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Liu Q, Gao S, Fang J, Gong Y, Zheng Y, Xu Y, Zhang D, Wei J, Liao L, Yao M, Wang W, Han X, Chen F, Molnár I, Yang X. Novel fungal diphenyl ether biosynthetic gene clusters encode a promiscuous oxidase for elevated antibacterial activities. Chem Sci 2024:d4sc01435a. [PMID: 39144458 PMCID: PMC11320064 DOI: 10.1039/d4sc01435a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 07/22/2024] [Indexed: 08/16/2024] Open
Abstract
Diphenyl ethers (DPEs) are produced by filamentous fungi using polyketide synthases (PKSs) directly, or via Cu oxidase-catalyzed oxidative rearrangements of benzophenone intermediates. Here, we use heterologous expression to reveal a third route towards DPEs in Preussia isomera that relies on an oxidative multienzyme cascade to convert a PKS-generated, ester-linked didepside to depsidones and further to DPEs, and apply comparative genomics to identify conserved biosynthetic gene clusters for this pathway in multiple fungi. The distribution of DPE products is modulated by the expression chassis upon pathway reconstitution. Among the post-PKS enzymes, the DpeH tyrosinase shows considerable substrate promiscuity towards synthetic DPE analogues. By creating hybrid enzymes with a DpeH orthologue from Aspergillus nidulans, we identify the C-terminal region of DpeH to alter substrate recognition. Our work highlights an evolutionarily conserved way to produce DPEs, and provides enzymatic tools to generate DPE analogues with broad spectrum antibiotic activity against multidrug-resistant human pathogens.
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Affiliation(s)
- Qingpei Liu
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Shuaibiao Gao
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Jin Fang
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Yifu Gong
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Yiling Zheng
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Yao Xu
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Dan Zhang
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Jiayuan Wei
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Liangxiu Liao
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Ming Yao
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Wenjing Wang
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Xiaole Han
- School of Chemistry and Materials Science, South-Central Minzu University Wuhan 430074 P.R. China
| | - Fusheng Chen
- School of Life Sciences, Guizhou Normal University Guiyang 550025 P.R. China
- College of Food Science and Technology, Huazhong Agricultural University Wuhan 430070 P.R. China
| | - István Molnár
- VTT Technical Research Centre of Finland FI-02044 VTT Espoo Finland
| | - Xiaolong Yang
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
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2
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Skellam E, Rajendran S, Li L. Combinatorial biosynthesis for the engineering of novel fungal natural products. Commun Chem 2024; 7:89. [PMID: 38637654 PMCID: PMC11026467 DOI: 10.1038/s42004-024-01172-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
Natural products are small molecules synthesized by fungi, bacteria and plants, which historically have had a profound effect on human health and quality of life. These natural products have evolved over millions of years resulting in specific biological functions that may be of interest for pharmaceutical, agricultural, or nutraceutical use. Often natural products need to be structurally modified to make them suitable for specific applications. Combinatorial biosynthesis is a method to alter the composition of enzymes needed to synthesize a specific natural product resulting in structurally diversified molecules. In this review we discuss different approaches for combinatorial biosynthesis of natural products via engineering fungal enzymes and biosynthetic pathways. We highlight the biosynthetic knowledge gained from these studies and provide examples of new-to-nature bioactive molecules, including molecules synthesized using combinations of fungal and non-fungal enzymes.
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Affiliation(s)
- Elizabeth Skellam
- Department of Chemistry, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
- Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
| | - Sanjeevan Rajendran
- Department of Chemistry, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
| | - Lei Li
- Department of Chemistry, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
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3
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Li L, Zhong W, Liu H, Espinosa-Artiles P, Xu YM, Wang C, Robles JMV, Paz TA, Inácio MC, Chen F, Xu Y, Gunatilaka AAL, Molnár I. Biosynthesis of Cytosporones in Leotiomycetous Filamentous Fungi. J Am Chem Soc 2024; 146:6189-6198. [PMID: 38386630 PMCID: PMC11106036 DOI: 10.1021/jacs.3c14066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Polyketides with the isochroman-3-one pharmacophore are rare among fungal natural products as their biosynthesis requires an unorthodox S-type aromatic ring cyclization. Genome mining uncovered a conserved gene cluster in select leotiomycetous fungi that encodes the biosynthesis of cytosporones, including isochroman-3-one congeners. Combinatorial biosynthesis in total biosynthetic and biocatalytic formats in Saccharomyces cerevisiae and in vitro reconstitution of key reactions with purified enzymes revealed how cytosporone structural and bioactivity diversity is generated. The S-type acyl dihydroxyphenylacetic acid (ADA) core of cytosporones is assembled by a collaborating polyketide synthase pair. Thioesterase domain-catalyzed transesterification releases ADA esters, some of which are known Nur77 modulators. Alternatively, hydrolytic release allows C6 hydroxylation by a flavin-dependent monooxygenase, yielding a trihydroxybenzene moiety. Reduction of the C9 carbonyl by a short chain dehydrogenase/reductase initiates isochroman-3-one formation, affording cytosporones with cytotoxic and antimicrobial activity. Enoyl di- or trihydroxyphenylacetic acids are generated as shunt products, while isocroman-3,4-diones are formed by autoxidation. The cytosporone pathway offers novel polyketide biosynthetic enzymes for combinatorial synthetic biology to advance the production of "unnatural" natural products for drug discovery.
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Affiliation(s)
- Li Li
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
- College of Life Science, Yangtze University, Jingzhou 434025, P. R. China
| | - Weimao Zhong
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
| | - Hang Liu
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Patricia Espinosa-Artiles
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
| | - Ya-ming Xu
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
| | - Chen Wang
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Jose Manuel Verdugo Robles
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
| | - Tiago Antunes Paz
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil
| | - Marielle Cascaes Inácio
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
| | - Fusheng Chen
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, P. R. China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Yuquan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - A. A. Leslie Gunatilaka
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, Tucson 85719, Arizona, United States
- VTT Technical Research Center of Finland Ltd., Espoo 02150, Finland
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Huang S, Ji H, Zheng J. Structural and computational insights into the regioselectivity of SpnK involved in rhamnose methylation of spinosyn. Int J Biol Macromol 2023; 253:126763. [PMID: 37703985 DOI: 10.1016/j.ijbiomac.2023.126763] [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: 07/16/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023]
Abstract
Rhamnose methylation of spinosyn critical for insecticidal activity is orchestrated by substrate specificity of three S-adenosyl-L-methionine (SAM) dependent methyltransferases (MTs). Previous in vitro enzymatic assays indicate that 3'-O-MT SpnK accepts the rhamnosylated aglycone (RAGL) and 2'-O-methylated RAGL as substrates, but does not tolerate the presence of a methoxy moiety at the O-4' position of the rhamnose unit. Here we solved the crystal structures of apo and ligand-bound SpnK, and used molecular dynamic (MD) simulations to decipher the molecular basis of substrate specificity. SpnK assembles into a tetramer, with each set of three monomers forming an integrated substrate binding pocket. The MD simulations of SpnK complexed with RAGL or 2'-O-methylated RAGL revealed that the 4'-hydroxyl of the rhamnose unit formed a hydrogen bond with a conserved Asp299 of the catalytic center, which is disrupted in structures of SpnK complexed with 4'-O-methylated RAGL or 2',4'-di-O-methylated RAGL. Comparison with SpnI methylating the C2'-hydroxyl of RAGL reveals a correlation between a DLQT/DLWT motif and the selectivity of rhamnose O-MTs. Together, our structural and computational results revealed the structural basis of substrate specificity of rhamnose O-MTs and would potentially help the engineering of spinosyn derivatives.
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Affiliation(s)
- Shuxin Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huining Ji
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.
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5
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Abstract
The ability to site-selectively modify equivalent functional groups in a molecule has the potential to streamline syntheses and increase product yields by lowering step counts. Enzymes catalyze site-selective transformations throughout primary and secondary metabolism, but leveraging this capability for non-native substrates and reactions requires a detailed understanding of the potential and limitations of enzyme catalysis and how these bounds can be extended by protein engineering. In this review, we discuss representative examples of site-selective enzyme catalysis involving functional group manipulation and C-H bond functionalization. We include illustrative examples of native catalysis, but our focus is on cases involving non-native substrates and reactions often using engineered enzymes. We then discuss the use of these enzymes for chemoenzymatic transformations and target-oriented synthesis and conclude with a survey of tools and techniques that could expand the scope of non-native site-selective enzyme catalysis.
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Affiliation(s)
- Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harrison M Snodgrass
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christian A Gomez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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6
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Li Y, Lin P, Lu X, Yan H, Wei H, Liu C, Liu X, Yang Y, Molnár I, Bai Z. Plasmid Copy Number Engineering Accelerates Fungal Polyketide Discovery upon Unnatural Polyketide Biosynthesis. ACS Synth Biol 2023; 12:2226-2235. [PMID: 37463503 DOI: 10.1021/acssynbio.3c00178] [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] [Indexed: 07/20/2023]
Abstract
Saccharomyces cerevisiae has been extensively used as a convenient synthetic biology chassis to reconstitute fungal polyketide biosynthetic pathways. Despite progress in refactoring these pathways for expression and optimization of the yeast production host by metabolic engineering, product yields often remain unsatisfactory. Such problems are especially acute when synthetic biological production is used for bioprospecting via genome mining or when chimeric fungal polyketide synthases (PKSs) are employed to produce novel bioactive compounds. In this work, we demonstrate that empirically balancing the expression levels of the two collaborating PKS subunits that afford benzenediol lactone (BDL)-type fungal polyketides is a facile strategy to improve the product yields. This is accomplished by systematically and independently altering the copy numbers of the two plasmids that express these PKS subunits. We applied this plasmid copy number engineering strategy to two orphan PKSs from genome mining where the yields of the presumed BDL products in S. cerevisiae were far too low for product isolation. This optimization resulted in product yield improvements of up to 10-fold, allowing for the successful isolation and structure elucidation of new BDL analogues. Heterocombinations of these PKS subunits from genome mining with those from previously identified BDL pathways led to the combinatorial biosynthesis of several additional novel BDL-type polyketides.
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Affiliation(s)
- Ye Li
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Pingxin Lin
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Xuan Lu
- School of Life Science and Biotechnology, Dalian University, Dalian 116622, China
| | - Hao Yan
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Huan Wei
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Chunli Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Xiuxia Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Yankun Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, Tucson, Arizona 85706, United States
- VTT Technical Research Centre of Finland Ltd., Espoo 02044, Finland
| | - Zhonghu Bai
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
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7
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Cox RJ. Curiouser and curiouser: progress in understanding the programming of iterative highly-reducing polyketide synthases. Nat Prod Rep 2023; 40:9-27. [PMID: 35543313 DOI: 10.1039/d2np00007e] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 1996-2022Investigations over the last 2 decades have begun to reveal how fungal iterative highly-reducing polyketide synthases are programmed. Both in vitro and in vivo experiments have revealed the interplay of intrinsic and extrinsic selectivity of the component catalytic domains of these systems. Structural biology has begun to provide high resolution structures of hr-PKS that can be used as the basis for their engineering and reprogramming, but progress to-date remains rudimentary. However, significant opportunities exist for translating the current level of understanding into the ability to rationally re-engineer these highly efficient systems for the production of important biologically active compounds through biotechnology.
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Affiliation(s)
- Russell J Cox
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167, Hannover, Germany.
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8
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Endowing homodimeric carbamoyltransferase GdmN with iterative functions through structural characterization and mechanistic studies. Nat Commun 2022; 13:6617. [PMID: 36329057 PMCID: PMC9633730 DOI: 10.1038/s41467-022-34387-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Iterative enzymes, which catalyze sequential reactions, have the potential to improve the atom economy and diversity of industrial enzymatic processes. Redesigning one-step enzymes to be iterative biocatalysts could further enhance these processes. Carbamoyltransferases (CTases) catalyze carbamoylation, an important modification for the bioactivity of many secondary metabolites with pharmaceutical applications. To generate an iterative CTase, we determine the X-ray structure of GdmN, a one-step CTase involved in ansamycin biosynthesis. GdmN forms a face-to-face homodimer through unusual C-terminal domains, a previously unknown functional form for CTases. Structural determination of GdmN complexed with multiple intermediates elucidates the carbamoylation process and identifies key binding residues within a spacious substrate-binding pocket. Further structural and computational analyses enable multi-site enzyme engineering, resulting in an iterative CTase with the capacity for successive 7-O and 3-O carbamoylations. Our findings reveal a subclade of the CTase family and exemplify the potential of protein engineering for generating iterative enzymes.
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9
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Dippe M, Davari MD, Weigel B, Heinke R, Vogt T, Wessjohann LA. Altering the Regiospecificity of a Catechol
O
‐methyltransferase through Rational Design: Vanilloid vs. Isovanilloid Motifs in the B‐ring of Flavonoids. ChemCatChem 2022. [DOI: 10.1002/cctc.202200511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Martin Dippe
- Department of Bioorganic Chemistry Leibniz-Institute of Plant Biochemistry Weinberg 3 D-06120 Halle Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry Leibniz-Institute of Plant Biochemistry Weinberg 3 D-06120 Halle Germany
| | - Benjamin Weigel
- Department of Bioorganic Chemistry Leibniz-Institute of Plant Biochemistry Weinberg 3 D-06120 Halle Germany
| | - Ramona Heinke
- Department of Bioorganic Chemistry Leibniz-Institute of Plant Biochemistry Weinberg 3 D-06120 Halle Germany
| | - Thomas Vogt
- Department of Cell and Metabolic Biology Leibniz-Institute of Plant Biochemistry Weinberg 3 D-06120 Halle Germany
| | - Ludger A. Wessjohann
- Department of Bioorganic Chemistry Leibniz-Institute of Plant Biochemistry Weinberg 3 D-06120 Halle Germany
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10
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Poudel PB, Pandey RP, Dhakal D, Kim TS, Nguyen TTH, Jung HJ, Shin HJ, Timalsina B, Sohng JK. Functional Characterization of a Regiospecific Sugar- O-Methyltransferase from Nocardia. Appl Environ Microbiol 2022; 88:e0075422. [PMID: 35703553 PMCID: PMC9275233 DOI: 10.1128/aem.00754-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
Methyltransferases transfer a methyl group to a diverse group of natural products, thus providing structural diversity, stability, and altered pharmacological properties to the molecules. A limited number of regiospecific sugar-O-methyltransferases are functionally characterized. Thus, discovery of such an enzyme could solve the difficulties of biological production of methoxy derivatives of glycosylated molecules. In the current study, a regiospecific sugar-O-methyltransferase, ThnM1, belonging to the biosynthetic gene cluster (BGC) of 1-(α-L-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene produced by Nocardia sp. strain CS682, was analyzed and functionally characterized. ThnM1 demonstrated promiscuity to diverse chemical structures such as rhamnose-containing anthraquinones and flavonoids with regiospecific methylation at the 2'-hydroxyl group of the sugar moiety. Compared with other compounds, anthraquinone rhamnosides were found to be the preferred substrates for methylation. Thus, the enzyme was further employed for whole-cell biotransformation using engineered Escherichia coli to produce a methoxy-rhamnosyl derivative of quinizarin, an anthraquinone derivative. The structure of the newly generated derivative from Escherichia coli fermentation was elucidated by liquid chromatography-mass spectrometry and nuclear magnetic resonance spectroscopic analyses and identified as quinizarin-4-O-α-l-2-O-methylrhamnoside (QRM). Further, the biological impact of methylation was studied by comparing the cytotoxicity of QRM with that of quinizarin against the U87MG, SNU-1, and A375SM cancer cell lines. IMPORTANCE ThnM1 is a putative sugar-O-methyltransferase produced by the Nocardia sp. strain CS682 and is encoded by a gene belonging to the biosynthetic gene cluster (BGC) of 1-(α-l-(2-O-methyl)-6-deoxymannopyranosyloxy)-3,6,8-trimethoxynaphthalene. We demonstrated that ThnM1 is a promiscuous enzyme with regiospecific activity at the 2'-OH of rhamnose. As regiospecific methylation of sugars by chemical synthesis is a challenging step, ThnM1 may fill the gap in the potential diversification of natural products by methylating the rhamnose moiety attached to them.
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Affiliation(s)
- Purna Bahadur Poudel
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Ramesh Prasad Pandey
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Dipesh Dhakal
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Tae-Su Kim
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Trang Thi Huyen Nguyen
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Hye Jin Jung
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
- Department of Biotechnology and Pharmaceutical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Hee Jeong Shin
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
| | - Binod Timalsina
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, Republic of Korea
| | - Jae Kyung Sohng
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
- Department of Biotechnology and Pharmaceutical Engineering, Sun Moon University, Asan-si, Chungnam, Republic of Korea
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11
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Abdelraheem E, Thair B, Varela RF, Jockmann E, Popadić D, Hailes HC, Ward JM, Iribarren AM, Lewkowicz ES, Andexer JN, Hagedoorn PL, Hanefeld U. Methyltransferases, functions and applications. Chembiochem 2022; 23:e202200212. [PMID: 35691829 PMCID: PMC9539859 DOI: 10.1002/cbic.202200212] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/10/2022] [Indexed: 11/25/2022]
Abstract
In this review the current state‐of‐the‐art of S‐adenosylmethionine (SAM)‐dependent methyltransferases and SAM are evaluated. Their structural classification and diversity is introduced and key mechanistic aspects presented which are then detailed further. Then, catalytic SAM as a target for drugs, and approaches to utilise SAM as a cofactor in synthesis are introduced with different supply and regeneration approaches evaluated. The use of SAM analogues are also described. Finally O‐, N‐, C‐ and S‐MTs, their synthetic applications and potential for compound diversification is given.
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Affiliation(s)
| | - Benjamin Thair
- University College London Faculty of Mathematical and Physical Sciences, department of Chemistry, UNITED KINGDOM
| | - Romina Fernández Varela
- Universidad nacional di Quilmes, 3Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | - Emely Jockmann
- Albert-Ludwigs-Universitat Freiburg Universitatsbibliothek Freiburg, Pharmacie, GERMANY
| | | | - Helen C Hailes
- University College London Faculty of Mathematical and Physical Sciences, department of Chemistry, UNITED KINGDOM
| | - John M Ward
- University College London, Department of Biochemical Engineering, UNITED KINGDOM
| | - Adolfo M Iribarren
- Universidad Nacional de Quilmes, 3Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | - Elizabeth S Lewkowicz
- Universidad Nacional de Quilmes, Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | | | | | - Ulf Hanefeld
- Technische Universiteit Delft, Gebouw voor Scheikunde, Julianalaan 136, 2628 BL, Delft, NETHERLANDS
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12
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Kačar D, Schleissner C, Cañedo LM, Rodríguez P, de la Calle F, Cuevas C, Galán B, García JL. In vivo production of pederin by labrenzin pathway expansion. Metab Eng Commun 2022; 14:e00198. [PMID: 35517715 PMCID: PMC9062313 DOI: 10.1016/j.mec.2022.e00198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/01/2022] [Accepted: 04/20/2022] [Indexed: 11/21/2022] Open
Abstract
Pederin is a potent polyketide toxin that causes severe skin lesions in humans after contact with insects of genus Paederus. Due to its potent anticancer activities, pederin family compounds have raised the interest of pharmaceutical industry. Despite the extensive studies on the cluster of biosynthetic genes responsible for the production of pederin, it has not yet been possible to isolate and cultivate its bacterial endosymbiont producer. However, the marine bacterium Labrenzia sp. PHM005 was recently reported to produce labrenzin, the closest pederin analog. By cloning a synthetic pedO gene encoding one of the three O-methyltraferase of the pederin cluster into Labrenzia sp. PHM005 we have been able to produce pederin for the first time by fermentation in the new recombinant strain.
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Affiliation(s)
- Dina Kačar
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | | | - Pilar Rodríguez
- Research and Development Department, PharmaMar S.A, Madrid, Spain
| | | | - Carmen Cuevas
- Research and Development Department, PharmaMar S.A, Madrid, Spain
| | - Beatriz Galán
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - José Luis García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
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13
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Liu Q, Zhang D, Xu Y, Gao S, Gong Y, Cai X, Yao M, Yang X. Cloning and Functional Characterization of the Polyketide Synthases Based on Genome Mining of Preussia isomera XL-1326. Front Microbiol 2022; 13:819086. [PMID: 35602042 PMCID: PMC9116485 DOI: 10.3389/fmicb.2022.819086] [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: 11/20/2021] [Accepted: 03/31/2022] [Indexed: 11/21/2022] Open
Abstract
Fungal polyketides (PKs) are one of the largest families of structurally diverse bioactive natural products biosynthesized by multidomain megasynthases, in which thioesterase (TE) domains act as nonequivalent decision gates determining both the shape and the yield of the polyketide intermediate. The endophytic fungus Preussia isomera XL-1326 was discovered to have an excellent capacity for secreting diverse bioactive PKs, i.e., the hot enantiomers (±)-preuisolactone A with antibacterial activity, the single-spiro minimoidione B with α-glucosidase inhibition activity, and the uncommon heptaketide setosol with antifungal activity, which drive us to illustrate how the unique PKs are biosynthesized. In this study, we first reported the genome sequence information of P. isomera. Based on genome mining, we discovered nine transcriptionally active genes encoding polyketide synthases (PKSs), Preu1–Preu9, of which those of Preu3, Preu4, and Preu6 were cloned and functionally characterized due to possessing complete sets of synthetic and release domains. Through heterologous expression in Saccharomyces cerevisiae, Preu3 and Preu6 could release high yields of orsellinic acid (OA) derivatives [3-methylorsellinic acid (3-MOA) and lecanoric acid, respectively]. Correspondingly, we found that Preu3 and Preu6 were clustered into OA derivative synthase groups by phylogenetic analysis. Next, with TE domain swapping, we constructed a novel “non-native” PKS, Preu6-TEPreu3, which shared a very low identity with OA synthase, OrsA, from Aspergillus nidulans but could produce a large amount of OA. In addition, with the use of Preu6-TEPreu3, we synthesized methyl 3-methylorsellinate (synthetic oak moss of great economic value) from 3-MOA as the substrate, and interestingly, 3-MOA exhibited remarkable antibacterial activities, while methyl 3-methylorsellinate displayed broad-spectrum antifungal activity. Taken together, we identified two novel PKSs to biosynthesize 3-MOA and lecanoric acid, respectively, with information on such kinds of PKSs rarely reported, and constructed one novel “non-native” PKS to largely biosynthesize OA. This work is our first step to explore the biosynthesis of the PKs in P. isomera, and it also provides a new platform for high-level environment-friendly production of OA derivatives and the development of new antimicrobial agents.
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Affiliation(s)
- Qingpei Liu
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Dan Zhang
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Yao Xu
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Shuaibiao Gao
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Yifu Gong
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Xianhua Cai
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Ming Yao
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Xiaolong Yang
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
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14
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Hao Y, Wei Z, Wang Z, Li G, Yao Y, Dun B. Biotransformation of Flavonoids Improves Antimicrobial and Anti-Breast Cancer Activities In Vitro. Foods 2021; 10:foods10102367. [PMID: 34681416 PMCID: PMC8535490 DOI: 10.3390/foods10102367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 01/15/2023] Open
Abstract
Coarse cereals are rich in flavonoids, which are bioactive substances with a wide range of functions. Biotransformation is considered an emerging approach to methylate flavonoids, displaying prominent regio- and stereoselectivity. In the current study, liquiritigenin, naringenin, and hesperidin flavonoids were biotransformed using O-methyltransferases that were heterologously expressed in Saccharomyces cerevisiae BJ5464-NpgA. Nuclear magnetic resonance (NMR) spectroscopy was used together with high-resolution mass spectroscopy analysis to determine the structures of the resulting methylated transformants, and their antimicrobial and antiproliferation activities were also characterized. Among the five methylated flavonoids obtained, 7-methoxy-liquiritigenin had the strongest inhibitory effect on Candida albicans SC5314 (C. albicans SC5314), Staphylococcus aureus ATCC6538 (S. aureus ATCC6538), and Escherichia coli ATCC25922 (E. coli ATCC25922), which increased 7.65-, 1.49-, and 0.54-fold in comparison to the values of their unmethylated counterparts at 200, 250, and 400 μM, respectively. The results suggest that 3′-methoxyhesperetin showed the best antiproliferative activity against MCF-7 cells with IC50 values of 10.45 ± 0.45 µM, which was an increase of more than 14.35-fold compared to that of hesperetin. These results indicate that methylation enhances the antimicrobial activities and antiproliferative effects of flavonoids. The current study provides an experimental basis for further research on flavonoids as well as flavonoid-containing crops in the development of antimicrobial and anti-breast cancer drugs in addition to supplementary and health foods. The biotransformation method is ideal, as it represents a means for the sustainable production of bioactive flavonoids.
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Affiliation(s)
- Yanpeng Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China; (Y.H.); (Z.W.); (Z.W.); (G.L.); (Y.Y.)
| | - Zuchen Wei
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China; (Y.H.); (Z.W.); (Z.W.); (G.L.); (Y.Y.)
- Laboratory for Green Cultivation and Deep Processing of Three Gorges Reservoir Area’s Medicinal Herbs, College of Life Science & Engineering, The Chongqing Engineering, Chongqing Three Gorges University, No. 666 Tianxing Road, Wanzhou District, Chongqing 404000, China
| | - Zhi Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China; (Y.H.); (Z.W.); (Z.W.); (G.L.); (Y.Y.)
| | - Guiying Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China; (Y.H.); (Z.W.); (Z.W.); (G.L.); (Y.Y.)
| | - Yang Yao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China; (Y.H.); (Z.W.); (Z.W.); (G.L.); (Y.Y.)
| | - Baoqing Dun
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China; (Y.H.); (Z.W.); (Z.W.); (G.L.); (Y.Y.)
- Correspondence:
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15
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Romero E, Jones BS, Hogg BN, Rué Casamajo A, Hayes MA, Flitsch SL, Turner NJ, Schnepel C. Enzymatic Late-Stage Modifications: Better Late Than Never. Angew Chem Int Ed Engl 2021; 60:16824-16855. [PMID: 33453143 PMCID: PMC8359417 DOI: 10.1002/anie.202014931] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/15/2021] [Indexed: 12/16/2022]
Abstract
Enzyme catalysis is gaining increasing importance in synthetic chemistry. Nowadays, the growing number of biocatalysts accessible by means of bioinformatics and enzyme engineering opens up an immense variety of selective reactions. Biocatalysis especially provides excellent opportunities for late-stage modification often superior to conventional de novo synthesis. Enzymes have proven to be useful for direct introduction of functional groups into complex scaffolds, as well as for rapid diversification of compound libraries. Particularly important and highly topical are enzyme-catalysed oxyfunctionalisations, halogenations, methylations, reductions, and amide bond formations due to the high prevalence of these motifs in pharmaceuticals. This Review gives an overview of the strengths and limitations of enzymatic late-stage modifications using native and engineered enzymes in synthesis while focusing on important examples in drug development.
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Affiliation(s)
- Elvira Romero
- Compound Synthesis and ManagementDiscovery Sciences, BioPharmaceuticals R&DAstraZenecaGothenburgSweden
| | - Bethan S. Jones
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Bethany N. Hogg
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Arnau Rué Casamajo
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Martin A. Hayes
- Compound Synthesis and ManagementDiscovery Sciences, BioPharmaceuticals R&DAstraZenecaGothenburgSweden
| | - Sabine L. Flitsch
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Nicholas J. Turner
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
| | - Christian Schnepel
- School of ChemistryThe University of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUnited Kingdom
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16
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Pompei S, Grimm C, Farnberger JE, Schober L, Kroutil W. Regioselectivity of Cobalamin-Dependent Methyltransferase Can Be Tuned by Reaction Conditions and Substrate. ChemCatChem 2020; 12:5977-5983. [PMID: 33442427 PMCID: PMC7783988 DOI: 10.1002/cctc.202001296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/06/2020] [Indexed: 12/21/2022]
Abstract
Regioselective reactions represent a significant challenge for organic chemistry. Here the regioselective methylation of a single hydroxy group of 4-substituted catechols was investigated employing the cobalamin-dependent methyltransferase from Desulfitobacterium hafniense. Catechols substituted in position four were methylated either in meta- or para-position to the substituent depending whether the substituent was polar or apolar. While the biocatalytic cobalamin dependent methylation was meta-selective with 4-substituted catechols bearing hydrophilic groups, it was para-selective for hydrophobic substituents. Furthermore, the presence of water miscible co-solvents had a clear improving influence, whereby THF turned out to enable the formation of a single regioisomer in selected cases. Finally, it was found that also the pH led to an enhancement of regioselectivity for the cases investigated.
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Affiliation(s)
- Simona Pompei
- Institute of ChemistryNAWI GrazUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Christopher Grimm
- Institute of ChemistryNAWI GrazUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Judith E. Farnberger
- Austrian Centre of Industrial Biotechnologyc/o Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Lukas Schober
- Institute of ChemistryNAWI GrazUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Wolfgang Kroutil
- Institute of ChemistryNAWI GrazUniversity of GrazHeinrichstrasse 288010GrazAustria
- Field of Excellence BioHealthUniversity of Graz8010GrazAustria
- BioTechMed Graz8010GrazAustria
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17
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Xie L, Xiao D, Wang X, Wang C, Bai J, Yue Q, Yue H, Li Y, Molnár I, Xu Y, Zhang L. Combinatorial Biosynthesis of Sulfated Benzenediol Lactones with a Phenolic Sulfotransferase from Fusarium graminearum PH-1. mSphere 2020; 5:e00949-20. [PMID: 33239367 PMCID: PMC7690957 DOI: 10.1128/msphere.00949-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/04/2020] [Indexed: 11/20/2022] Open
Abstract
Total biosynthesis or whole-cell biocatalytic production of sulfated small molecules relies on the discovery and implementation of appropriate sulfotransferase enzymes. Although fungi are prominent biocatalysts and have been used to sulfate drug-like phenolics, no gene encoding a sulfotransferase enzyme has been functionally characterized from these organisms. Here, we identify a phenolic sulfotransferase, FgSULT1, by genome mining from the plant-pathogenic fungus Fusarium graminearum PH-1. We expressed FgSULT1 in a Saccharomyces cerevisiae chassis to modify a broad range of benzenediol lactones and their nonmacrocyclic congeners, together with an anthraquinone, with the resulting unnatural natural product (uNP) sulfates displaying increased solubility. FgSULT1 shares low similarity with known animal and plant sulfotransferases. Instead, it forms a sulfotransferase family with putative bacterial and fungal enzymes for phase II detoxification of xenobiotics and allelochemicals. Among fungi, putative FgSULT1 homologues are encoded in the genomes of Fusarium spp. and a few other genera in nonsyntenic regions, some of which may be related to catabolic sulfur recycling. Computational structure modeling combined with site-directed mutagenesis revealed that FgSULT1 retains the key catalytic residues and the typical fold of characterized animal and plant sulfotransferases. Our work opens the way for the discovery of hitherto unknown fungal sulfotransferases and provides a synthetic biological and enzymatic platform that can be adapted to produce bioactive sulfates, together with sulfate ester standards and probes for masked mycotoxins, precarcinogenic toxins, and xenobiotics.IMPORTANCE Sulfation is an expedient strategy to increase the solubility, bioavailability, and bioactivity of nutraceuticals and clinically important drugs. However, chemical or biological synthesis of sulfoconjugates is challenging. Genome mining, heterologous expression, homology structural modeling, and site-directed mutagenesis identified FgSULT1 of Fusarium graminearum PH-1 as a cytosolic sulfotransferase with the typical fold and active site architecture of characterized animal and plant sulfotransferases, despite low sequence similarity. FgSULT1 homologues are sparse in fungi but form a distinct clade with bacterial sulfotransferases. This study extends the functionally characterized sulfotransferase superfamily to the kingdom Fungi and demonstrates total biosynthetic and biocatalytic synthetic biological platforms to produce unnatural natural product (uNP) sulfoconjugates. Such uNP sulfates may be utilized for drug discovery in human and veterinary medicine and crop protection. Our synthetic biological methods may also be adapted to generate masked mycotoxin standards for food safety and environmental monitoring applications and to expose precarcinogenic xenobiotics.
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Affiliation(s)
- Linan Xie
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Dongliang Xiao
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Xiaojing Wang
- Southwest Center for Natural Products Research, University of Arizona, Tucson, Arizona, USA
- Microbial Pharmacology Laboratory, Shanghai University of Medicine and Health Sciences, Shanghai, People's Republic of China
| | - Chen Wang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Jing Bai
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
- School of Chemistry, Biology and Material Engineering, Suzhou University of Science and Technology, Suzhou City, Jiangsu Province, People's Republic of China
| | - Qun Yue
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Haitao Yue
- Department of Biology and Biotechnology, Xinjiang University, Urumqi, People's Republic of China
| | - Ye Li
- Southwest Center for Natural Products Research, University of Arizona, Tucson, Arizona, USA
- National Engineering Lab for Cereal Fermentation Technology, Jiangnan University, Wuxi, People's Republic of China
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, Tucson, Arizona, USA
| | - Yuquan Xu
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Liwen Zhang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
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18
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Blaby IK, Cheng JF. Building a custom high-throughput platform at the Joint Genome Institute for DNA construct design and assembly-present and future challenges. Synth Biol (Oxf) 2020; 5:ysaa023. [PMID: 34746437 PMCID: PMC7737003 DOI: 10.1093/synbio/ysaa023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 11/11/2023] Open
Abstract
The rapid design and assembly of synthetic DNA constructs have become a crucial component of biological engineering projects via iterative design-build-test-learn cycles. In this perspective, we provide an overview of the workflows used to generate the thousands of constructs and libraries produced each year at the U.S. Department of Energy Joint Genome Institute. Particular attention is paid to describing pipelines, tools used, types of scientific projects enabled by the platform and challenges faced in further scaling output.
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Affiliation(s)
- Ian K Blaby
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jan-Fang Cheng
- US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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19
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Bang S, Shim SH. Beta resorcylic acid lactones (RALs) from fungi: chemistry, biology, and biosynthesis. Arch Pharm Res 2020; 43:1093-1113. [PMID: 33113097 DOI: 10.1007/s12272-020-01275-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/21/2020] [Indexed: 11/29/2022]
Abstract
β-Resorcylic acid lactones (RALs) are one of the major polyketides produced by fungi, and some of them have a diverse array of biological activities. Most RALs feature a 14-membered macrocyclic ring fused to β-resorcylic acid (2,4-dihydroxybenzoic acid). In this review, more than 100 RAL-type of compounds are structurally classified into three groups; 14-membered RALs with 17R configuration, 14-membered RALs with 17S configuration, and benzopyranones/benzofuranones, and they are reviewed comprehensively in terms of chemistry, biological activities, and biosynthetic pathways.
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Affiliation(s)
- Sunghee Bang
- College of Pharmacy, Duksung Women's University, Seoul, 01369, Republic of Korea
| | - Sang Hee Shim
- College of Pharmacy, Duksung Women's University, Seoul, 01369, Republic of Korea.
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20
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Wang C, Wang X, Zhang L, Yue Q, Liu Q, Xu YM, Gunatilaka AAL, Wei X, Xu Y, Molnár I. Intrinsic and Extrinsic Programming of Product Chain Length and Release Mode in Fungal Collaborating Iterative Polyketide Synthases. J Am Chem Soc 2020; 142:17093-17104. [PMID: 32833442 DOI: 10.1021/jacs.0c07050] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Combinatorial biosynthesis with fungal polyketide synthases (PKSs) promises to produce unprecedented bioactive "unnatural" natural products (uNPs) for drug discovery. Genome mining of the dothideomycete Rhytidhysteron rufulum uncovered a collaborating highly reducing PKS (hrPKS)-nonreducing PKS (nrPKS) pair. These enzymes produce trace amounts of rare S-type benzenediol macrolactone congeners with a phenylacetate core in a heterologous host. However, subunit shuffling and domain swaps with voucher enzymes demonstrated that all PKS domains are highly productive. This contradiction led us to reveal novel programming layers exerted by the starter unit acyltransferase (SAT) and the thioesterase (TE) domains on the PKS system. First, macrocyclic vs linear product formation is dictated by the intrinsic biosynthetic program of the TE domain. Next, the chain length of the hrPKS product is strongly influenced in trans by the off-loading preferences of the nrPKS SAT domain. Last, TE domains are size-selective filters that facilitate or obstruct product formation from certain priming units. Thus, the intrinsic programs of the SAT and TE domains are both part of the extrinsic program of the hrPKS subunit and modulate the observable metaprogram of the whole PKS system. Reconstruction of SAT and TE phylogenies suggests that these domains travel different evolutionary trajectories, with the resulting divergence creating potential conflicts in the PKS metaprogram. Such conflicts often emerge in chimeric PKSs created by combinatorial biosynthesis, reducing biosynthetic efficiency or even incapacitating the system. Understanding the points of failure for such engineered biocatalysts is pivotal to advance the biosynthetic production of uNPs.
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Affiliation(s)
- Chen Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.,Southwest Center for Natural Products Research, University of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United States
| | - Xiaojing Wang
- Microbial Pharmacology Laboratory, Shanghai University of Medicine and Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai 201318, P. R. China
| | - Liwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Qun Yue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Qingpei Liu
- Southwest Center for Natural Products Research, University of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United States.,School of Pharmaceutical Sciences, South-Central University for Nationalities, 182 Minyuan Road, Hongshan District, Wuhan 430074, P. R. China
| | - Ya-Ming Xu
- Southwest Center for Natural Products Research, University of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United States
| | - A A Leslie Gunatilaka
- Southwest Center for Natural Products Research, University of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United States
| | - Xiaoyi Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Yuquan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United States
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21
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Malico AA, Nichols L, Williams GJ. Synthetic biology enabling access to designer polyketides. Curr Opin Chem Biol 2020; 58:45-53. [PMID: 32758909 DOI: 10.1016/j.cbpa.2020.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/08/2020] [Accepted: 06/11/2020] [Indexed: 12/18/2022]
Abstract
The full potential of polyketide discovery has yet to be reached owing to a lack of suitable technologies and knowledge required to advance engineering of polyketide biosynthesis. Recent investigations on the discovery, enhancement, and non-natural use of these biosynthetic gene clusters via computational biology, metabolic engineering, structural biology, and enzymology-guided approaches have facilitated improved access to designer polyketides. Here, we discuss recent successes in gene cluster discovery, host strain engineering, precursor-directed biosynthesis, combinatorial biosynthesis, polyketide tailoring, and high-throughput synthetic biology, as well as challenges and outlooks for rapidly generating useful target polyketides.
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Affiliation(s)
- Alexandra A Malico
- Department of Chemistry, NC State University, Raleigh, NC, 27695, United States
| | - Lindsay Nichols
- Department of Chemistry, NC State University, Raleigh, NC, 27695, United States
| | - Gavin J Williams
- Department of Chemistry, NC State University, Raleigh, NC, 27695, United States; Comparative Medicine Institute, NC State University, Raleigh, NC, 27695, United States.
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22
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Yuan S, Gopal JV, Ren S, Chen L, Liu L, Gao Z. Anticancer fungal natural products: Mechanisms of action and biosynthesis. Eur J Med Chem 2020; 202:112502. [PMID: 32652407 DOI: 10.1016/j.ejmech.2020.112502] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/20/2020] [Accepted: 05/25/2020] [Indexed: 01/07/2023]
Abstract
Many fungal metabolites show promising anticancer properties both in vitro and in animal models, and some synthetic analogs of those metabolites have progressed into clinical trials. However, currently, there are still no fungi-derived agents approved as anticancer drugs. Two potential reasons could be envisioned: 1) lacking a clear understanding of their anticancer mechanism of action, 2) unable to supply enough materials to support the preclinical and clinic developments. In this review, we will summarize recent efforts on elucidating the anticancer mechanisms and biosynthetic pathways of several promising anticancer fungal natural products.
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Affiliation(s)
- Siwen Yuan
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jannu Vinay Gopal
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Shuya Ren
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Litong Chen
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Lan Liu
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Zhizeng Gao
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
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23
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Zhou J, Gao Y, Chang JL, Yu HY, Chen J, Zhou M, Meng XG, Ruan HL. Resorcylic Acid Lactones from an Ilyonectria sp. JOURNAL OF NATURAL PRODUCTS 2020; 83:1505-1514. [PMID: 32323537 DOI: 10.1021/acs.jnatprod.9b01167] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Twelve new resorcylic acid lactones (RALs) including three new 16-membered RALs (1a, 1b and 2), eight new 14-membered RALs (3-10), and one new 12-membered RAL (11), along with five known 14-membered RALs (12-16), were identified from the fermentation of the soil-derived fungus Ilyonectria sp. sb65. Their structures were established by detailed analyses of 1D and 2D NMR, HRESIMS, and X-ray diffraction crystallography. All new compounds were evaluated for their cytotoxic effects against three human cancer cell lines, along with their potential as TRAIL sensitizers in TRAIL-resistant A549 human lung adenocarcinoma cells and their in vitro immunosuppressive effects against ConA-induced T-cell and LPS-induced B-cell proliferation.
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Affiliation(s)
- Jia Zhou
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Wuhan 430030, People's Republic of China
| | - Ying Gao
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Wuhan 430030, People's Republic of China
| | - Jin-Ling Chang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Wuhan 430030, People's Republic of China
| | - Heng-Yi Yu
- Department of Pharmacy, Tongji Hospital Affiliated Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Juan Chen
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Wuhan 430030, People's Republic of China
| | - Ming Zhou
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Wuhan 430030, People's Republic of China
| | - Xiang-Gao Meng
- College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Han-Li Ruan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Wuhan 430030, People's Republic of China
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The versatile O-methyltransferase LrOMT catalyzes multiple O-methylation reactions in amaryllidaceae alkaloids biosynthesis. Int J Biol Macromol 2019; 141:680-692. [PMID: 31494163 DOI: 10.1016/j.ijbiomac.2019.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/03/2019] [Accepted: 09/03/2019] [Indexed: 12/19/2022]
Abstract
Amaryllidaceae alkaloids are unique benzylphenethylamine derivatives that comprise of more than 600 members with a huge chemical diversity. Most of them showed interesting bioactivities, for instance, galanthamine (GAL) is clinically used for Alzheimer's disease treatment. All Amaryllidaceae alkaloids had been thought to be derived from 4'-O-methylnorbelladine originated from norbelladine catalyzed by norbelladine 4'-O-methyltransferase (N4OMT). Herein we mined the transcriptome datasets of Lycoris radiata, a GAL-producing plant. LrOMT was cloned, overexpressed in Escherichia coli, and purified to homogeneity. Bioinformatics analysis and enzymatic activity assays revealed that LrOMT is an S-adenosylmethionine-dependent Class I OMT. LrOMT exhibited both para- and meta-O-methylation activities toward norbelladine to give 4'- and 3'-O-methylnorbelladine. Twenty-four analogues, including the proposed biosynthetic intermediates, were introduced to investigate the substrate scope of LrOMT and it showed that the aromatic substrates should have two vicinal hydroxyl groups. The LrOMT-catalyzed O-methylation preference is dependent on the properties of the binding group of the substrates. The transcription levels of LrOMT were positively associated with the accumulation of the Amaryllidaceae alkaloids and the biosynthetic intermediates in L. radiata. The present work revealed that LrOMT catalyzes multiple O-methylation reactions and its characterization will be helpful to uncover novel biosynthetic genes for Amaryllidaceae alkaloids biosynthesis.
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