1
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Wu Y, Wang M, Liu L. Advances on structure, bioactivity, and biosynthesis of amino acid-containing trans-AT polyketides. Eur J Med Chem 2023; 262:115890. [PMID: 37907023 DOI: 10.1016/j.ejmech.2023.115890] [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: 08/19/2023] [Revised: 10/01/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023]
Abstract
Trans-AT polyketides represent a class of natural compounds utilizing independent acyltransferase during their biosynthesis. They are well known for their diverse chemical structures and potent bioactivities. Trans-AT polyketides are synthesized through biosynthetic gene clusters predominantly composed of polyketide synthases (PKS), but often found in hybrid with non-ribosomal peptide synthetases (NRPS). This genetic hybridization results in the incorporation of amino acid residues into polyketide structures, significantly enhancing their structural diversity. Numerous amino acid-containing trans-AT polyketides have been identified, drawing significant attention to the mechanisms underlying amino acid incorporation and their impact on the biological activity of polyketides. Here, we discussed their origins, structures, biological activities, and the specific roles of amino acids in modulating both the bioactivity and biosynthesis of 38 trans-AT polyketides containing amino acids for the first time. This comprehensive analysis will serve as a crucial reference for the exploration of novel compounds and the improvement of structures and activities.
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Affiliation(s)
- Yunqiang Wu
- Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China; Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China
| | - Min Wang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.
| | - Liwei Liu
- Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China; Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China.
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2
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Adaikpoh BI, Romanowski SB, Eustáquio AS. Understanding Autologous Spliceostatin Transcriptional Regulation to Derive Parts for Heterologous Expression in a Burkholderia Bacterial Host. ACS Synth Biol 2023; 12:1952-1960. [PMID: 37338297 PMCID: PMC10527236 DOI: 10.1021/acssynbio.3c00228] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Burkholderia β-Proteobacteria are emerging sources of natural products. We are interested in developing Burkholderia sp. FERM BP-3421 into a synthetic biology chassis to facilitate natural product discovery. FERM BP-3421 produces autologous spliceostatins on gram per liter scale. We reasoned that transcription factors and promoters that regulate spliceostatin biosynthesis would provide valuable parts for heterologous expression. Herein we demonstrate that fr9A encodes a pathway-specific transcriptional activator of spliceostatin biosynthesis. In-frame deletion of fr9A abolished spliceostatin production, which was restored by genetic complementation. Using transcriptomics and green fluorescent protein (GFP) reporter assays, we identified four fr9 promoters, three of which are activated by LuxR-type regulator Fr9A. We then constructed an Fr9A-regulated promoter system that was compared to benchmarks and effectively applied for GFP and capistruin lasso peptide expression in an optimized host background. Our findings enrich the genetic toolbox for optimizing heterologous expression and promoting the discovery and development of natural products from Burkholderia bacteria.
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Affiliation(s)
- Barbara I. Adaikpoh
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, 60607, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Sean B. Romanowski
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, 60607, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Alessandra S. Eustáquio
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, 60607, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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3
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Jang JP, Kim GS, Oh TH, Park B, Kim M, Hwang GJ, Lee HW, Lee JG, Hong YS, Ahn JS, Ko SK, Jang JH. Jejuketomycins A and B, polyketide glycosides with cancer cell migration inhibitory activity from Streptomyces sp. KCB15JA151. RSC Adv 2022; 12:22360-22366. [PMID: 36105948 PMCID: PMC9364360 DOI: 10.1039/d2ra04039e] [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: 06/30/2022] [Accepted: 07/30/2022] [Indexed: 11/21/2022] Open
Abstract
Two new polyketide glycosides jejuketomycins A (1) and B (2), were isolated from a culture of Streptomyces sp. KCB15JA151. Their chemical structures including the absolute configurations were determined by detailed analyses of the NMR and HRMS data and ECD calculations and spectral data. Compounds 1 and 2 possess an unusual 6/6/8 tricyclic ring system. Biological evaluation with the wound healing assay and time-lapse cell tracking analysis revealed that compounds 1 and 2 have significant inhibitory activities against cancer cell migration with low cytotoxicity. Two new polyketide glycosides jejuketomycins A (1) and B (2), were isolated from a culture of Streptomyces sp. KCB15JA151.![]()
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Affiliation(s)
- Jun-Pil Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Gil Soo Kim
- Central Research and Development, HanpoongPharm. Co., LTD., Wanju 54843, Korea
| | - Tae Hoon Oh
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- College of Pharmacy, Chungbuk National University, Cheongju, 28160, Korea
| | - Beomcheol Park
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- College of Pharmacy, Chungbuk National University, Cheongju, 28160, Korea
| | - Minhee Kim
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- College of Pharmacy, Chungbuk National University, Cheongju, 28160, Korea
| | - Gwi Ja Hwang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Hyeok-Won Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Korea
| | - Jin-Gyeom Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Korea
| | - Young-Soo Hong
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea
| | - Jong Seog Ahn
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea
| | - Sung-Kyun Ko
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea
| | - Jae-Hyuk Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea
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4
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Sulheim S, Fossheim FA, Wentzel A, Almaas E. Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters. BMC Bioinformatics 2021; 22:81. [PMID: 33622234 PMCID: PMC7901079 DOI: 10.1186/s12859-021-03985-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/18/2021] [Indexed: 12/17/2022] Open
Abstract
Background A wide range of bioactive compounds is produced by enzymes and enzymatic complexes encoded in biosynthetic gene clusters (BGCs). These BGCs can be identified and functionally annotated based on their DNA sequence. Candidates for further research and development may be prioritized based on properties such as their functional annotation, (dis)similarity to known BGCs, and bioactivity assays. Production of the target compound in the native strain is often not achievable, rendering heterologous expression in an optimized host strain as a promising alternative. Genome-scale metabolic models are frequently used to guide strain development, but large-scale incorporation and testing of heterologous production of complex natural products in this framework is hampered by the amount of manual work required to translate annotated BGCs to metabolic pathways. To this end, we have developed a pipeline for an automated reconstruction of BGC associated metabolic pathways responsible for the synthesis of non-ribosomal peptides and polyketides, two of the dominant classes of bioactive compounds. Results The developed pipeline correctly predicts 72.8% of the metabolic reactions in a detailed evaluation of 8 different BGCs comprising 228 functional domains. By introducing the reconstructed pathways into a genome-scale metabolic model we demonstrate that this level of accuracy is sufficient to make reliable in silico predictions with respect to production rate and gene knockout targets. Furthermore, we apply the pipeline to a large BGC database and reconstruct 943 metabolic pathways. We identify 17 enzymatic reactions using high-throughput assessment of potential knockout targets for increasing the production of any of the associated compounds. However, the targets only provide a relative increase of up to 6% compared to wild-type production rates. Conclusion With this pipeline we pave the way for an extended use of genome-scale metabolic models in strain design of heterologous expression hosts. In this context, we identified generic knockout targets for the increased production of heterologous compounds. However, as the predicted increase is minor for any of the single-reaction knockout targets, these results indicate that more sophisticated strain-engineering strategies are necessary for the development of efficient BGC expression hosts.
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Affiliation(s)
- Snorre Sulheim
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Sem Sælands vei 8, 7034, Trondheim, Norway. .,Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands vei 3, 7034, Trondheim, Norway.
| | - Fredrik A Fossheim
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Sem Sælands vei 8, 7034, Trondheim, Norway
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands vei 3, 7034, Trondheim, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Sem Sælands vei 8, 7034, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, Håkon Jarls gate 11, 7030, Trondheim, Norway
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5
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Yin Z, Dickschat JS. Cis double bond formation in polyketide biosynthesis. Nat Prod Rep 2021; 38:1445-1468. [PMID: 33475122 DOI: 10.1039/d0np00091d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covering: up to 2020Polyketides form a large group of bioactive secondary metabolites that usually contain one or more double bonds. Although most of the double bonds found in polyketides are trans or E-configured, several cases are known in which cis or Z-configurations are observed. Double bond formation by polyketide synthases (PKSs) is widely recognised to be catalysed by ketoreduction and subsequent dehydration of the acyl carrier protein (ACP)-tethered 3-ketoacyl intermediate in the PKS biosynthetic assembly line with a specific stereochemical course in which the ketoreduction step determines the usual trans or more rare cis double bond configuration. Occasionally, other mechanisms for the installation of cis double bonds such as double bond formation during chain release or post-PKS modifications including, amongst others, isomerisations or double bond installations by oxidation are observed. This review discusses the peculiar mechanisms of cis double bond formation in polyketide biosynthesis.
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Affiliation(s)
- Zhiyong Yin
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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6
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Walker PD, Weir ANM, Willis CL, Crump MP. Polyketide β-branching: diversity, mechanism and selectivity. Nat Prod Rep 2021; 38:723-756. [PMID: 33057534 DOI: 10.1039/d0np00045k] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 2008 to August 2020 Polyketides are a family of natural products constructed from simple building blocks to generate a diverse range of often complex chemical structures with biological activities of both pharmaceutical and agrochemical importance. Their biosynthesis is controlled by polyketide synthases (PKSs) which catalyse the condensation of thioesters to assemble a functionalised linear carbon chain. Alkyl-branches may be installed at the nucleophilic α- or electrophilic β-carbon of the growing chain. Polyketide β-branching is a fascinating biosynthetic modification that allows for the conversion of a β-ketone into a β-alkyl group or functionalised side-chain. The overall transformation is catalysed by a multi-protein 3-hydroxy-3-methylglutaryl synthase (HMGS) cassette and is reminiscent of the mevalonate pathway in terpene biosynthesis. The first step most commonly involves the aldol addition of acetate to the electrophilic carbon of the β-ketothioester catalysed by a 3-hydroxy-3-methylglutaryl synthase (HMGS). Subsequent dehydration and decarboxylation selectively generates either α,β- or β,γ-unsaturated β-alkyl branches which may be further modified. This review covers 2008 to August 2020 and summarises the diversity of β-branch incorporation and the mechanistic details of each catalytic step. This is extended to discussion of polyketides containing multiple β-branches and the selectivity exerted by the PKS to ensure β-branching fidelity. Finally, the application of HMGS in data mining, additional β-branching mechanisms and current knowledge of the role of β-branches in this important class of biologically active natural products is discussed.
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Affiliation(s)
- P D Walker
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - A N M Weir
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - C L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - M P Crump
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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7
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Bressin RK, Osman S, Pohorilets I, Basu U, Koide K. Total Synthesis of Meayamycin B. J Org Chem 2020; 85:4637-4647. [DOI: 10.1021/acs.joc.9b03370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Robert K. Bressin
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Sami Osman
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Ivanna Pohorilets
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Upamanyu Basu
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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8
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Nivina A, Yuet KP, Hsu J, Khosla C. Evolution and Diversity of Assembly-Line Polyketide Synthases. Chem Rev 2019; 119:12524-12547. [PMID: 31838842 PMCID: PMC6935866 DOI: 10.1021/acs.chemrev.9b00525] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Indexed: 12/11/2022]
Abstract
Assembly-line polyketide synthases (PKSs) are among the most complex protein machineries known in nature, responsible for the biosynthesis of numerous compounds used in the clinic. Their present-day diversity is the result of an evolutionary path that has involved the emergence of a multimodular architecture and further diversification of assembly-line PKSs. In this review, we provide an overview of previous studies that investigated PKS evolution and propose a model that challenges the currently prevailing view that gene duplication has played a major role in the emergence of multimodularity. We also analyze the ensemble of orphan PKS clusters sequenced so far to evaluate how large the entire diversity of assembly-line PKS clusters and their chemical products could be. Finally, we examine the existing techniques to access the natural PKS diversity in natural and heterologous hosts and describe approaches to further expand this diversity through engineering.
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Affiliation(s)
- Aleksandra Nivina
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
| | - Kai P. Yuet
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
| | - Jake Hsu
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
| | - Chaitan Khosla
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
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9
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Liang H, Jiang L, Jiang Q, Shi J, Xiang J, Yan X, Zhu X, Zhao L, Shen B, Duan Y, Huang Y. A 3‐hydroxy‐3‐methylglutaryl‐CoA synthase‐based probe for the discovery of the acyltransferase‐less type I polyketide synthases. Environ Microbiol 2019; 21:4270-4282. [DOI: 10.1111/1462-2920.14787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/08/2019] [Accepted: 08/20/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Haoyu Liang
- Xiangya International Academy of Translational Medicine at Central South University Changsha Hunan China
| | - Lin Jiang
- Xiangya International Academy of Translational Medicine at Central South University Changsha Hunan China
| | - Qiyun Jiang
- School of Geosciences and Info‐physics at Central South University Changsha Hunan China
| | - Jie Shi
- Xiangya International Academy of Translational Medicine at Central South University Changsha Hunan China
| | - Jingxi Xiang
- Xiangya International Academy of Translational Medicine at Central South University Changsha Hunan China
| | - Xiaohui Yan
- Xiangya International Academy of Translational Medicine at Central South University Changsha Hunan China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery Changsha Hunan China
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine at Central South University Changsha Hunan China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery Changsha Hunan China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery Changsha Hunan China
| | - Lixing Zhao
- Yunnan Institute of Microbiology, Yunnan University Kunming Yunnan China
| | - Ben Shen
- Department of Chemistry The Scripps Research Institute Jupiter FL USA
- Molecular Medicine The Scripps Research Institute Jupiter FL USA
- Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute Jupiter FL USA
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine at Central South University Changsha Hunan China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery Changsha Hunan China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery Changsha Hunan China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine at Central South University Changsha Hunan China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery Changsha Hunan China
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10
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Zhao H, Zhang B, Ma LF, Shi LM, Zhan ZJ. Cytotoxic Spliceostatin Analogs from Pseudomonas sp. Chem Biodivers 2019; 16:e1900266. [PMID: 31298476 DOI: 10.1002/cbdv.201900266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 07/11/2019] [Indexed: 12/14/2022]
Abstract
Two new spliceostatin analogs, designed as spliceostatins J and K (1 and 2), were isolated and identified from the culture of Pseudomonas sp., along with two known ones, FR901464 (3) and spliceostatin E (4). Their structures were elucidated by detailed interpretation of their spectroscopic data, especially 2D-NMR and HR-ESI-MS. Spliceostatin J (1) represented the first example of spliceostatins bearing an unusual hexahydrofuro[3,4-b]furan moiety. Biological assay showed all the isolated compounds except 1 displayed potent cytotoxic activities against two cancer cell lines (MDA-MB-231 and A-549). Structure-activity-relationship studies revealed that the tetrahydropyran ring in spliceostatin analogs was necessary for their bioactive retention.
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Affiliation(s)
- Hong Zhao
- First Clinical Medicine College, Zhejiang Chinese Medical University, Hangzhou, 310006, P. R. China
| | - Bei Zhang
- First Clinical Medicine College, Zhejiang Chinese Medical University, Hangzhou, 310006, P. R. China
| | - Lie-Feng Ma
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Lin-Mei Shi
- Lishui Technology College, Lishui, 323000, P. R. China
| | - Zha-Jun Zhan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
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11
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Abstract
Burkholderia bacteria are multifaceted organisms that are ecologically and metabolically diverse. The Burkholderia genus has gained prominence because it includes human pathogens; however, many strains are nonpathogenic and have desirable characteristics such as beneficial plant associations and degradation of pollutants. The diversity of the Burkholderia genus is reflected within the large genomes that feature multiple replicons. Burkholderia genomes encode a plethora of natural products with potential therapeutic relevance and biotechnological applications. This review highlights Burkholderia as an emerging source of natural products. An overview of the taxonomy of the Burkholderia genus, which is currently being revised, is provided. We then present a curated compilation of natural products isolated from Burkholderia sensu lato and analyze their characteristics in terms of biosynthetic class, discovery method, and bioactivity. Finally, we describe and discuss genome characteristics and highlight the biosynthesis of a select number of natural products that are encoded in unusual biosynthetic gene clusters. The availability of >1000 Burkholderia genomes in public databases provides an opportunity to realize the genetic potential of this underexplored taxon for natural product discovery.
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Affiliation(s)
- Sylvia Kunakom
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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12
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Tolmie C, Smit MS, Opperman DJ. Native roles of Baeyer–Villiger monooxygenases in the microbial metabolism of natural compounds. Nat Prod Rep 2019; 36:326-353. [DOI: 10.1039/c8np00054a] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Baeyer–Villiger monooxygenases function in the primary metabolism of atypical carbon sources, as well as the synthesis of complex microbial metabolites.
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Affiliation(s)
- Carmien Tolmie
- Department of Biotechnology
- University of the Free State
- Bloemfontein
- South Africa
| | - Martha S. Smit
- Department of Biotechnology
- University of the Free State
- Bloemfontein
- South Africa
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13
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Abstract
Enzymes that catalyze a Michael-type addition in polyketide biosynthesis are summarized and discussed.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
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14
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Auerbach D, Yan F, Zhang Y, Müller R. Characterization of an Unusual Glycerate Esterification Process in Vioprolide Biosynthesis. ACS Chem Biol 2018; 13:3123-3130. [PMID: 30286293 DOI: 10.1021/acschembio.8b00826] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteria produce a large number of secondary metabolites with extraordinary chemical structures and bioactivities. Vioprolides are promising anticancer and antifungal lead compounds produced by the myxobacterium Cystobacter violaceus Cb vi35, which are initially synthesized as acylated precursors (previoprolides) by nonribosomal peptide synthetases (NRPS). Here, we describe and characterize an unprecedented glycerate esterification process in the biosynthesis of vioprolides. In vitro biochemical investigations revealed that the fatty acyl chain of previoprolides is adenylated by the starting fatty acyl-AMP ligase (FAAL) domain, while the glycerate moiety is incorporated by the FkbH domain. An unusual ester-bond forming condensation domain is shown responsible for the acylation of glycerate. LC-MS analysis and bioactivity assays suggest that the acylation serves for directed membrane transport rather than representing a prodrug mechanism.
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Affiliation(s)
- David Auerbach
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
| | - Fu Yan
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
| | - Youming Zhang
- Shandong University-Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao, People’s Republic of China
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Department of Pharmacy, Saarland University, Saarland University Campus, Building E8.1, 66123 Saarbrücken, Germany
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15
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Wagner DT, Zhang Z, Meoded RA, Cepeda AJ, Piel J, Keatinge-Clay AT. Structural and Functional Studies of a Pyran Synthase Domain from a trans-Acyltransferase Assembly Line. ACS Chem Biol 2018; 13:975-983. [PMID: 29481043 DOI: 10.1021/acschembio.8b00049] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
trans-Acyltransferase assembly lines possess enzymatic domains often not observed in their better characterized cis-acyltransferase counterparts. Within this repertoire of largely unexplored biosynthetic machinery is a class of enzymes called the pyran synthases that catalyze the formation of five- and six-membered cyclic ethers from diverse polyketide chains. The 1.55 Å resolution crystal structure of a pyran synthase domain excised from the ninth module of the sorangicin assembly line highlights the similarity of this enzyme to the ubiquitous dehydratase domain and provides insight into the mechanism of ring formation. Functional assays of point mutants reveal the central importance of the active site histidine that is shared with the dehydratases as well as the supporting role of a neighboring semiconserved asparagine.
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Affiliation(s)
- Drew T. Wagner
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhicheng Zhang
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Roy A. Meoded
- Institut für Mikrobiologie, Eidgenössiche Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Alexis J. Cepeda
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jörn Piel
- Institut für Mikrobiologie, Eidgenössiche Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Adrian T. Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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16
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Slocum ST, Lowell AN, Tripathi A, Shende VV, Smith JL, Sherman DH. Chemoenzymatic Dissection of Polyketide β-Branching in the Bryostatin Pathway. Methods Enzymol 2018; 604:207-236. [PMID: 29779653 PMCID: PMC6327954 DOI: 10.1016/bs.mie.2018.01.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
β-Branching is an expansion upon canonical polyketide synthase extension that allows for the installation of diverse chemical moieties in several natural products. Several of these moieties are unique among natural products, including the two vinyl methylesters found in the core structure of bryostatins. This family of molecules is derived from an obligate bacterial symbiont of a sessile marine bryozoan, Bugula neritina. Within this family, bryostatin 1 has been investigated as an anticancer, neuroprotective, and immunomodulatory compound. We have turned to the biosynthetic gene cluster within the bacterial symbiont to investigate the biosynthesis of bryostatins. Recent sequencing efforts resulted in the annotation of two missing genes: bryT and bryU. Using novel chemoenzymatic techniques, we have validated these as the missing enoyl-CoA hydratase and donor acyl carrier protein, essential components of the β-branching cassette of the bryostatin pathway. Together, this cassette installs the vinyl methylester moieties essential to the activity of bryostatins.
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Affiliation(s)
- Samuel T Slocum
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Andrew N Lowell
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - Vikram V Shende
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Chemistry, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, United States.
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17
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Ghosh AK, Brindisi M. Achmatowicz Reaction and its Application in the Syntheses of Bioactive Molecules. RSC Adv 2016; 6:111564-111598. [PMID: 28944049 PMCID: PMC5603243 DOI: 10.1039/c6ra22611f] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Substituted pyranones and tetrahydropyrans are structural subunits of many bioactive natural products. Considerable efforts are devoted toward the chemical synthesis of these natural products due to their therapeutic potential as well as low natural abundance. These embedded pyranones and tetrahydropyran structural motifs have been the subject of synthetic interest over the years. While there are methods available for the syntheses of these subunits, there are issues related to regio and stereochemical outcomes, as well as versatility and compatibility of reaction conditions and functional group tolerance. The Achmatowicz reaction, an oxidative ring enlargement of furyl alcohol, was developed in the 1970s. The reaction provides a unique entry to a variety of pyranone derivatives from functionalized furanyl alcohols. These pyranones provide convenient access to substituted tetrahydropyran derivatives. This review outlines general approaches to the synthesis of tetrahydropyrans, covering general mechanistic aspects of the Achmatowicz reaction or rearrangement with an overview of the reagents utilized for the Achmatowicz reaction. The review then focuses on the synthesis of functionalized tetrahydropyrans and pyranones and their applications in the synthesis of natural products and medicinal agents.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Margherita Brindisi
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
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18
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Wu LF, Meng S, Tang GL. Ferrous iron and α-ketoglutarate-dependent dioxygenases in the biosynthesis of microbial natural products. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:453-70. [DOI: 10.1016/j.bbapap.2016.01.012] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/22/2016] [Accepted: 01/29/2016] [Indexed: 01/29/2023]
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Liu X, Zhu H, Biswas S, Cheng YQ. Improved production of cytotoxic thailanstatins A and D through metabolic engineering of Burkholderia thailandensis MSMB43 and pilot scale fermentation. Synth Syst Biotechnol 2016; 1:34-38. [PMID: 29062925 PMCID: PMC5640593 DOI: 10.1016/j.synbio.2016.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 01/26/2016] [Accepted: 02/12/2016] [Indexed: 01/11/2023] Open
Abstract
Thailanstatin A (TST-A) is a potent antiproliferative natural product discovered by our group from Burkholderia thailandensis MSMB43 through a genome-guided approach. The limited supply of TST-A, due to its low titer in bacterial fermentation, modest stability and very low recovery rate during purification, has hindered the investigations of TST-A as an anticancer drug candidate. Here we report the significant yield improvement of TST-A and its direct precursor, thailanstatin D (TST-D), through metabolic engineering of the thailanstatin biosynthetic pathway in MSMB43. Deletion of tstP, which encodes a dioxygenase involved in converting TST-A to downstream products including FR901464 (FR), resulted in 58% increase of the TST-A titer to 144.7 ± 2.3 mg/L and 132% increase of the TST-D titer to 14.6 ± 0.5 mg/L in the fermentation broth, respectively. Deletion of tstR, which encodes a cytochrome P450 involved in converting TST-D to TST-A, resulted in more than 7-fold increase of the TST-D titer to 53.2 ± 12.1 mg/L in the fermentation broth. An execution of 90 L pilot-scale fed-batch fermentation of the tstP deletion mutant in a 120-L fermentor led to the preparation of 714 mg of TST-A with greater than 98.5% purity. The half-life of TST-D in a phosphate buffer was found to be at least 202 h, significantly longer than that of TST-A or FR, suggesting superior stability. However, the IC50 values of TST-D against representative human cancer cell lines were determined to be greater than those of TST-A, indicating weaker antiproliferative activity. This work enabled us to prepare sufficient quantities of TST-A and TST-D for our ongoing translational research.
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Affiliation(s)
- Xiangyang Liu
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA.,Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Hui Zhu
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Sreya Biswas
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Yi-Qiang Cheng
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, USA.,Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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20
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Abstract
This highlight provides an overview of recent advances in understanding the diversity of polyketide synthase (PKS) substrate building blocks. Substrates functioning as starter units and extender units contribute significantly to the chemical complexity and structural diversity exhibited by this class of natural products. This article complements and extends upon the current comprehensive reviews that have been published on these two topics (Moore and Hertweck, Nat. Prod. Rep., 2002, 19, 70; Chan et al., Nat. Prod. Rep., 2009, 1, 90; Wilson and Moore, Nat. Prod. Rep., 2012, 29, 72).
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Affiliation(s)
- Lauren Ray
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093-0204, USA
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21
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Helfrich EJN, Piel J. Biosynthesis of polyketides by trans-AT polyketide synthases. Nat Prod Rep 2016; 33:231-316. [DOI: 10.1039/c5np00125k] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review discusses the biosynthesis of natural products that are generated bytrans-AT polyketide synthases, a family of catalytically versatile enzymes that represents one of the major group of proteins involved in the production of bioactive polyketides.
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Affiliation(s)
- Eric J. N. Helfrich
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
| | - Jörn Piel
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
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22
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Eustáquio AS, Chang LP, Steele GL, O׳Donnell CJ, Koehn FE. Biosynthetic engineering and fermentation media development leads to gram-scale production of spliceostatin natural products in Burkholderia sp. Metab Eng 2016; 33:67-75. [DOI: 10.1016/j.ymben.2015.11.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 09/25/2015] [Accepted: 11/18/2015] [Indexed: 12/18/2022]
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23
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Tian N, Tang Y, Chen Y, Zhen Z, Long J, Liu Z, Liu S. WITHDRAWN: Identification of an antimycin gene cluster and characterization of the tryptophan 2,3-dioxygenase from the deep sea-derived Streptomyces somaliensis HND1201. Biochem Biophys Res Commun 2015:S0006-291X(15)30788-9. [PMID: 26525851 DOI: 10.1016/j.bbrc.2015.10.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 10/18/2015] [Indexed: 11/29/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Na Tian
- Hunan Collaborative Innovation for Utilization of Botanical Functional Ingredients, National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, College of Horticulture and Hardening, Hunan Agricultural University, Changsha 410128, China
| | - Yuwei Tang
- Hunan Collaborative Innovation for Utilization of Botanical Functional Ingredients, National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, College of Horticulture and Hardening, Hunan Agricultural University, Changsha 410128, China
| | - Yuhong Chen
- Key Lab of Tea Science, Ministry of Education, Changsha 410128, China
| | - Zehua Zhen
- Hunan Collaborative Innovation for Utilization of Botanical Functional Ingredients, National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, College of Horticulture and Hardening, Hunan Agricultural University, Changsha 410128, China
| | - Jinhua Long
- Hunan Collaborative Innovation for Utilization of Botanical Functional Ingredients, National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, College of Horticulture and Hardening, Hunan Agricultural University, Changsha 410128, China
| | - Zhonghua Liu
- Hunan Collaborative Innovation for Utilization of Botanical Functional Ingredients, National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, College of Horticulture and Hardening, Hunan Agricultural University, Changsha 410128, China; Key Lab of Tea Science, Ministry of Education, Changsha 410128, China
| | - Shuoqian Liu
- Hunan Collaborative Innovation for Utilization of Botanical Functional Ingredients, National Research Center of Engineering Technology for Utilization of Functional Ingredients from Botanicals, College of Horticulture and Hardening, Hunan Agricultural University, Changsha 410128, China; Key Lab of Tea Science, Ministry of Education, Changsha 410128, China.
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24
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He HY, Yuan H, Tang MC, Tang GL. An Unusual Dehydratase Acting on Glycerate and a Ketoreducatse Stereoselectively Reducing α-Ketone in Polyketide Starter Unit Biosynthesis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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25
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He HY, Yuan H, Tang MC, Tang GL. An unusual dehydratase acting on glycerate and a ketoreducatse stereoselectively reducing α-ketone in polyketide starter unit biosynthesis. Angew Chem Int Ed Engl 2014; 53:11315-9. [PMID: 25160004 DOI: 10.1002/anie.201406602] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Indexed: 11/06/2022]
Abstract
Polyketide synthases (PKSs) usually employ a ketoreductase (KR) to catalyze the reduction of a β-keto group, followed by a dehydratase (DH) that drives the dehydration to form a double bond between the α- and β-carbon atoms. Herein, a DH*-KR* involved in FR901464 biosynthesis was characterized: DH* acts on glyceryl-S-acyl carrier protein (ACP) to yield ACP-linked pyruvate; subsequently KR* reduces α-ketone that yields L-lactyl-S-ACP as starter unit for polyketide biosynthesis. Genetic and biochemical evidence was found to support a similar pathway that is involved in the biosynthesis of lankacidins. These results not only identified new PKS domains acting on different substrates, but also provided additional options for engineering the PKS starter pathway or biocatalysis.
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Affiliation(s)
- Hai-Yan He
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032 (China)
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26
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Spliceostatin hemiketal biosynthesis in Burkholderia spp. is catalyzed by an iron/α-ketoglutarate-dependent dioxygenase. Proc Natl Acad Sci U S A 2014; 111:E3376-85. [PMID: 25097259 DOI: 10.1073/pnas.1408300111] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Spliceostatins are potent spliceosome inhibitors biosynthesized by a hybrid nonribosomal peptide synthetase-polyketide synthase (NRPS-PKS) system of the trans-acyl transferase (AT) type. Burkholderia sp. FERM BP-3421 produces hemiketal spliceostatins, such as FR901464, as well as analogs containing a terminal carboxylic acid. We provide genetic and biochemical evidence for hemiketal biosynthesis by oxidative decarboxylation rather than the previously hypothesized Baeyer-Villiger oxidative release postulated to be catalyzed by a flavin-dependent monooxygenase (FMO) activity internal to the last module of the PKS. Inactivation of Fe(II)/α-ketoglutarate-dependent dioxygenase gene fr9P led to loss of hemiketal congeners, whereas the mutant was still able to produce all major carboxylic acid-type compounds. FMO mutants, on the other hand, produced both hemiketal and carboxylic acid analogs containing an exocyclic methylene instead of an epoxide, indicating that the FMO is involved in epoxidation rather than Baeyer-Villiger oxidation. Moreover, recombinant Fr9P enzyme was shown to catalyze hydroxylation to form β-hydroxy acids, which upon decarboxylation led to hemiketal FR901464. Finally, a third oxygenase activity encoded in the biosynthetic gene cluster, the cytochrome P450 monooxygenase Fr9R, was assigned as a 4-hydroxylase based on gene inactivation results. Identification and deletion of the gene involved in hemiketal formation allowed us to generate a strain--the dioxygenase fr9P(-) mutant--that accumulates only the carboxylic acid-type spliceostatins, which are as potent as the hemiketal analogs, when derivatized to increase cell permeability, but are chemically more stable.
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27
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Ghosh AK, Chen ZH, Effenberger KA, Jurica MS. Enantioselective total syntheses of FR901464 and spliceostatin A and evaluation of splicing activity of key derivatives. J Org Chem 2014; 79:5697-709. [PMID: 24873648 PMCID: PMC4066912 DOI: 10.1021/jo500800k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
FR901464
(1) and spliceostatin A (2)
are potent inhibitors of spliceosomes. These compounds have shown
remarkable anticancer activity against multiple human cancer cell
lines. Herein, we describe efficient, enantioselective syntheses of
FR901464, spliceostatin A, six corresponding diastereomers and an
evaluation of their splicing activity. Syntheses of spliceostatin
A and FR901464 were carried out in the longest linear sequence of
9 and 10 steps, respectively. To construct the highly functionalized
tetrahydropyran A-ring, we utilized
CBS reduction, Achmatowicz rearrangement, Michael addition, and reductive
amination as key steps. The remarkable diastereoselectivity of the
Michael addition was specifically demonstrated with different substrates
under various reaction conditions. The side chain B was prepared from an optically active alcohol, followed
by acetylation and hydrogenation over Lindlar’s catalyst. The
other densely functionalized tetrahydropyran C-ring was derived from readily available (R)-isopropylidene glyceraldehyde through a route featuring 1,2-addition,
cyclic ketalization, and regioselective epoxidation. These fragments
were coupled together at a late stage through amidation and cross-metathesis
in a convergent manner. Six key diastereomers were then synthesized
to probe the importance of specific stereochemical features of FR901464
and spliceostatin A, with respect to their in vitro splicing activity.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University , 560 Oval Drive, West Lafayette, Indiana 4790, United States
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28
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He HY, Tang MC, Zhang F, Tang GL. Cis-Double Bond Formation by Thioesterase and Transfer by Ketosynthase in FR901464 Biosynthesis. J Am Chem Soc 2014; 136:4488-91. [DOI: 10.1021/ja500942y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hai-Yan He
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Man-Cheng Tang
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Feng Zhang
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Gong-Li Tang
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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29
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Xu P, Wang W, Li L, Bhan N, Zhang F, Koffas MAG. Design and kinetic analysis of a hybrid promoter-regulator system for malonyl-CoA sensing in Escherichia coli. ACS Chem Biol 2014; 9:451-8. [PMID: 24191643 DOI: 10.1021/cb400623m] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Malonyl-CoA is the rate-limiting precursor involved in the chain elongation reaction of a range of value-added pharmaceuticals and biofuels. Development of malonyl-CoA responsive sensors holds great promise in overcoming critical pathway limitations and optimizing production titers and yields. By incorporating the Bacillus subtilis trans-regulatory protein FapR and the cis-regulatory element fapO, we constructed a hybrid promoter-regulatory system that responds to a broad range of intracellular malonyl-CoA concentrations (from 0.1 to 1.1 nmol/mgDW) in Escherichia coli. Elimination of regulatory protein and nonspecific DNA cross-communication leads to a sensor construct that exhibits malonyl-CoA-dependent linear phase kinetics with increased dynamic response range. The sensors reported in this study could potentially control and optimize carbon flux leading to robust biosynthetic pathways for the production of malonyl-CoA-derived compounds.
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Affiliation(s)
- Peng Xu
- Department
of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Wenya Wang
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- College
of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lingyun Li
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Department
of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Namita Bhan
- Department
of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Fuming Zhang
- Department
of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Mattheos A. G. Koffas
- Department
of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Department
of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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30
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Till M, Race PR. Progress challenges and opportunities for the re-engineering of trans-AT polyketide synthases. Biotechnol Lett 2014; 36:877-88. [PMID: 24557077 DOI: 10.1007/s10529-013-1449-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 12/23/2013] [Indexed: 12/13/2022]
Abstract
Polyketides are a structurally and functionally diverse family of bioactive natural products that are used extensively as pharmaceuticals and agrochemicals. In bacteria these molecules are biosynthesized by giant, multi-functional enzymatic complexes, termed modular polyketide synthases (PKSs), that function in assembly-line like fashion to fuse and tailor simple carboxylic acid monomers into a vast array of elaborate chemical scaffolds. Modifying PKSs through targeted synthase re-engineering is a promising approach for accessing functionally-optimized polyketides. Due to their highly mosaic architectures the recently identified trans-AT family of modular synthases appear inherently more amenable to re-engineering than their well studied cis-AT counterparts. Here, we review recent progress in the re-engineering of trans-AT PKSs, summarize opportunities for harnessing the biosynthetic potential of these systems, and highlight challenges that such re-engineering approaches present.
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Affiliation(s)
- M Till
- School of Biochemistry, Medical Sciences, University of Bristol, Bristol, BS8 1TD, UK
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31
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Liu X, Cheng YQ. Genome-guided discovery of diverse natural products from Burkholderia sp. J Ind Microbiol Biotechnol 2013; 41:275-84. [PMID: 24212473 DOI: 10.1007/s10295-013-1376-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 10/24/2013] [Indexed: 01/09/2023]
Abstract
Burkholderia species have emerged as a new source of diverse natural products. This mini-review covers all of the natural products discovered in recent years from Burkholderia sp. by genome-guided approaches--these refer to the use of bacterial genome sequence as an entry point for in silico structural prediction, wet lab experimental design, and execution. While reliable structural prediction based on cryptic biosynthetic gene cluster sequence was not always possible due to noncanonical domains and/or module organization of a deduced biosynthetic pathway, a molecular genetic method was often employed to detect or alter the expression level of the gene cluster to achieve an observable phenotype, which facilitated downstream natural product purification and identification. Those examples of natural product discovery from Burkholderia sp. provide practical guidance for future exploration of Gram-negative bacteria as a new source of natural products.
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Affiliation(s)
- Xiangyang Liu
- UNT System College of Pharmacy, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX, 76107, USA
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32
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Ghosh AK, Chen ZH. Enantioselective syntheses of FR901464 and spliceostatin A: potent inhibitors of spliceosome. Org Lett 2013; 15:5088-91. [PMID: 24050251 PMCID: PMC3827971 DOI: 10.1021/ol4024634] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enantioselective syntheses of FR901464 and spliceostatin A, potent spliceosome inhibitors, are described. The synthesis of FR901464 has been accomplished in a convergent manner in 10 linear steps (20 total steps). The A-tetrahydropyran ring was constructed from (R)-isopropylidene glyceraldehyde. The functionalized tetrahydropyran B-ring was synthesized utilizing a Corey-Bakshi-Shibata reduction, an Achmatowicz reaction, and a stereoselective Michael addition as the key steps. Coupling of A- and B-ring fragments was accomplished via cross-metathesis.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Zhi-Hua Chen
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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33
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Identification of the incednine biosynthetic gene cluster: characterization of novel β-glutamate-β-decarboxylase IdnL3. J Antibiot (Tokyo) 2013; 66:691-9. [DOI: 10.1038/ja.2013.76] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 06/11/2013] [Accepted: 06/21/2013] [Indexed: 12/18/2022]
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34
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Arens JC, Berrué F, Pearson JK, Kerr RG. Isolation and structure elucidation of satosporin A and B: new polyketides from Kitasatospora griseola. Org Lett 2013; 15:3864-7. [PMID: 23875542 DOI: 10.1021/ol401598f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Satosporins A and B, two novel glucosylated polyketides, were isolated from the actinomycete Kitasatospora griseola MF730-N6. The polyketides possess an unprecedented tricyclic ring system that was fully characterized using a combination of spectroscopic analyses and computational calculations. Satosporin A was quantitatively converted into its aglycon homologue, satosporin C, using a β-glucosidase. The determination of the absolute stereochemistry was achieved using solution TDDFT/ECD calculations and chemical derivatization methods.
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Affiliation(s)
- Jennifer C Arens
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown PEI C1A 4P3, Canada
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Liu X, Biswas S, Berg MG, Antapli CM, Xie F, Wang Q, Tang MC, Tang GL, Zhang L, Dreyfuss G, Cheng YQ. Genomics-guided discovery of thailanstatins A, B, and C As pre-mRNA splicing inhibitors and antiproliferative agents from Burkholderia thailandensis MSMB43. JOURNAL OF NATURAL PRODUCTS 2013; 76:685-93. [PMID: 23517093 PMCID: PMC3696399 DOI: 10.1021/np300913h] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Mining the genome sequence of Burkholderia thailandensis MSMB43 revealed a cryptic biosynthetic gene cluster resembling that of FR901464 (4), a prototype spliceosome inhibitor produced by Pseudomonas sp. No. 2663. Transcriptional analysis revealed a cultivation condition in which a regulatory gene of the cryptic gene cluster is adequately expressed. Consequently, three new compounds, named thailanstatins A (1), B (2), and C (3), were isolated from the fermentation broth of B. thailandensis MSMB43. Thailanstatins are proposed to be biosynthesized by a hybrid polyketide synthase-nonribosomal peptide synthetase pathway. They differ from 4 by lacking an unstable hydroxyl group and by having an extra carboxyl moiety; those differences endow thailanstatins with a significantly greater stability than 4 as tested in phosphate buffer at pH 7.4. In vitro assays showed that thailanstatins inhibit pre-mRNA splicing as potently as 4, with half-maximal inhibitory concentrations in the single to sub-μM range. Cell culture assays indicated that thailanstatins also possess potent antiproliferative activities in representative human cancer cell lines, with half-maximal growth inhibitory concentrations in the single nM range. This work provides new chemical entities for research and development and new structure-activity information for chemical optimization of related spliceosome inhibitors.
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Affiliation(s)
- Xiangyang Liu
- Department of Biological Sciences, and Department of Chemistry and Biochemistry, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin 53201, United States
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Sreya Biswas
- Department of Biological Sciences, and Department of Chemistry and Biochemistry, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Michael G. Berg
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Christopher M. Antapli
- Department of Biological Sciences, and Department of Chemistry and Biochemistry, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin 53201, United States
| | - Feng Xie
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Qi Wang
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Man-Cheng Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lixin Zhang
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Gideon Dreyfuss
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Yi-Qiang Cheng
- Department of Biological Sciences, and Department of Chemistry and Biochemistry, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin 53201, United States
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
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Zou Y, Yin H, Kong D, Deng Z, Lin S. ATrans-Acting Ketoreductase in Biosynthesis of a Symmetric Polyketide Dimer SIA7248. Chembiochem 2013; 14:679-83. [DOI: 10.1002/cbic.201300068] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Indexed: 11/07/2022]
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Tang MC, He HY, Zhang F, Tang GL. Baeyer–Villiger Oxidation of Acyl Carrier Protein-Tethered Thioester to Acyl Carrier Protein-Linked Thiocarbonate Catalyzed by a Monooxygenase Domain in FR901464 Biosynthesis. ACS Catal 2013. [DOI: 10.1021/cs300819e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Man-Cheng Tang
- State Key
Laboratory of Bioorganic and Natural Products
Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032,
China
| | - Hai-Yan He
- State Key
Laboratory of Bioorganic and Natural Products
Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032,
China
| | - Feng Zhang
- State Key
Laboratory of Bioorganic and Natural Products
Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032,
China
| | - Gong-Li Tang
- State Key
Laboratory of Bioorganic and Natural Products
Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032,
China
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Crosby J, Crump MP. The structural role of the carrier protein--active controller or passive carrier. Nat Prod Rep 2012; 29:1111-37. [PMID: 22930263 DOI: 10.1039/c2np20062g] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Common to all FASs, PKSs and NRPSs is a remarkable component, the acyl or peptidyl carrier protein (A/PCP). These take the form of small individual proteins in type II systems or discrete folded domains in the multi-domain type I systems and are characterized by a fold consisting of three major α-helices and between 60-100 amino acids. This protein is central to these biosynthetic systems and it must bind and transport a wide variety of functionalized ligands as well as mediate numerous protein-protein interactions, all of which contribute to efficient enzyme turnover. This review covers the structural and biochemical characterization of carrier proteins, as well as assessing their interactions with different ligands, and other synthase components. Finally, their role as an emerging tool in biotechnology is discussed.
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Affiliation(s)
- John Crosby
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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Go MK, Chow JY, Cheung VWN, Lim YP, Yew WS. Establishing a toolkit for precursor-directed polyketide biosynthesis: exploring substrate promiscuities of acid-CoA ligases. Biochemistry 2012; 51:4568-79. [PMID: 22587726 DOI: 10.1021/bi300425j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyketides are chemically diverse and medicinally important biochemicals that are biosynthesized from acyl-CoA precursors by polyketide synthases. One of the limitations to combinatorial biosynthesis of polyketides has been the lack of a toolkit that describes the means of delivering novel acyl-CoA precursors necessary for polyketide biosynthesis. Using five acid-CoA ligases obtained from various plants and microorganisms, we biosynthesized an initial library of 79 acyl-CoA thioesters by screening each of the acid-CoA ligases against a library of 123 carboxylic acids. The library of acyl-CoA thioesters includes derivatives of cinnamyl-CoA, 3-phenylpropanoyl-CoA, benzoyl-CoA, phenylacetyl-CoA, malonyl-CoA, saturated and unsaturated aliphatic CoA thioesters, and bicyclic aromatic CoA thioesters. In our search for the biosynthetic routes of novel acyl-CoA precursors, we discovered two previously unreported malonyl-CoA derivatives (3-thiophenemalonyl-CoA and phenylmalonyl-CoA) that cannot be produced by canonical malonyl-CoA synthetases. This report highlights the utility and importance of determining substrate promiscuities beyond conventional substrate pools and describes novel enzymatic routes for the establishment of precursor-directed combinatorial polyketide biosynthesis.
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Affiliation(s)
- Maybelle Kho Go
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
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Thibodeaux CJ, Chang WC, Liu HW. Enzymatic chemistry of cyclopropane, epoxide, and aziridine biosynthesis. Chem Rev 2012; 112:1681-709. [PMID: 22017381 PMCID: PMC3288687 DOI: 10.1021/cr200073d] [Citation(s) in RCA: 202] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Wei-chen Chang
- College of Pharmacy and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| | - Hung-wen Liu
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
- College of Pharmacy and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
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Wong FT, Khosla C. Combinatorial biosynthesis of polyketides--a perspective. Curr Opin Chem Biol 2012; 16:117-23. [PMID: 22342766 DOI: 10.1016/j.cbpa.2012.01.018] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 12/19/2011] [Accepted: 01/27/2012] [Indexed: 12/29/2022]
Abstract
Since their discovery, polyketide synthases have been attractive targets of biosynthetic engineering to make 'unnatural' natural products. Although combinatorial biosynthesis has made encouraging advances over the past two decades, the field remains in its infancy. In this enzyme-centric perspective, we discuss the scientific and technological challenges that could accelerate the adoption of combinatorial biosynthesis as a method of choice for the preparation of encoded libraries of bioactive small molecules. Borrowing a page from the protein structure prediction community, we propose a periodic challenge program to vet the most promising methods in the field, and to foster the collective development of useful tools and algorithms.
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Affiliation(s)
- Fong T Wong
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, United States
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Kang Q, Bai L, Deng Z. Toward steadfast growth of antibiotic research in China: from natural products to engineered biosynthesis. Biotechnol Adv 2011; 30:1228-41. [PMID: 21930196 DOI: 10.1016/j.biotechadv.2011.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 09/04/2011] [Accepted: 09/05/2011] [Indexed: 11/30/2022]
Abstract
Antibiotics are widely used for clinical treatment and preventing or curing diseases in agriculture. Cloning and studies of their biosynthetic gene clusters are vital for yield enhancement and engineering new derivatives with new and prominent activities. In recent years, research in this aspect is impressively active in China. This article reviews biosynthetic progress on 28 antibiotics, including polyketides, nonribosomal peptides, hybrid polyketide-nonribosomal peptides, peptidyl nucleoside, nucleoside, and others. Their biosynthetic mechanisms were disclosed, and their derivatives with new structures/activities were obtained by gene inactivation, mutasynthesis and combinatorial biosynthesis.
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Affiliation(s)
- Qianjin Kang
- State key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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