol and dimethylallyl diphosphate (DMAPP) as substrates. To investigate the interaction between nanoparticles and NovQ, we characterized the nanocomposite, and revealed that carboxymethyl cellulose (CMC) and Fe3O4 formed a core-shell structure to absorb NovQ in the reaction systems, resulting from the high affinity of immobilized materials. Meanwhile, NCMNs with excellent pH and temperature tolerance, enhanced prenylated activity, and improved stability were found. Molecular docking analysis was also conducted to justify the contribution of multiple amino acids and effect of nanoparticles on catalytic properties of NovQ. Taken together, our study introduces a promising strategy to prepare magnetic nanoparticles and improve the performance of catalyst, which aims for opening new orientations for synthesis of magnetic nanoparticles used for prenyltransferase immobilization.
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Affiliation(s)
- Wenfeng Ni
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Comprehensive Laboratory Building, 350 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China; University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Zhiming Zheng
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Comprehensive Laboratory Building, 350 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China.
| | - Hui Liu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Comprehensive Laboratory Building, 350 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Peng Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Comprehensive Laboratory Building, 350 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Li Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Comprehensive Laboratory Building, 350 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Han Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Comprehensive Laboratory Building, 350 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China; University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Xiaowen Sun
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Comprehensive Laboratory Building, 350 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China; University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Qiang Yang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Comprehensive Laboratory Building, 350 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China; University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Hengfang Tang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Comprehensive Laboratory Building, 350 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China; University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Genhai Zhao
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Comprehensive Laboratory Building, 350 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China.
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22
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He J, Hu Z, Dong Z, Li B, Chen K, Shang Z, Zhang M, Qiao X, Ye M. Enzymatic
O
‐Prenylation of Diverse Phenolic Compounds by a Permissive
O
‐Prenyltransferase from the Medicinal Mushroom
Antrodia camphorata. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201901396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Junbin He
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 People's Republic of China
| | - Zhimin Hu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 People's Republic of China
| | - Zeyuan Dong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 People's Republic of China
| | - Bin Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 People's Republic of China
| | - Kuan Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 People's Republic of China
| | - Zhanpeng Shang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 People's Republic of China
| | - Meng Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 People's Republic of China
| | - Xue Qiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 People's Republic of China
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences Peking University 38 Xueyuan Road Beijing 100191 People's Republic of China
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23
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Awakawa T, Abe I. Molecular basis for the plasticity of aromatic prenyltransferases in hapalindole biosynthesis. Beilstein J Org Chem 2019; 15:1545-1551. [PMID: 31354873 PMCID: PMC6632223 DOI: 10.3762/bjoc.15.157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/02/2019] [Indexed: 12/25/2022] Open
Abstract
Aromatic prenyltransferases (PTases) are enzymes that catalyze Friedel–Crafts reactions between aromatic compounds and isoprenoid diphosphates. In hapalindole biosynthesis, the aromatic PTases AmbP1 and AmbP3 exhibit surprisingly plastic selectivities. AmbP1 not only transfers the geranyl group on the C-3 of cis-indolylvinyl isonitrile, but also on the C-2, which is supressed in the presence of Mg2+ ions. AmbP3 transfers the dimethylallyl group on C-2 of hapalindole U in the reverse manner, but on C-2 of its C-10 stereoisomer in the normal manner. This review highlights the molecular bases of the AmbP1 and AmbP3 functions, elucidated through their X-ray crystal structures. The knowledge presented here will contribute to the understanding of aromatic PTase reactions and will enhance their uses as biocatalysts.
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Affiliation(s)
- Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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24
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Bandari C, Scull EM, Bavineni T, Nimmo SL, Gardner ED, Bensen RC, Burgett AW, Singh S. FgaPT2, a biocatalytic tool for alkyl-diversification of indole natural products. MEDCHEMCOMM 2019; 10:1465-1475. [PMID: 31534661 PMCID: PMC6748273 DOI: 10.1039/c9md00177h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/05/2019] [Indexed: 01/02/2023]
Abstract
Demonstration of FgaPT2 catalyzed alkyl-diversification of indole containing natural products.
Aromatic prenyltransferases from natural product biosynthetic pathways display relaxed specificity for their aromatic substrates. While a growing body of evidence suggests aromatic prenyltransferases to be more tolerant towards their alkyl-donor substrates, most studies aimed at probing their donor-substrate specificity are limited to only a small set of alkyl pyrophosphate donors, restricting their broader utility as biocatalysts for synthetic applications. Here, we assess the donor substrate specificity of an l-tryptophan C4-prenyltransferase, also known as C4-dimethylallyltryptophan synthase, FgaPT2 from Aspergillus fumigatus, using an array of 34 synthetic unnatural alkyl-pyrophosphate analogues, and demonstrate FgaPT2 can catalyze the transfer of 25 of the 34 non-native alkyl groups from their corresponding synthetic alkyl-pyrophosphate analogues at N1, C3, C4 and C5 position of tryptophan in a normal and reverse manner. The kinetic studies and regio-chemical analysis of the alkyl-l-tryptophan products suggest that the alkyl-donor transfer by FgaPT2 is a function of the stability of the carbocation and the steric factors in the active site of the enzyme. Further, to demonstrate the biocatalytic utility of FgaPT2, this study also highlights the FgaPT2-catalyzed synthesis of a small set of alkyl-diversified indolocarbazole analogues. These results reveal FgaPT2 to be more tolerant to diverse non-native alkyl-donor substrates beyond their known acceptor substrate promiscuity and set the stage for its development as a novel biocatalytic tool for the differential alkylation of natural products for drug discovery and other synthetic applications.
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Affiliation(s)
- Chandrasekhar Bandari
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
| | - Erin M Scull
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
| | - Tejaswi Bavineni
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
| | - Susan L Nimmo
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
| | - Eric D Gardner
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
| | - Ryan C Bensen
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
| | - Anthony W Burgett
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
| | - Shanteri Singh
- Department of Chemistry and Biochemistry , University of Oklahoma , Stephenson Life Sciences Research Center , 101 Stephenson Parkway , Norman , Oklahoma 73019 , USA .
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25
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Sukumaran A, McDowell T, Chen L, Renaud J, Dhaubhadel S. Isoflavonoid-specific prenyltransferase gene family in soybean: GmPT01, a pterocarpan 2-dimethylallyltransferase involved in glyceollin biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:966-981. [PMID: 30195273 DOI: 10.1111/tpj.14083] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 08/30/2018] [Accepted: 09/03/2018] [Indexed: 05/27/2023]
Abstract
Phytoalexin glyceollins are soybean-specific antimicrobial compounds that are derived from the isoflavonoid pathway. They are synthesized by soybean in response to extrinsic stress such as pathogen attack or injury, thereby conferring partial resistance if synthesized rapidly at the site of infection and at the required concentration. Soybean produces multiple forms of glyceollins that result from the differential prenylation reaction catalyzed by prenyltransferases (PTs) on either the C-2 or C-4 carbon of a pterocarpan glycinol. The soybean genome contains 77 PT-encoding genes (GmPTs) where at least 11 are (iso)flavonoid-specific. Transcript accumulation of five candidates GmPTs was increased in response to Phytophthora sojae infection, suggesting their role in phytoalexin synthesis. The induced GmPTs localize to plastids and display tissue-specific expression. We have in this study identified two additional GmPTs: an isoflavone dimethylallyltransferase 3 (IDT3); and a glycinol 2-dimethylallyl transferase GmPT01. GmPT01 prenylates (-)-glycinol at the C-2 position, localizes in the plastid, and exhibits root-specific gene expression. Furthermore, its expression is induced rapidly in response to stress, and is associated with a quantitative trait loci linked with resistance to P. sojae. Based on these results, we conclude that GmPT01 are possibly one of the loci involved in conferring partial resistance against stem and root rot disease in soybean.
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Affiliation(s)
- Arjun Sukumaran
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford Street, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Tim McDowell
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford Street, London, ON, Canada
| | - Ling Chen
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford Street, London, ON, Canada
| | - Justin Renaud
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford Street, London, ON, Canada
| | - Sangeeta Dhaubhadel
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford Street, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
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26
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Ni W, Liu H, Wang P, Wang L, Sun X, Wang H, Zhao G, Zheng Z. Evaluation of multiple fused partners on enhancing soluble level of prenyltransferase NovQ in Escherichia coli. Bioprocess Biosyst Eng 2018; 42:465-474. [DOI: 10.1007/s00449-018-2050-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 11/23/2018] [Indexed: 01/18/2023]
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27
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Dalponte L, Parajuli A, Younger E, Mattila A, Jokela J, Wahlsten M, Leikoski N, Sivonen K, Jarmusch SA, Houssen WE, Fewer DP. N-Prenylation of Tryptophan by an Aromatic Prenyltransferase from the Cyanobactin Biosynthetic Pathway. Biochemistry 2018; 57:6860-6867. [DOI: 10.1021/acs.biochem.8b00879] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Luca Dalponte
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, U.K
- Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Aberdeen AB25 2ZD, U.K
| | - Anirudra Parajuli
- Department of Microbiology, University of Helsinki, Viikki Biocenter 1, Viikinkaari 9, 00014 Helsinki, Finland
| | - Ellen Younger
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, U.K
- Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Aberdeen AB25 2ZD, U.K
| | - Antti Mattila
- Department of Microbiology, University of Helsinki, Viikki Biocenter 1, Viikinkaari 9, 00014 Helsinki, Finland
| | - Jouni Jokela
- Department of Microbiology, University of Helsinki, Viikki Biocenter 1, Viikinkaari 9, 00014 Helsinki, Finland
| | - Matti Wahlsten
- Department of Microbiology, University of Helsinki, Viikki Biocenter 1, Viikinkaari 9, 00014 Helsinki, Finland
| | - Niina Leikoski
- Department of Microbiology, University of Helsinki, Viikki Biocenter 1, Viikinkaari 9, 00014 Helsinki, Finland
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Viikki Biocenter 1, Viikinkaari 9, 00014 Helsinki, Finland
| | - Scott A. Jarmusch
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, U.K
| | - Wael E. Houssen
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, U.K
- Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Aberdeen AB25 2ZD, U.K
- Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - David P. Fewer
- Department of Microbiology, University of Helsinki, Viikki Biocenter 1, Viikinkaari 9, 00014 Helsinki, Finland
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He BB, Bu XL, Zhou T, Li SM, Xu MJ, Xu J. Combinatory Biosynthesis of Prenylated 4-Hydroxybenzoate Derivatives by Overexpression of the Substrate-Promiscuous Prenyltransferase XimB in Engineered E. coli. ACS Synth Biol 2018; 7:2094-2104. [PMID: 30103600 DOI: 10.1021/acssynbio.8b00070] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Prenylated aromatic compounds are important intermediates in the biosynthesis of bioactive molecules such as 3-chromanols from plants, ubiquinones from prokaryotes and meroterpenoids from sponges. Biosynthesis of prenylated aromatic compounds using prokaryotic microorganisms has attracted increasing attention in the field of synthetic biology. In this study, we demonstrated that the production of 3-geranyl-4-hydroxybenzoic acid (GBA) and a variety of GBA analogues was feasible in a metabolically engineered E. coli by using XimB, a special prenyltransferase involved in the biosynthesis of xiamenmycin A in Streptomyces xiamenensis 318. XimB exhibits broad substrate specificity and can catalyze the transfer reaction of prenyl moieties with different carbon chain lengths to both the natural substrate 4-hydroxybenzoate (4-HBA) and to different substituted 4-HBA derivatives at C-2 and C-3. Feeding 4-HBA to an engineered E. coli equipped with a hybrid mevalonate pathway increased the production of GBA up to 94.30 mg/L. Considerable amounts of other GBA derivatives, compounds 4, 5, 6, 7, and 9, can be achieved by feeding precursors. The plug-and-play design for inserting C5, C15, and C20 prenyl diphosphate synthetases under the control of the T7 promoter resulted in targeted production of 3-dimethylallyl, 3-farnesyl-, and 3-geranylgeranyl-4-hydroxybenzoic acid, respectively. Furthermore, the valuable benzopyran xiamenmycin B was successfully produced in E. coli R7-MVA by coexpression of a complete biosynthetic gene cluster, which contains ximBDE.
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Affiliation(s)
| | | | | | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, Marburg, 35037, Germany
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Pan Y, Liu L, Guan F, Li E, Jin J, Li J, Che Y, Liu G. Characterization of a Prenyltransferase for Iso-A82775C Biosynthesis and Generation of New Congeners of Chloropestolides. ACS Chem Biol 2018; 13:703-711. [PMID: 29384350 DOI: 10.1021/acschembio.7b01059] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chloropupukeananin and chloropestolides are novel metabolites of the plant endophyte Pestalotiopsis fici, showing antimicrobial, antitumor, and anti-HIV activities. Their highly complex and unique skeletons were generated from the coisolated pestheic acid (1) and iso-A82775C (10) based on our previous studies. Here, we identified the biosynthetic gene cluster iac of 10 and characterized an iacE encoded prenyltransferase. Deletion of iacE abolished iso-A82775C production, accumulated the prenyl group-lacking siccayne (2), and generated four new chloropestolides (3-6). Compounds 5 and 6 showed antibacterial effects against Staphylococcus aureus and Bacillus subtilis, and 5 was also cytotoxic to human tumor cell lines HeLa, MCF-7, and SW480. These results provided the first genetic and biochemical insights into the biosynthesis of natural prenylepoxycyclohexanes and demonstrated the feasibility for generation of diversified congeners by manipulating the biosynthetic genes of 10.
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Affiliation(s)
- Yuanyuan Pan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ling Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Feifei Guan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Erwei Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jin Jin
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Jinyang Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongsheng Che
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Gang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Biogenetic Relationships of Bioactive Sponge Merotriterpenoids. Mar Drugs 2017; 15:md15090285. [PMID: 28891968 PMCID: PMC5618424 DOI: 10.3390/md15090285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/07/2017] [Accepted: 09/07/2017] [Indexed: 02/01/2023] Open
Abstract
Hydroquinone meroterpenoids, especially those derived from marine sponges, display a wide range of biological activities. However, use of these compounds is limited by their inaccessibility; there is no sustainable supply of these compounds. Furthermore, our knowledge of their metabolic origin remains completely unstudied. In this review, an in depth structural analysis of sponge merotriterpenoids, including the adociasulfate family of kinesin motor protein inhibitors, provides insight into their biosynthesis. Several key structural features provide clues to the relationships between compounds. All adociasulfates appear to be derived from only four different hydroquinone hexaprenyl diphosphate precursors, each varying in the number and position of epoxidations. Proton-initiated cyclization of these precursors can lead to all carbon skeletons observed amongst sponge merotriterpenoids. Consideration of the enzymes involved in the proposed biosynthetic route suggests a bacterial source, and a hypothetical gene cluster was constructed that may facilitate discovery of the authentic pathway from the sponge metagenome. A similar rationale can be extended to other sponge meroterpenoids, for which no biosynthetic pathways have yet been identified.
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Li Z, Zhao G, Liu H, Guo Y, Wu H, Sun X, Wu X, Zheng Z. Biotransformation of menadione to its prenylated derivative MK-3 using recombinant Pichia pastoris. ACTA ACUST UNITED AC 2017; 44:973-985. [DOI: 10.1007/s10295-017-1931-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/23/2017] [Indexed: 12/17/2022]
Abstract
Abstract
Prenylated quinones, especially menaquinones, have significant physiological activities, but are arduous to synthesize efficiently. Due to the relaxed aromatic substrate specificity and prenylation regiospecificity at the ortho- site of the phenolic hydroxyl group, the aromatic prenyltransferase NovQ from Streptomyces may be useful in menaquinone synthesis from menadione. In this study, NovQ was overexpressed in Pichia pastoris. After fermentation optimization, NovQ production increased by 1617%. Then the different effects of metal ions, detergents and pH on the activity of purified NovQ were investigated to optimize the prenylation reaction. Finally, purified NovQ and cells containing NovQ were used for menadione prenylation in vitro and in vivo, respectively. Menaquinone-1 (MK-1) was detected as the only product in vitro with γ,γ-dimethylallyl pyrophosphate and menadione hydroquinol substrates. MK-3 at a concentration of 90.53 mg/L was detected as the major product of whole cell catalysis with 3-methyl-2-buten-1-ol and menadione hydroquinol substrates. This study realized whole cell catalysis converting menadione to menaquinones.
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Affiliation(s)
- Zhemin Li
- grid.454811.d 0000 0004 1792 7603 Institute of Technical Biology and Agriculture Engineering, Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science Chinese Academy of Sciences and Anhui Province 230031 Hefei Anhui People’s Republic of China
| | - Genhai Zhao
- grid.454811.d 0000 0004 1792 7603 Institute of Technical Biology and Agriculture Engineering, Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science Chinese Academy of Sciences and Anhui Province 230031 Hefei Anhui People’s Republic of China
| | - Hui Liu
- grid.454811.d 0000 0004 1792 7603 Institute of Technical Biology and Agriculture Engineering, Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science Chinese Academy of Sciences and Anhui Province 230031 Hefei Anhui People’s Republic of China
| | - Yugang Guo
- 0000000121679639 grid.59053.3a The CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Biology, School of Life Sciences University of Science and Technology of China 230026 Hefei People’s Republic of China
| | - Hefang Wu
- grid.454811.d 0000 0004 1792 7603 Institute of Technical Biology and Agriculture Engineering, Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science Chinese Academy of Sciences and Anhui Province 230031 Hefei Anhui People’s Republic of China
| | - Xiaowen Sun
- grid.454811.d 0000 0004 1792 7603 Institute of Technical Biology and Agriculture Engineering, Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science Chinese Academy of Sciences and Anhui Province 230031 Hefei Anhui People’s Republic of China
| | - Xihua Wu
- grid.454811.d 0000 0004 1792 7603 Institute of Technical Biology and Agriculture Engineering, Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science Chinese Academy of Sciences and Anhui Province 230031 Hefei Anhui People’s Republic of China
| | - Zhiming Zheng
- grid.454811.d 0000 0004 1792 7603 Institute of Technical Biology and Agriculture Engineering, Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science Chinese Academy of Sciences and Anhui Province 230031 Hefei Anhui People’s Republic of China
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Araya-Cloutier C, Martens B, Schaftenaar G, Leipoldt F, Gruppen H, Vincken JP. Structural basis for non-genuine phenolic acceptor substrate specificity of Streptomyces roseochromogenes prenyltransferase CloQ from the ABBA/PT-barrel superfamily. PLoS One 2017; 12:e0174665. [PMID: 28355308 PMCID: PMC5371340 DOI: 10.1371/journal.pone.0174665] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/13/2017] [Indexed: 12/03/2022] Open
Abstract
Acceptor substrate specificity of Streptomyces roseochromogenes prenyltransferase SrCloQ was investigated using different non-genuine phenolic compounds. RP-UHPLC-UV-MSn was used for the tentative annotation and quantification of the prenylated products. Flavonoids, isoflavonoids and stilbenoids with different types of substitution were prenylated by SrCloQ, although with less efficiency than the genuine substrate 4-hydroxyphenylpyruvate. The isoflavan equol, followed by the flavone 7,4’-dihydroxyflavone, were the best non-genuine acceptor substrates. B-ring C-prenylation was in general preferred over A-ring C-prenylation (ratio 5:1). Docking studies of non-genuine acceptor substrates with the B-ring oriented towards the donor substrate dimethylallyl pyrophosphate, showed that the carbonyl group of the C-ring was able to make stabilizing interactions with the residue Arg160, which might determine the preference observed for B-ring prenylation. No reaction products were formed when the acceptor substrate had no phenolic hydroxyl groups. This preference can be explained by the essential hydrogen bond needed between a phenolic hydroxyl group and the residue Glu281. Acceptor substrates with an additional hydroxyl group at the C3’ position (B-ring), were mainly O3’-prenylated (> 80% of the reaction products). This can be explained by the proximity of the C3’ hydroxyl group to the donor substrate at the catalytic site. Flavones were preferred over isoflavones by SrCloQ. Docking studies suggested that the orientation of the B-ring and of the phenolic hydroxyl group at position C7 (A-ring) of flavones towards the residue Tyr233 plays an important role in this observed preference. Finally, the insights obtained on acceptor substrate specificity and regioselectivity for SrCloQ were extended to other prenyltransferases from the CloQ/NhpB family.
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Affiliation(s)
- Carla Araya-Cloutier
- Laboratory of Food Chemistry, Wageningen University, Wageningen, The Netherlands
| | - Bianca Martens
- Laboratory of Food Chemistry, Wageningen University, Wageningen, The Netherlands
| | - Gijs Schaftenaar
- Nijmegen Centre for Molecular Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Franziska Leipoldt
- Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Harry Gruppen
- Laboratory of Food Chemistry, Wageningen University, Wageningen, The Netherlands
| | - Jean-Paul Vincken
- Laboratory of Food Chemistry, Wageningen University, Wageningen, The Netherlands
- * E-mail:
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Molecular insights into the enzyme promiscuity of an aromatic prenyltransferase. Nat Chem Biol 2016; 13:226-234. [PMID: 27992881 DOI: 10.1038/nchembio.2263] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 11/02/2016] [Indexed: 11/08/2022]
Abstract
Aromatic prenyltransferases (aPTases) transfer prenyl moieties from isoprenoid donors to various aromatic acceptors, some of which have the rare property of extreme enzymatic promiscuity toward both a variety of prenyl donors and a large diversity of acceptors. In this study, we discovered a new aPTase, AtaPT, from Aspergillus terreus that exhibits unprecedented promiscuity toward diverse aromatic acceptors and prenyl donors and also yields products with a range of prenylation patterns. Systematic crystallographic studies revealed various discrete conformations for ligand binding with donor-dependent acceptor specificity and multiple binding sites within a spacious hydrophobic substrate-binding pocket. Further structure-guided mutagenesis of active sites at the substrate-binding pocket is responsible for altering the specificity and promiscuity toward substrates and the diversity of product prenylations. Our study reveals the molecular mechanism underlying the promiscuity of AtaPT and suggests an efficient protein engineering strategy to generate new prenylated derivatives in drug discovery applications.
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Yang Y, Ke N, Liu S, Li W. Methods for Structural and Functional Analyses of Intramembrane Prenyltransferases in the UbiA Superfamily. Methods Enzymol 2016; 584:309-347. [PMID: 28065269 DOI: 10.1016/bs.mie.2016.10.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The UbiA superfamily is a group of intramembrane prenyltransferases that generate lipophilic compounds essential in biological membranes. These compounds, which include various quinones, hemes, chlorophylls, and vitamin E, participate in electron transport and function as antioxidants, as well as acting as structural lipids of microbial cell walls and membranes. Prenyltransferases producing these compounds are involved in important physiological processes and human diseases. These UbiA superfamily members differ significantly in their enzymatic activities and substrate selectivities. This chapter describes examples of methods that can be used to group these intramembrane enzymes, analyze their activity, and screen and crystallize homolog proteins for structure determination. Recent structures of two archaeal homologs are compared with structures of soluble prenyltransferases to show distinct mechanisms used by the UbiA superfamily to control enzymatic activity in membranes.
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Affiliation(s)
- Y Yang
- Washington University School of Medicine, St. Louis, MO, United States
| | - N Ke
- New England Biolabs, Ipswich, MA, United States
| | - S Liu
- Washington University School of Medicine, St. Louis, MO, United States
| | - W Li
- Washington University School of Medicine, St. Louis, MO, United States.
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Leipoldt F, Zeyhle P, Kulik A, Kalinowski J, Heide L, Kaysser L. Diversity of ABBA Prenyltransferases in Marine Streptomyces sp. CNQ-509: Promiscuous Enzymes for the Biosynthesis of Mixed Terpenoid Compounds. PLoS One 2015; 10:e0143237. [PMID: 26659564 PMCID: PMC4684245 DOI: 10.1371/journal.pone.0143237] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/01/2015] [Indexed: 11/19/2022] Open
Abstract
Terpenoids are arguably the largest and most diverse family of natural products, featuring prominently in e.g. signalling, self-defence, UV-protection and electron transfer. Prenyltransferases are essential players in terpenoid and hybrid isoprenoid biosynthesis that install isoprene units on target molecules and thereby often modulate their bioactivity. In our search for new prenyltransferase biocatalysts we focused on the marine-derived Streptomyces sp. CNQ-509, a particularly rich source of meroterpenoid chemistry. Sequencing and analysis of the genome of Streptomyces sp. CNQ-509 revealed seven putative phenol/phenazine-specific ABBA prenyltransferases, and one putative indole-specific ABBA prenyltransferase. To elucidate the substrate specificity of the ABBA prenyltransferases and to learn about their role in secondary metabolism, CnqP1 -CnqP8 were produced in Escherichia coli and incubated with various aromatic and isoprenoid substrates. Five of the eight prenyltransferases displayed enzymatic activity. The efficient conversion of dihydroxynaphthalene derivatives by CnqP3 (encoded by AA958_24325) and the co-location of AA958_24325 with genes characteristic for the biosynthesis of THN (tetrahydroxynaphthalene)-derived natural products indicates that the enzyme is involved in the formation of debromomarinone or other naphthoquinone-derived meroterpenoids. Moreover, CnqP3 showed high flexibility towards a range of aromatic and isoprenoid substrates and thus represents an interesting new tool for biocatalytic applications.
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Affiliation(s)
- Franziska Leipoldt
- Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Philipp Zeyhle
- Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Andreas Kulik
- Microbial Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Lutz Heide
- Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Leonard Kaysser
- Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- * E-mail:
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36
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Gallagher KA, Jensen PR. Genomic insights into the evolution of hybrid isoprenoid biosynthetic gene clusters in the MAR4 marine streptomycete clade. BMC Genomics 2015; 16:960. [PMID: 26578069 PMCID: PMC4650096 DOI: 10.1186/s12864-015-2110-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/19/2015] [Indexed: 01/17/2023] Open
Abstract
Background Considerable advances have been made in our understanding of the molecular genetics of secondary metabolite biosynthesis. Coupled with increased access to genome sequence data, new insight can be gained into the diversity and distributions of secondary metabolite biosynthetic gene clusters and the evolutionary processes that generate them. Here we examine the distribution of gene clusters predicted to encode the biosynthesis of a structurally diverse class of molecules called hybrid isoprenoids (HIs) in the genus Streptomyces. These compounds are derived from a mixed biosynthetic origin that is characterized by the incorporation of a terpene moiety onto a variety of chemical scaffolds and include many potent antibiotic and cytotoxic agents. Results One hundred and twenty Streptomyces genomes were searched for HI biosynthetic gene clusters using ABBA prenyltransferases (PTases) as queries. These enzymes are responsible for a key step in HI biosynthesis. The strains included 12 that belong to the ‘MAR4’ clade, a largely marine-derived lineage linked to the production of diverse HI secondary metabolites. We found ABBA PTase homologs in all of the MAR4 genomes, which averaged five copies per strain, compared with 21 % of the non-MAR4 genomes, which averaged one copy per strain. Phylogenetic analyses suggest that MAR4 PTase diversity has arisen by a combination of horizontal gene transfer and gene duplication. Furthermore, there is evidence that HI gene cluster diversity is generated by the horizontal exchange of orthologous PTases among clusters. Many putative HI gene clusters have not been linked to their secondary metabolic products, suggesting that MAR4 strains will yield additional new compounds in this structure class. Finally, we confirm that the mevalonate pathway is not always present in genomes that contain HI gene clusters and thus is not a reliable query for identifying strains with the potential to produce HI secondary metabolites. Conclusions We found that marine-derived MAR4 streptomycetes possess a relatively high genetic potential for HI biosynthesis. The combination of horizontal gene transfer, duplication, and rearrangement indicate that complex evolutionary processes account for the high level of HI gene cluster diversity in these bacteria, the products of which may provide a yet to be defined adaptation to the marine environment. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2110-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kelley A Gallagher
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0204, USA.
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0204, USA.
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Schmidt B, Riemer M, Schilde U. Tandem Claisen Rearrangement/6-endoCyclization Approach to Allylated and Prenylated Chromones. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501151] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Gao B, Chen R, Liu X, Dai J, Sun F. Expression, purification, crystallization and crystallographic study of the Aspergillus terreus aromatic prenyltransferase AtaPT. Acta Crystallogr F Struct Biol Commun 2015; 71:889-94. [PMID: 26144234 PMCID: PMC4498710 DOI: 10.1107/s2053230x15008882] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 05/07/2015] [Indexed: 11/10/2022] Open
Abstract
Prenylated aromatics are produced by aromatic prenyltransferases during the secondary metabolism of bacteria, fungi and plants. The prenylation of nonprenylated precursors can lead to great chemical diversity and extensive biological properties. Aspergillus terreus aromatic prenyltransferase (AtaPT), which has recently been discovered and characterized, is such an enzyme and is responsible for the prenylation of various aromatic compounds. Here, recombinant AtaPT was overexpressed in Escherichia coli, purified and crystallized. Diffraction data were collected to a resolution of 1.71 Å and the crystal belonged to space group P2(1)2(1)2, with unit-cell parameters a = 96.2, b = 135.8, c = 69.5 Å, α = β = γ = 90°. Analysis of the calculated Matthews coefficient and the self-rotation function suggested that there are two AtaPT molecules in the asymmetric unit.
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Affiliation(s)
- Bingquan Gao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Ridao Chen
- State Key Laboratory of Bioactive Substances and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, People’s Republic of China
| | - Xiao Liu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, People’s Republic of China
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, People’s Republic of China
| | - Jungui Dai
- State Key Laboratory of Bioactive Substances and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, People’s Republic of China
| | - Fei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
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Zhou J, Wang X, Kuang M, Wang L, Luo HB, Mo Y, Wu R. Protonation-Triggered Carbon-Chain Elongation in Geranyl Pyrophosphate Synthase (GPPS). ACS Catal 2015. [DOI: 10.1021/acscatal.5b00947] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jingwei Zhou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Xiaoming Wang
- Program in Public Health, College of Healthy Sciences, University of California—Irvine, Irvine, California 92697,United States
| | - Ming Kuang
- Institute of Chinese Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Laiyou Wang
- Institute of Chinese Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
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Wang J, Chu S, Zhu Y, Cheng H, Yu D. Positive selection drives neofunctionalization of the UbiA prenyltransferase gene family. PLANT MOLECULAR BIOLOGY 2015; 87:383-94. [PMID: 25605655 DOI: 10.1007/s11103-015-0285-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 01/12/2015] [Indexed: 05/05/2023]
Abstract
Gene duplication provides the key materials for new genes and novel functions. However, the mechanism underlying functional innovation remains unknown. In this study, we revealed the evolutionary pattern of the prenyltransferases of the UbiA gene family in 15 higher plants. Prenyltransferases of the UbiA gene family are involved in many important biological processes of both primary and secondary metabolism. Based on the phylogenetic relationships of the UbiA genes, seven subfamilies are classified. Confirming this classification, genes within each subfamily are characterized by similar exon numbers, exon lengths and patterns of motif combinations. Similar numbers of UbiA genes are found in different species within each subfamily except for Subfamily I, in which a Phaseoleae-specific expansion is detected in clade I-A. Homologous genes in clade I-A evolve rapidly, exchange sequences frequently and experience positive selection. Genes in clade I-A function as flavonoid prenyltransferase synthesis secondary compounds, while other genes from Subfamily I encode homogentisate phytyltransferase, which plays a role in primary metabolism. Thus, our results suggest that the secondary metabolism genes acquire new functions from those of primary metabolism through gene duplication and neofunctionalization driven by positive selection.
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Affiliation(s)
- Jiao Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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Pan LL, Yang Y, Merz KM. Origin of product selectivity in a prenyl transfer reaction from the same intermediate: exploration of multiple FtmPT1-catalyzed prenyl transfer pathways. Biochemistry 2014; 53:6126-38. [PMID: 25188320 PMCID: PMC4179596 DOI: 10.1021/bi500747z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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FtmPT1 is a fungal indole prenyltransferase
that catalyzes the
reaction of tryptophan derivatives with dimethylallyl pyrophosphate
to form various biologically active compounds. Herein, we describe
detailed studies of FtmPT1 catalysis involving dimethylallyl pyrophosphate
and Brevianamide F following the native pathway (yielding Tryprostatin
B) and an alternate pathway observed in the Gly115Thr mutant of FtmPT1
yielding a novel cyclized product. Importantly, these two products
arise from the same intermediate state, meaning that a step other
than the cleavage of the dimethylallyl pyrophosphate (DMAPP; C–O)
bond is differentiating between the two product reaction channels.
From detailed potential of mean force (PMF) and two-dimensional PMF
analyses, we conclude that the rate-limiting step is the cleavage
of the C–O bond in DMAPP, while the deprotonation/cyclization
step determines the final product distribution. Hence, in the case
of FtmPT1, the optimization of the necessary catalytic machinery guides
the generation of the final product after formation of the intermediate
carbocation.
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Affiliation(s)
- Li-Li Pan
- Quantum Theory Project and Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
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42
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Teufel R, Kaysser L, Villaume MT, Diethelm S, Carbullido MK, Baran PS, Moore BS. One-Pot Enzymatic Synthesis of Merochlorin A and B. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405694] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Teufel R, Kaysser L, Villaume MT, Diethelm S, Carbullido MK, Baran PS, Moore BS. One-pot enzymatic synthesis of merochlorin A and B. Angew Chem Int Ed Engl 2014; 53:11019-22. [PMID: 25115835 DOI: 10.1002/anie.201405694] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 11/06/2022]
Abstract
The polycycles merochlorin A and B are complex halogenated meroterpenoid natural products with significant antibacterial activities and are produced by the marine bacterium Streptomyces sp. strain CNH-189. Heterologously produced enzymes and chemical synthesis are employed herein to fully reconstitute the merochlorin biosynthesis in vitro. The interplay of a dedicated type III polyketide synthase, a prenyl diphosphate synthase, and an aromatic prenyltransferase allow formation of a highly unusual aromatic polyketide-terpene hybrid intermediate which features an unprecedented branched sesquiterpene moiety from isosesquilavandulyl diphosphate. As supported by in vivo experiments, this precursor is furthermore chlorinated and cyclized to merochlorin A and isomeric merochlorin B by a single vanadium-dependent haloperoxidase, thus completing the remarkably efficient pathway.
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Affiliation(s)
- Robin Teufel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037 (USA) http://scrippsscholars.ucsd.edu/bsmoore
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44
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Bayse CA, Merz KM. Mechanistic insights into Mg2+-independent prenylation by CloQ from classical molecular mechanics and hybrid quantum mechanics/molecular mechanics molecular dynamics simulations. Biochemistry 2014; 53:5034-41. [PMID: 25020142 DOI: 10.1021/bi500531p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the mechanism of prenyltransferases is important to the design of engineered proteins capable of synthesizing derivatives of naturally occurring therapeutic agents. CloQ is a Mg(2+)-independent aromatic prenyltransferase (APTase) that transfers a dimethylallyl group to 4-hydroxyphenylpyruvate in the biosynthetic pathway for clorobiocin. APTases consist of a common ABBA fold that defines a β-barrel containing the reaction cavity. Positively charged basic residues line the inside of the β-barrel of CloQ to activate the pyrophosphate leaving group to replace the function of the Mg(2+) cofactor in other APTases. Classical molecular dynamics simulations of CloQ, its E281G and F68S mutants, and the related NovQ were used to explore the binding of the 4-hydroxyphenylpyruvate (4HPP) and dimethylallyl diphosphate substrates in the reactive cavity and the role of various conserved residues. Hybrid quantum mechanics/molecular mechanics potential of mean force (PMF) calculations show that the effect of the replacement of the Mg(2+) cofactor with basic residues yields a similar activation barrier for prenylation to Mg(2+)-dependent APTases like NphB. The topology of the binding pocket for 4HPP is important for selective prenylation at the ortho position of the ring. Methylation at this position alters the conformation of the substrate for O-prenylation at the phenol group. Further, a two-dimensional PMF scan shows that a "reverse" prenylation product may be a possible target for protein engineering.
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Affiliation(s)
- Craig A Bayse
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23518, United States
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45
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Liu C, Noike M, Minami A, Oikawa H, Dairi T. A fungal prenyltransferase catalyzes the regular di-prenylation at positions 20 and 21 of paxilline. Biosci Biotechnol Biochem 2014; 78:448-54. [DOI: 10.1080/09168451.2014.882759] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
A putative indole diterpene biosynthetic gene cluster composed of eight genes was identified in a genome database of Phomopsis amygdali, and from it, biosynthetic genes of fusicoccin A were cloned and characterized. The six genes showed significant similarities to pax genes, which are essential to paxilline biosynthesis in Penicillium paxilli. Recombinants of the three putative prenyltransferase genes in the cluster were overexpressed in Escherichia coli and characterized by means of in vitro experiments. AmyG is perhaps a GGDP synthase. AmyC and AmyD were confirmed to be prenyltransferases catalyzing the transfer of GGDP to IGP and a regular di-prenylation at positions 20 and 21 of paxilline, respectively. AmyD is the first know example of an enzyme with this function. The Km values for AmyD were calculated to be 7.6 ± 0.5 μM for paxilline and 17.9 ± 1.7 μM for DMAPP at a kcat of 0.12 ± 0.003/s.
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Affiliation(s)
- Chengwei Liu
- Graduate School of Engineering, Hokkaido University, Sapporo, Japan
| | - Motoyoshi Noike
- Graduate School of Engineering, Hokkaido University, Sapporo, Japan
| | - Atsushi Minami
- Graduate School of Science, Hokkaido University, Sapporo, Japan
| | - Hideaki Oikawa
- Graduate School of Science, Hokkaido University, Sapporo, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, Sapporo, Japan
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Schmidt-Dannert C. Biosynthesis of terpenoid natural products in fungi. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 148:19-61. [PMID: 25414054 DOI: 10.1007/10_2014_283] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tens of thousands of terpenoid natural products have been isolated from plants and microbial sources. Higher fungi (Ascomycota and Basidiomycota) are known to produce an array of well-known terpenoid natural products, including mycotoxins, antibiotics, antitumor compounds, and phytohormones. Except for a few well-studied fungal biosynthetic pathways, the majority of genes and biosynthetic pathways responsible for the biosynthesis of a small number of these secondary metabolites have only been discovered and characterized in the past 5-10 years. This chapter provides a comprehensive overview of the current knowledge on fungal terpenoid biosynthesis from biochemical, genetic, and genomic viewpoints. Enzymes involved in synthesizing, transferring, and cyclizing the prenyl chains that form the hydrocarbon scaffolds of fungal terpenoid natural products are systematically discussed. Genomic information and functional evidence suggest differences between the terpenome of the two major fungal phyla--the Ascomycota and Basidiomycota--which will be illustrated for each group of terpenoid natural products.
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Affiliation(s)
- Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minneapolis, MN, 55108, USA,
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47
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Rudolf JD, Poulter CD. Tyrosine O-prenyltransferase SirD catalyzes S-, C-, and N-prenylations on tyrosine and tryptophan derivatives. ACS Chem Biol 2013; 8:2707-14. [PMID: 24083562 DOI: 10.1021/cb400691z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The tyrosine O-prenyltransferase SirD in Leptosphaeria maculans catalyzes normal prenylation of the hydroxyl group in tyrosine as the first committed step in the biosynthesis of the phytotoxin sirodesmin PL. SirD also catalyzes normal N-prenylation of 4-aminophenylalanine and normal C-prenylation at C7 of tryptophan. In this study, we found that 4-mercaptophenylalanine and several derivatives of tryptophan are also substrates for prenylation by dimethylallyl diphosphate. Incubation of SirD with 4-mercaptophenylalanine gave normal S-prenylated mercaptophenylalanine. We found that incubation of the enzyme with tryptophan gave reverse prenylation at N1 in addition to the previously reported normal prenylation at C7. 4-Methyltryptophan also gave normal prenylation at C7 and reverse prenylation at N1, whereas 4-methoxytryptophan gave normal and reverse prenylation at C7, and 7-methyltryptophan gave normal prenylation at C6 and reverse prenylation at N1. The ability of SirD to prenylate at three different sites on the indole nucleus, with normal and reverse prenylation at one of the sites, is similar to behavior seen for dimethylallyltryptophan synthase. The multiple products produced by SirD suggests it and dimethylallyltryptophan synthase use a dissociative electrophilic mechanism for alkylation of amino acid substrates.
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Affiliation(s)
- Jeffrey D. Rudolf
- Department of Chemistry, University of Utah, 315 South 1400
East, Salt Lake City, Utah 84112, United States
| | - C. Dale Poulter
- Department of Chemistry, University of Utah, 315 South 1400
East, Salt Lake City, Utah 84112, United States
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48
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Regiospecificities and prenylation mode specificities of the fungal indole diterpene prenyltransferases AtmD and PaxD. Appl Environ Microbiol 2013; 79:7298-304. [PMID: 24038699 DOI: 10.1128/aem.02496-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We recently reported the function of paxD, which is involved in the paxilline (compound 1) biosynthetic gene cluster in Penicillium paxilli. Recombinant PaxD catalyzed a stepwise regular-type diprenylation at the 21 and 22 positions of compound 1 with dimethylallyl diphosphate (DMAPP) as the prenyl donor. In this study, atmD, which is located in the aflatrem (compound 2) biosynthetic gene cluster in Aspergillus flavus and encodes an enzyme with 32% amino acid identity to PaxD, was characterized using recombinant enzyme. When compound 1 and DMAPP were used as substrates, two major products and a trace of minor product were formed. The structures of the two major products were determined to be reversely monoprenylated compound 1 at either the 20 or 21 position. Because compound 2 and β-aflatrem (compound 3), both of which are compound 1-related compounds produced by A. flavus, have the same prenyl moiety at the 20 and 21 position, respectively, AtmD should catalyze the prenylation in compound 2 and 3 biosynthesis. More importantly and surprisingly, AtmD accepted paspaline (compound 4), which is an intermediate of compound 1 biosynthesis that has a structure similar to that of compound 1, and catalyzed a regular monoprenylation of compound 4 at either the 21 or 22 position, though the reverse prenylation was observed with compound 1. This suggests that fungal indole diterpene prenyltransferases have the potential to alter their position and regular/reverse specificities for prenylation and could be applicable for the synthesis of industrially useful compounds.
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49
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Functional analysis of a prenyltransferase gene (paxD) in the paxilline biosynthetic gene cluster. Appl Microbiol Biotechnol 2013; 98:199-206. [DOI: 10.1007/s00253-013-4834-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 02/27/2013] [Accepted: 03/05/2013] [Indexed: 10/27/2022]
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50
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Dunbar KL, Mitchell DA. Revealing nature's synthetic potential through the study of ribosomal natural product biosynthesis. ACS Chem Biol 2013; 8:473-87. [PMID: 23286465 DOI: 10.1021/cb3005325] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribosomally synthesized posttranslationally modified peptides (RiPPs) are a rapidly growing class of natural products with diverse structures and activities. In recent years, a great deal of progress has been made in elucidating the biosynthesis of various RiPP family members. As with the study of nonribosomal peptide and polyketide biosynthetic enzymes, these investigations have led to the discovery of entirely new biological chemistry. With each unique enzyme investigated, a more complex picture of Nature's synthetic potential is revealed. This Review focuses on recent reports (since 2008) that have changed the way that we think about ribosomal natural product biosynthesis and the enzymology of complex bond-forming reactions.
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Affiliation(s)
- Kyle L. Dunbar
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
| | - Douglas A. Mitchell
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
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