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Gao J, Li L, Shen S, Ai G, Wang B, Guo F, Yang T, Han H, Xu Z, Pan G, Fan K. Cofactor-independent C-C bond cleavage reactions catalyzed by the AlpJ family of oxygenases in atypical angucycline biosynthesis. Beilstein J Org Chem 2024; 20:1198-1206. [PMID: 38887580 PMCID: PMC11181247 DOI: 10.3762/bjoc.20.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 05/07/2024] [Indexed: 06/20/2024] Open
Abstract
Biosynthesis of atypical angucyclines involves unique oxidative B-ring cleavage and rearrangement reactions, which are catalyzed by AlpJ-family oxygenases, including AlpJ, JadG, and GilOII. Prior investigations established the essential requirement for FADH2/FMNH2 as cofactors when utilizing the quinone intermediate dehydrorabelomycin as a substrate. In this study, we unveil a previously unrecognized facet of these enzymes as cofactor-independent oxygenases when employing the hydroquinone intermediate CR1 as a substrate. The enzymes autonomously drive oxidative ring cleavage and rearrangement reactions of CR1, yielding products identical to those observed in cofactor-dependent reactions of AlpJ-family oxygenases. Furthermore, the AlpJ- and JadG-catalyzed reactions of CR1 could be quenched by superoxide dismutase, supporting a catalytic mechanism wherein the substrate CR1 reductively activates molecular oxygen, generating a substrate radical and the superoxide anion O2 •-. Our findings illuminate a substrate-controlled catalytic mechanism of AlpJ-family oxygenases, expanding the realm of cofactor-independent oxygenases. Notably, AlpJ-family oxygenases stand as a pioneering example of enzymes capable of catalyzing oxidative reactions in either an FADH2/FMNH2-dependent or cofactor-independent manner.
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Affiliation(s)
- Jinmin Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
- University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Beijing 101408, China
| | - Liyuan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
| | - Shijie Shen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
- University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Beijing 101408, China
| | - Guomin Ai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
| | - Bin Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
- University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Beijing 101408, China
| | - Fang Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
| | - Tongjian Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
- University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Beijing 101408, China
| | - Hui Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
| | - Zhengren Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Guohui Pan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
- University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Beijing 101408, China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
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2
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Wang Y, Zhou L, Pan X, Liao Z, Qi N, Sun M, Zhang H, Ju J, Ma J. Metabolic Blockade-Based Genome Mining of Sea Anemone-Associated Streptomyces sp. S1502 Identifies Atypical Angucyclines WS-5995 A-E: Isolation, Identification, Biosynthetic Investigation, and Bioactivities. Mar Drugs 2024; 22:195. [PMID: 38786587 PMCID: PMC11122949 DOI: 10.3390/md22050195] [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: 03/27/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Marine symbiotic and epiphyte microorganisms are sources of bioactive or structurally novel natural products. Metabolic blockade-based genome mining has been proven to be an effective strategy to accelerate the discovery of natural products from both terrestrial and marine microorganisms. Here, the metabolic blockade-based genome mining strategy was applied to the discovery of other metabolites in a sea anemone-associated Streptomyces sp. S1502. We constructed a mutant Streptomyces sp. S1502/Δstp1 that switched to producing the atypical angucyclines WS-5995 A-E, among which WS-5995 E is a new compound. A biosynthetic gene cluster (wsm) of the angucyclines was identified through gene knock-out and heterologous expression studies. The biosynthetic pathways of WS-5995 A-E were proposed, the roles of some tailoring and regulatory genes were investigated, and the biological activities of WS-5995 A-E were evaluated. WS-5995 A has significant anti-Eimeria tenell activity with an IC50 value of 2.21 μM. The production of antibacterial streptopyrroles and anticoccidial WS-5995 A-E may play a protective role in the mutual relationship between Streptomyces sp. S1502 and its host.
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Affiliation(s)
- Yuyang Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Haizhu District, Guangzhou 510301, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Le Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Haizhu District, Guangzhou 510301, China
| | - Xiaoting Pan
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zhangjun Liao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Laboratory Medicine, Guangdong Medical University, Dongguan 523808, China
| | - Nanshan Qi
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Mingfei Sun
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Key Laboratory of Avian Influenza and Other Major Poultry Diseases Prevention and Control, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Hua Zhang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Laboratory Medicine, Guangdong Medical University, Dongguan 523808, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Haizhu District, Guangzhou 510301, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
| | - Junying Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Haizhu District, Guangzhou 510301, China
- College of Oceanology, University of Chinese Academy of Sciences, Qingdao 266400, China
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3
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Kouprina N, Larionov V. Transformation-associated recombination (TAR) cloning and its applications for gene function; genome architecture and evolution; biotechnology and biomedicine. Oncotarget 2023; 14:1009-1033. [PMID: 38147065 PMCID: PMC10750837 DOI: 10.18632/oncotarget.28546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023] Open
Abstract
Transformation-associated recombination (TAR) cloning represents a unique tool to selectively and efficiently recover a given chromosomal segment up to several hundred kb in length from complex genomes (such as animals and plants) and simple genomes (such as bacteria and viruses). The technique exploits a high level of homologous recombination in the yeast Sacharomyces cerevisiae. In this review, we summarize multiple applications of the pioneering TAR cloning technique, developed previously for complex genomes, for functional, evolutionary, and structural studies, and extended the modified TAR versions to isolate biosynthetic gene clusters (BGCs) from microbes, which are the major source of pharmacological agents and industrial compounds, and to engineer synthetic viruses with novel properties to design a new generation of vaccines. TAR cloning was adapted as a reliable method for the assembly of synthetic microbe genomes for fundamental research. In this review, we also discuss how the TAR cloning in combination with HAC (human artificial chromosome)- and CRISPR-based technologies may contribute to the future.
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Affiliation(s)
- Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
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4
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Elsayed SS, van der Heul HU, Xiao X, Nuutila A, Baars LR, Wu C, Metsä-Ketelä M, van Wezel GP. Unravelling key enzymatic steps in C-ring cleavage during angucycline biosynthesis. Commun Chem 2023; 6:281. [PMID: 38110491 PMCID: PMC10728087 DOI: 10.1038/s42004-023-01059-1] [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: 06/30/2023] [Accepted: 11/08/2023] [Indexed: 12/20/2023] Open
Abstract
Angucyclines are type II polyketide natural products, often characterized by unusual structural rearrangements through B- or C-ring cleavage of their tetracyclic backbone. While the enzymes involved in B-ring cleavage have been extensively studied, little is known of the enzymes leading to C-ring cleavage. Here, we unravel the function of the oxygenases involved in the biosynthesis of lugdunomycin, a highly rearranged C-ring cleaved angucycline derivative. Targeted deletion of the oxygenase genes, in combination with molecular networking and structural elucidation, showed that LugOI is essential for C12 oxidation and maintaining a keto group at C6 that is reduced by LugOII, resulting in a key intermediate towards C-ring cleavage. An epoxide group is then inserted by LugOIII, and stabilized by the novel enzyme LugOV for the subsequent cleavage. Thus, for the first time we describe the oxidative enzymatic steps that form the basis for a wide range of rearranged angucycline natural products.
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Affiliation(s)
- Somayah S Elsayed
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333BE, Leiden, The Netherlands.
| | - Helga U van der Heul
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333BE, Leiden, The Netherlands
| | - Xiansha Xiao
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Aleksi Nuutila
- Department of Life Technologies, University of Turku, Tykistökatu 6, FIN-20014, Turku, Finland
| | - Laura R Baars
- Department of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237, Qingdao, P.R. China
| | - Mikko Metsä-Ketelä
- Department of Life Technologies, University of Turku, Tykistökatu 6, FIN-20014, Turku, Finland
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333BE, Leiden, The Netherlands.
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708PB, Wageningen, The Netherlands.
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5
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Schwitalla JW, Le NTH, Um S, Schalk F, Brönstrup M, Baunach M, Beemelmanns C. Heterologous expression of the cryptic mdk gene cluster and structural revision of maduralactomycin A. RSC Adv 2023; 13:34136-34144. [PMID: 38019997 PMCID: PMC10663993 DOI: 10.1039/d3ra05931f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
After conducting an in silico analysis of the cryptic mdk cluster region and performing transcriptomic studies, an integrative Streptomyces BAC Vector containing the mdk gene sequence was constructed. The heterologous expression of the mdk cluster in Streptomyces albus J1074 resulted in the production of the angucyclic product, seongomycin, which allowed for the assesment of its antibacterial, antiproliferative, and antiviral activities. Heterologous production was further confirmed by targeted knock-out experiments involving key regulators of the biosynthetic pathways. We were further able to revise the core structure of maduralactomycin A, using a computational approach.
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Affiliation(s)
- Jan W Schwitalla
- Chemical Biology of Microbe-Host Interactions, Hans-Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) Campus E8 66123 Saarbrücken Germany
| | - Ngoc-Thao-Hien Le
- Department of Pharmaceutical Sciences, Natural Products and Food Research and Analysis (NatuRA), University of Antwerp Universiteitsplein 1 B-2610 Antwerp Belgium
| | - Soohyun Um
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University Incheon 21983 South Korea
| | - Felix Schalk
- Chemical Biology of Microbe-Host Interactions, Hans-Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research Inhoffenstrasse 7 D-38124 Braunschweig Germany
| | - Martin Baunach
- Institute of Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| | - Christine Beemelmanns
- Chemical Biology of Microbe-Host Interactions, Hans-Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) Campus E8 66123 Saarbrücken Germany
- Saarland University 66123 Saarbrücken Germany
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6
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Yang C, Zhang L, Zhang W, Huang C, Zhu Y, Jiang X, Liu W, Zhao M, De BC, Zhang C. Biochemical and structural insights of multifunctional flavin-dependent monooxygenase FlsO1-catalyzed unexpected xanthone formation. Nat Commun 2022; 13:5386. [PMID: 36104338 PMCID: PMC9474520 DOI: 10.1038/s41467-022-33131-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 09/02/2022] [Indexed: 11/18/2022] Open
Abstract
Xanthone-containing natural products display diverse pharmacological properties. The biosynthetic mechanisms of the xanthone formation have not been well documented. Here we show that the flavoprotein monooxygenase FlsO1 in the biosynthesis of fluostatins not only functionally compensates for the monooxygenase FlsO2 in converting prejadomycin to dehydrorabelomycin, but also unexpectedly converts prejadomycin to xanthone-containing products by catalyzing three successive oxidations including hydroxylation, epoxidation and Baeyer-Villiger oxidation. We also provide biochemical evidence to support the physiological role of FlsO1 as the benzo[b]-fluorene C5-hydrolase by using nenestatin C as a substrate mimic. Finally, we resolve the crystal structure of FlsO1 in complex with the cofactor flavin adenine dinucleotide close to the “in” conformation to enable the construction of reactive substrate-docking models to understand the basis of a single enzyme-catalyzed multiple oxidations. This study highlights a mechanistic perspective for the enzymatic xanthone formation in actinomycetes and sets an example for the versatile functions of flavoproteins. The biosynthesis of xanthones has not been well documented. Here, the authors report that monooxygenase FlsO1 catalyzes three successive oxidations – hydroxylation, epoxidation and Baeyer–Villiger oxidation—to form the xanthone scaffold in actinomycetes.
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7
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Flavin-enabled reductive and oxidative epoxide ring opening reactions. Nat Commun 2022; 13:4896. [PMID: 35986005 PMCID: PMC9391479 DOI: 10.1038/s41467-022-32641-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 08/08/2022] [Indexed: 12/23/2022] Open
Abstract
Epoxide ring opening reactions are common and important in both biological processes and synthetic applications and can be catalyzed in a non-redox manner by epoxide hydrolases or reductively by oxidoreductases. Here we report that fluostatins (FSTs), a family of atypical angucyclines with a benzofluorene core, can undergo nonenzyme-catalyzed epoxide ring opening reactions in the presence of flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide (NADH). The 2,3-epoxide ring in FST C is shown to open reductively via a putative enol intermediate, or oxidatively via a peroxylated intermediate with molecular oxygen as the oxidant. These reactions lead to multiple products with different redox states that possess a single hydroxyl group at C-2, a 2,3-vicinal diol, a contracted five-membered A-ring, or an expanded seven-membered A-ring. Similar reactions also take place in both natural products and other organic compounds harboring an epoxide adjacent to a carbonyl group that is conjugated to an aromatic moiety. Our findings extend the repertoire of known flavin chemistry that may provide new and useful tools for organic synthesis. Epoxide ring opening reactions are important in both biological processes and synthetic applications. Here, the authors show that flavin cofactors can catalyze reductive and oxidative epoxide ring opening reactions and propose the underlying mechanisms.
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8
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Wu C, Yin Y, Zhu L, Zhang Y, Li YZ. Metagenomic sequencing-driven multidisciplinary approaches to shed light on the untapped microbial natural products. Drug Discov Today 2021; 27:730-742. [PMID: 34775105 DOI: 10.1016/j.drudis.2021.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/07/2021] [Accepted: 11/08/2021] [Indexed: 11/17/2022]
Abstract
The advantage of metagenomics over the culture-based natural product (NP) discovery pipeline is the ability to access the biosynthetic potential of uncultivable microbes. Advances in DNA sequencing are revolutionizing conventional metagenomics approaches for microbial NP discovery. The genomes of (in)cultivable bugs can be resolved straightforwardly from environmental samples, enabling in situ prediction of biosynthetic gene clusters (BGCs). The predicted chemical diversities could be realized not only by heterologous expression of gene clusters originating from DNA synthesis or direct cloning, but also potentially by bioinformatic-directed organic synthesis or chemoenzymatic total synthesis. In this review, we suggest that metagenomic sequencing in tandem with multidisciplinary approaches will form a versatile platform to shed light on a plethora of microbial 'dark matter'.
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Affiliation(s)
- Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Yizhen Yin
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Lele Zhu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China.
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9
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Mohamed SS, Abdelhamid SA, Ali RH. Isolation and identification of marine microbial products. J Genet Eng Biotechnol 2021; 19:162. [PMID: 34665351 PMCID: PMC8526645 DOI: 10.1186/s43141-021-00259-3] [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: 05/30/2021] [Accepted: 10/02/2021] [Indexed: 11/16/2022]
Abstract
Background The ocean is one of the world’s most important sources of bioactive chemicals in the marine environment. Microbiologists, ecologists, agronomists, taxonomists, and evolutionary biologists have been increasingly interested in marine microbial natural products (MMNPs) in recent decades. Main body Diverse marine bacteria appear to get the ability to manufacture an astounding diversity of MMNPs with a wide range of biological actions, including anti-tumor, antimicrobial, and anti-cardiovascular agents according to numerous studies. Short conclusions Innovative isolation and culture methodologies, tactics for identifying novel MMNPs via routine screens, metagenomics, genomics, combinatorial biosynthesis, and synthetic biology are all discussed in this review. There is also a discussion of potential issues and future directions for studying MMNPs.
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Affiliation(s)
- Sahar Saleh Mohamed
- Microbial Biotechnology Department, Genetic Engineering Division, National Research Centre, Cairo, Egypt
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10
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Wang Z, Sun R, Li M, Liu L, Duan Y, Huang Y. Yield improvement of enediyne yangpumicins in Micromonospora yangpuensis through ribosome engineering and fermentation optimization. Biotechnol J 2021; 16:e2100250. [PMID: 34473904 DOI: 10.1002/biot.202100250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/22/2022]
Abstract
Yangpumicins (YPMs), for example, YPM A, F, and G, are newly discovered enediynes from Micromonospora yangpuensis DSM 45577, which could be exploited as promising payloads of antibody-drug conjugates. However, the low yield of YPMs in the wild-type strain (∼1 mg L-1 ) significantly hampers their further drug development. In this study, a combined ribosome engineering and fermentation optimization strategy has been used for yield improvement of YPMs. One gentamicin-resistant M. yangpuensis DSM 45577 strain (MY-G-1) showed higher YPMs production (7.4 ± 1.0 mg L-1 ), while it exhibits delayed sporulation and slender mycelium under scanning electron microscopy. Whole genome re-sequencing of MY-G-1 reveals several deletion and single nucleotide polymorphism mutations, which were confirmed by PCR and DNA sequencing. Further Box-Behnken experiment and regression analysis determined that the optimal medium concentrations of soluble starch, D-mannitol, and pharmamedia for YPMs production in shaking flasks (10.0 ± 0.8 mg L-1 ). Finally, the total titer of YPM A/F/G in MY-G-1 reached to 15.0 ± 2.5 mg L-1 in 3 L fermenters, which was about 11-fold higher than the original titer of 1.3 ± 0.3 mg L-1 in wild-type strain. Our study may be instrumental to develop YPMs into a clinical anticancer drug, and inspire the use of these multifaceted strategies for yield improvement in Micromonospora species. GRAPHICAL ABSTRACT LAY SUMMARY: ???
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Affiliation(s)
- Zilong Wang
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China
| | - Runze Sun
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China
| | - Miao Li
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China
| | - Ling Liu
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, Hunan, China.,National Engineering Research Center of Combinatorial Biosynthesis for 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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Huang C, Yang C, Zhang W, Zhang L, Zhu Y, Zhang C. Discovery of an Unexpected 1,4-Oxazepine-Linked seco-Fluostatin Heterodimer by Inactivation of the Oxidoreductase-Encoding Gene flsP. JOURNAL OF NATURAL PRODUCTS 2021; 84:2336-2344. [PMID: 34384027 DOI: 10.1021/acs.jnatprod.1c00461] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fluostatins belong to the atypical angucyclinone aromatic polyketides featuring a distinctive tetracyclic benzo[a]fluorene skeleton. To understand the formation of the heavily oxidized A-ring in fluostatins, a flavin adenine dinucleotide-binding oxidoreductase-encoding gene flsP was inactivated, leading to the production of an unprecedented 1,4-oxazepine-linked seco-fluostatin heterodimer difluostatin I (7) and five new fluostatin-related derivatives, fluostatins T-X (8-12). Their structures were elucidated by mass spectrometry, nuclear magnetic resonance, X-ray diffraction analysis, and biosynthetic considerations. Difluostatin I (7) represents the first example with an A-ring-cleaved 3',4'-seco-fluostatin skeleton. The absolute configuration of fluostatin T (8) was determined by X-ray diffraction analysis. Fluostatin W (11) contains an uncommon isoxazolinone ring. These findings highlight the structural diversity of fluostatins.
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Affiliation(s)
- Chunshuai Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Chunfang Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Oceanology, SCSIO, Yazhou Scientific Bay, Sanya 572000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Oceanology, SCSIO, Yazhou Scientific Bay, Sanya 572000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Sanya Institute of Oceanology, SCSIO, Yazhou Scientific Bay, Sanya 572000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Oceanology, SCSIO, Yazhou Scientific Bay, Sanya 572000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Oceanology, SCSIO, Yazhou Scientific Bay, Sanya 572000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
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12
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Sharma V, Kaur R, Salwan R. Streptomyces: host for refactoring of diverse bioactive secondary metabolites. 3 Biotech 2021; 11:340. [PMID: 34221811 DOI: 10.1007/s13205-021-02872-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/31/2021] [Indexed: 12/22/2022] Open
Abstract
Microbial secondary metabolites are intensively explored due to their demands in pharmaceutical, agricultural and food industries. Streptomyces are one of the largest sources of secondary metabolites having diverse applications. In particular, the abundance of secondary metabolites encoding biosynthetic gene clusters and presence of wobble position in Streptomyces strains make it potential candidate as a native or heterologous host for secondary metabolite production including several cryptic gene clusters expression. Here, we have discussed the developments in Streptomyces strains genome mining, its exploration as a suitable host and application of synthetic biology for refactoring genetic systems for developing chassis for enhanced as well as novel secondary metabolites with reduced genome and cleaned background.
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Affiliation(s)
- Vivek Sharma
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Randhir Kaur
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Richa Salwan
- College of Horticulture and Forestry, Dr YS Parmar University of Horticulture and Forestry, Neri, Hamirpur, Himachal Pradesh 177001 India
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13
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Yang C, Huang C, Fang C, Zhang L, Chen S, Zhang Q, Zhang C, Zhang W. Inactivation of Flavoenzyme-Encoding Gene flsO1 in Fluostatin Biosynthesis Leads to Diversified Angucyclinone Derivatives. J Org Chem 2021; 86:11019-11028. [DOI: 10.1021/acs.joc.0c02517] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Chunfang Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Oceanology, SCSIO, Yazhou
Scientific Bay, Sanya 572000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
| | - Chunshuai Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunyan Fang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Oceanology, SCSIO, Yazhou
Scientific Bay, Sanya 572000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
| | - Siqiang Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Oceanology, SCSIO, Yazhou
Scientific Bay, Sanya 572000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Oceanology, SCSIO, Yazhou
Scientific Bay, Sanya 572000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Oceanology, SCSIO, Yazhou
Scientific Bay, Sanya 572000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Yaragorla S, Rajesh P. In Situ Generation of Allenes and their Application to One‐Pot Assembly of Functionalized Fluoreno[3,2‐
b
]furans by Calcium‐Catalyzed, Regioselective, 3‐Component Reactions. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Srinivasarao Yaragorla
- School of Chemistry, Gurbaksh Building, W‐16, 17 University of Hyderabad P.O. Central University Gachibowli Hyderabad 5000046 Telangana State India
| | - Pallava Rajesh
- School of Chemistry, Gurbaksh Building, W‐16, 17 University of Hyderabad P.O. Central University Gachibowli Hyderabad 5000046 Telangana State India
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15
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Fang Z, Jiang X, Zhang Q, Zhang L, Zhang W, Yang C, Zhang H, Zhu Y, Zhang C. S-Bridged Thioether and Structure-Diversified Angucyclinone Derivatives from the South China Sea-Derived Micromonospora echinospora SCSIO 04089. JOURNAL OF NATURAL PRODUCTS 2020; 83:3122-3130. [PMID: 32970433 DOI: 10.1021/acs.jnatprod.0c00719] [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
Angucyclinces belong to the class of aromatic polyketides and display a wide variety of structure diversity and pharmaceutical significance. Herein we report the isolation, structure elucidation, and bioactivity evaluation of structure-diversified angucyclinone derivatives and anthracene from the South China Sea-derived Micromonospora echinospora SCSIO 04089, including a thioether, gephysulfuromycin (1), two new benzo[b]phenanthridines, homophenanthroviridone (2) and homophenanthridonamide (3), a new benzo[b]fluorene, homostealthin D (4), a new naphtho[2,3-b]benzofuran, nenesfuran (5), a new naphthoquinone, WS-5995 D (6) and a new anthracene, nenesophanol (7), together with three known compounds (8-10). Their structures were elucidated by extensive spectroscopic analyses. The structures of 1-3 and 5-8 were confirmed by X-ray crystallographic analyses. Gephysulfuromycin (1) featured a rare single S-bridged 3,12a-epithiotetraphene skeleton. Homophenanthroviridone (2) was found to be cytotoxic to SF-268, MCF-7, and HepG2 cell lines with IC50 values of 5.4 ± 0.4, 6.8 ± 0.3, and 1.4 ± 0.1 μM, respectively. Compound 2 was also active against Gram-positive bacteria with MIC (minimal inhibition concentration) values ranging 2-4 μg mL-1.
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Affiliation(s)
- Zhuangjie Fang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaodong Jiang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Chunfang Yang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Haibo Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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16
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Gore BS, Chiang CH, Lee CC, Shih YL, Wang JJ. De Novo Protocol for the Construction of Benzo[ a]fluorenes via Nitrile/Alkene Activation. Org Lett 2020; 22:7848-7852. [PMID: 33021802 DOI: 10.1021/acs.orglett.0c02739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Unprecedented chemo- and regioselective synthesis of benzo[a]fluorenes and naphthamide-substituted benzo[a]fluorenes were constructed from the reaction of (E)-2-aroyl-3-(2-(arylalkynes/alkenes)aryl)acrylonitrile scaffolds under metal-free conditions via the activation of nitriles and alkenes, respectively. A tentative reaction mechanism was proposed for this homofunctionalization of nitriles. Control experiments showed that the reaction proceeds via selective nitrile or alkene protonation, depending upon the substrates. Additionally, we demonstrated an alternative expeditious route for the synthesis of disubstituted benzo[a]fluorenes in the presence of TfOH alone.
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Affiliation(s)
- Babasaheb Sopan Gore
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, No. 100, Shiquan First Road, Sanmin District, Kaohsiung City 807, Taiwan
| | - Chun-Hsien Chiang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, No. 100, Shiquan First Road, Sanmin District, Kaohsiung City 807, Taiwan
| | - Chein Chung Lee
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, No. 100, Shiquan First Road, Sanmin District, Kaohsiung City 807, Taiwan
| | - Yi-Lun Shih
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, No. 100, Shiquan First Road, Sanmin District, Kaohsiung City 807, Taiwan
| | - Jeh-Jeng Wang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, No. 100, Shiquan First Road, Sanmin District, Kaohsiung City 807, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, No. 100, Tzyou First Road, Sanmin District, Kaohsiung City 807, Taiwan
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17
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Tao K, Ye T, Cao M, Meng X, Li Y, Wang H, Feng Z. Salumycin, a New Pyrazolequinone from a Streptomyces albus J1074 Mutant Strain. Molecules 2020; 25:molecules25184098. [PMID: 32911655 PMCID: PMC7570766 DOI: 10.3390/molecules25184098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 01/09/2023] Open
Abstract
Heterocyclic natural products with various bioactivities play significant roles in pharmaceuticals. Here, we isolated a heterocyclic compound salumycin (1) from a Streptomyces albus J1074 mutant strain. The structure of (1) was elucidated via single-crystal X-ray diffraction, mass spectrometry (MS), fourier transform infrared spectrometer (FTIR), and nuclear magnetic resonance (NMR) data analysis. Salumycin (1) contained a novel pyrazolequinone ring, which had never been previously reported in a natural product. Salumycin (1) exhibited moderate 2,2'-diphenyl-1-picrylhydrazyl (DPPH)-radical scavenging activity (EC50 = 46.3 ± 2.2 μM) compared with tert-butylhydroquinone (EC50 = 4.7 ± 0.3 μM). This study provides a new example of discovering novel natural products from bacteria.
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Affiliation(s)
- Kaixiang Tao
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (K.T.); (T.Y.); (M.C.); (X.M.)
| | - Taijia Ye
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (K.T.); (T.Y.); (M.C.); (X.M.)
| | - Mingming Cao
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (K.T.); (T.Y.); (M.C.); (X.M.)
| | - Xiaolu Meng
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (K.T.); (T.Y.); (M.C.); (X.M.)
| | - Yuqing Li
- School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China;
| | - Huan Wang
- School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China;
- Correspondence: (H.W.); (Z.F.); Tel./Fax: +86-025-89682133 (H.W.); +86-025-84399511 (Z.F.)
| | - Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; (K.T.); (T.Y.); (M.C.); (X.M.)
- Correspondence: (H.W.); (Z.F.); Tel./Fax: +86-025-89682133 (H.W.); +86-025-84399511 (Z.F.)
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18
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Wang Y, Zhang C, Zhao YL, Zhao R, Houk KN. Understand the Specific Regio- and Enantioselectivity of Fluostatin Conjugation in the Post-Biosynthesis. Biomolecules 2020; 10:E815. [PMID: 32466453 PMCID: PMC7355926 DOI: 10.3390/biom10060815] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/22/2022] Open
Abstract
Fluostatins, benzofluorene-containing aromatic polyketides in the atypical angucycline family, conjugate into dimeric and even trimeric compounds in the post-biosynthesis. The formation of the C-C bond involves a non-enzymatic stereospecific coupling reaction. In this work, the unusual regio- and enantioselectivities were rationalized by density functional theory calculations with the M06-2X (SMD, water)/6-311 + G(d,p)//6-31G(d) method. These DFT calculations reproduce the lowest energy C1-(R)-C10'-(S) coupling pathway observed in a nonenzymatic reaction. Bonding of the reactive carbon atoms (C1 and C10') of the two reactant molecules maximizes the HOMO-LUMO interactions and Fukui function involving the highest occupied molecular orbital (HOMO) of nucleophile p-QM and lowest unoccupied molecular orbital (LUMO) of electrophile FST2- anion. In particular, the significant π-π stacking interactions of the low-energy pre-reaction state are retained in the lowest energy pathway for C-C coupling. The distortion/interaction-activation strain analysis indicates that the transition state (TScp-I) of the lowest energy pathway involves the highest stabilizing interactions and small distortion among all possible C-C coupling reactions. One of the two chiral centers generated in this step is lost upon aromatization of the phenol ring in the final difluostatin products. Thus, the π-π stacking interactions between the fluostatin 6-5-6 aromatic ring system play a critical role in the stereoselectivity of the nonenzymatic fluostatin conjugation.
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Affiliation(s)
- Yuanqi Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China;
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resource and Ecology, Guangdong Key Laboratory of Marine Materia, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China;
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China;
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; (R.Z.); (K.N.H.)
| | - Rosalinda Zhao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; (R.Z.); (K.N.H.)
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; (R.Z.); (K.N.H.)
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19
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Selective isolation of large segments from individual microbial genomes and environmental DNA samples using transformation-associated recombination cloning in yeast. Nat Protoc 2020; 15:734-749. [PMID: 32005981 DOI: 10.1038/s41596-019-0280-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 12/05/2019] [Indexed: 11/08/2022]
Abstract
Here, we describe an extension of our original transformation-associated recombination (TAR) cloning protocol, enabling selective isolation of DNA segments from microbial genomes. The technique is based on the previously described TAR cloning procedure developed for isolation of a desirable region from mammalian genomes that are enriched in autonomously replicating sequence (ARS)-like sequences, elements that function as the origin of replication in yeast. Such sequences are not common in microbial genomes. In this Protocol Extension, an ARS is inserted into the TAR vector along with a counter-selectable marker, allowing for selection of cloning events against vector circularization. Pre-treatment of microbial DNA with CRISPR-Cas9 to generate double-stranded breaks near the targeted sequences greatly increases the yield of region-positive colonies. In comparison to other available methods, this Protocol Extension allows selective isolation of any region from microbial genomes as well as from environmental DNA samples. The entire procedure can be completed in 10 d.
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20
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Zhang JJ, Tang X, Moore BS. Genetic platforms for heterologous expression of microbial natural products. Nat Prod Rep 2019; 36:1313-1332. [PMID: 31197291 PMCID: PMC6750982 DOI: 10.1039/c9np00025a] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Covering: 2005 up to 2019Natural products are of paramount importance in human medicine. Not only are most antibacterial and anticancer drugs derived directly from or inspired by natural products, many other branches of medicine, such as immunology, neurology, and cardiology, have similarly benefited from natural product-based drugs. Typically, the genetic material required to synthesize a microbial specialized product is arranged in a multigene biosynthetic gene cluster (BGC), which codes for proteins associated with molecule construction, regulation, and transport. The ability to connect natural product compounds to BGCs and vice versa, along with ever-increasing knowledge of biosynthetic machineries, has spawned the field of genomics-guided natural product genome mining for the rational discovery of new chemical entities. One significant challenge in the field of natural product genome mining is how to rapidly link orphan biosynthetic genes to their associated chemical products. This review highlights state-of-the-art genetic platforms to identify, interrogate, and engineer BGCs from diverse microbial sources, which can be broken into three stages: (1) cloning and isolation of genomic loci, (2) heterologous expression in a host organism, and (3) genetic manipulation of cloned pathways. In the future, we envision natural product genome mining will be rapidly accelerated by de novo DNA synthesis and refactoring of whole biosynthetic pathways in combination with systematic heterologous expression methodologies.
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Affiliation(s)
- Jia Jia Zhang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Xiaoyu Tang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
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21
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Yaragorla S, Rajesh P. An efficient Benzannulation protocol for the synthesis of 9,9-Diphenyl-9H
-fluorenols using Intramolecular Allene Friedel-Crafts Annulation. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900895] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Srinivasarao Yaragorla
- School of Chemistry; Gurbaksh Building, W-16, 17; University of Hyderabad; P.O. Central University, Gachibowli 5000046 Hyderabad Telangana State India
| | - P. Rajesh
- School of Chemistry; Gurbaksh Building, W-16, 17; University of Hyderabad; P.O. Central University, Gachibowli 5000046 Hyderabad Telangana State India
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22
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Wang W, Li J, Li H, Fan K, Liu Y. Crystal structure of AlpK: An essential monooxygenase involved in the biosynthesis of kinamycin. Biochem Biophys Res Commun 2019; 510:601-605. [PMID: 30739782 DOI: 10.1016/j.bbrc.2019.01.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 01/16/2019] [Indexed: 12/23/2022]
Abstract
AlpK is an essential monooxygenase involved in the biosynthesis of kinamycin. It catalyzes the C5-hyfroxylattion of the crucial benzo[b]-fluorence intermediate in kinamycin synthesis. However, the structure and mechanism of AlpK is unclear. Here, we report the first structure of AlpK in complex with FAD. Our structure sheds light on the catalytic mechanism of AlpK.
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Affiliation(s)
- Wenpeng Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Li
- School of Medicine, Sun Yat-Sen University, Shenzhen, 510080, China
| | - HuanHuan Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Keqing Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yingfang Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, School of Medicine, Sun Yat-sen University, Guangzhou, China.
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23
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Huo L, Hug JJ, Fu C, Bian X, Zhang Y, Müller R. Heterologous expression of bacterial natural product biosynthetic pathways. Nat Prod Rep 2019. [DOI: 10.1039/c8np00091c [epub ahead of print]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The review highlights the 2013–2018 literature on the heterologous expression of bacterial natural product biosynthetic pathways and emphasises new techniques, heterologous hosts, and novel chemistry.
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Affiliation(s)
- Liujie Huo
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Joachim J. Hug
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Chengzhang Fu
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Xiaoying Bian
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Youming Zhang
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Rolf Müller
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
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Huo L, Hug JJ, Fu C, Bian X, Zhang Y, Müller R. Heterologous expression of bacterial natural product biosynthetic pathways. Nat Prod Rep 2019; 36:1412-1436. [DOI: 10.1039/c8np00091c] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The review highlights the 2013–2018 literature on the heterologous expression of bacterial natural product biosynthetic pathways and emphasises new techniques, heterologous hosts, and novel chemistry.
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Affiliation(s)
- Liujie Huo
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Joachim J. Hug
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Chengzhang Fu
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Xiaoying Bian
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Youming Zhang
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Rolf Müller
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
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25
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Akbar S, Tamilarasan VJ, Srinivasan K. Iodine-mediated synthesis of benzo[a]fluorenones from yne-enones. RSC Adv 2019; 9:23652-23657. [PMID: 35530623 PMCID: PMC9069471 DOI: 10.1039/c9ra02376c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/19/2019] [Indexed: 01/20/2023] Open
Abstract
The chalcones derived from o-alkynylacetophenones and aromatic aldehydes (yne-enones) when heated under reflux with iodine in acetic acid gave a range of benzo[a]fluorenone derivatives in moderate to good yields. The transformation involves the formation of a vinyl indenone intermediate through regioselective alkyne hydration and intramolecular aldol condensation followed by electrocyclic ring closure and aromatization. An iodine mediated synthesis of benzo[a]fluorenone derivatives from the chalcones derived from o-alkynylacetophenones and aromatic aldehydes is described.![]()
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26
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Fan K, Zhang Q. The functional differentiation of the post-PKS tailoring oxygenases contributed to the chemical diversities of atypical angucyclines. Synth Syst Biotechnol 2018; 3:275-282. [PMID: 30533539 PMCID: PMC6260466 DOI: 10.1016/j.synbio.2018.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/05/2018] [Accepted: 11/06/2018] [Indexed: 12/31/2022] Open
Abstract
Angucyclines are one of the largest families of aromatic polyketides with various chemical structures and bioactivities. Decades of studies have made it easy for us to depict the picture of their early biosynthetic pathways. Two families of oxygenases, the FAD-dependent oxygenases and the ring opening oxygenases, contribute to the formation of some unique skeletons of atypical angucyclines. The FAD-dependent oxygenases involved in the biosynthetic gene clusters of typical angucyclines catalyze two hydroxylation reactions at C-12 and C-12b of prejadomycin, while their homolog JadH in jadomycin gene cluster catalyze the C-12 hydroxylation and 4a,12b-dehydration reactions of prejadomycin, which leads to the production of dehydrorabelomycin, a common intermediate during the biosynthesis of atypical angucyclines. Ring opening oxygenases of a unique family of oxygenases catalyze the oxidative C—C bond cleavage reaction of dehydrorabelomycin, followed by different rearrangement reactions, resulting in the formation of the various chemical skeletons of atypical angucyclines. These results suggested that the functional differentiation of these oxygenases could apparently enrich the sources of aromatic polyketides with greater structure diversities.
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Affiliation(s)
- Keqiang Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Qian Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
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27
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Huang C, Yang C, Zhu Y, Zhang W, Yuan C, Zhang C. Marine Bacterial Aromatic Polyketides From Host-Dependent Heterologous Expression and Fungal Mode of Cyclization. Front Chem 2018; 6:528. [PMID: 30425983 PMCID: PMC6218434 DOI: 10.3389/fchem.2018.00528] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/11/2018] [Indexed: 11/23/2022] Open
Abstract
The structure diversity of type II polyketide synthases-derived bacterial aromatic polyketides is often enhanced by enzyme controlled or spontaneous cyclizations. Here we report the discovery of bacterial aromatic polyketides generated from 5 different cyclization modes and pathway crosstalk between the host and the heterologous fluostatin biosynthetic gene cluster derived from a marine bacterium. The discovery of new compound SEK43F (2) represents an unusual carbon skeleton resulting from a pathway crosstalk, in which a pyrrole-like moiety derived from the host Streptomyces albus J1074 is fused to an aromatic polyketide SEK43 generated from the heterologous fluostatin type II PKSs. The occurrence of a new congener, fluoquinone (3), highlights a bacterial aromatic polyketide that is exceptionally derived from a characteristic fungal F-mode first-ring cyclization. This study expands our knowledge on the power of bacterial type II PKSs in diversifying aromatic polyketides.
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Affiliation(s)
- Chunshuai Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, RNAM Center for Marine Microbiology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chunfang Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, RNAM Center for Marine Microbiology, Chinese Academy of Sciences, Guangzhou, China
| | - Yiguang Zhu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, RNAM Center for Marine Microbiology, Chinese Academy of Sciences, Guangzhou, China
| | - Wenjun Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, RNAM Center for Marine Microbiology, Chinese Academy of Sciences, Guangzhou, China
| | - Chengshan Yuan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, RNAM Center for Marine Microbiology, Chinese Academy of Sciences, Guangzhou, China
| | - Changsheng Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, RNAM Center for Marine Microbiology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
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28
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Huang C, Yang C, Zhang W, Zhang L, De BC, Zhu Y, Jiang X, Fang C, Zhang Q, Yuan CS, Liu HW, Zhang C. Molecular basis of dimer formation during the biosynthesis of benzofluorene-containing atypical angucyclines. Nat Commun 2018; 9:2088. [PMID: 29802272 PMCID: PMC5970136 DOI: 10.1038/s41467-018-04487-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/30/2018] [Indexed: 11/30/2022] Open
Abstract
Lomaiviticin A and difluostatin A are benzofluorene-containing aromatic polyketides in the atypical angucycline family. Although these dimeric compounds are potent antitumor agents, how nature constructs their complex structures remains poorly understood. Herein, we report the discovery of a number of fluostatin type dimeric aromatic polyketides with varied C−C and C−N coupling patterns. We also demonstrate that these dimers are not true secondary metabolites, but are instead derived from non-enzymatic deacylation of biosynthetic acyl fluostatins. The non-enzymatic deacylation proceeds via a transient quinone methide like intermediate which facilitates the subsequent C–C/C−N coupled dimerization. Characterization of this unusual property of acyl fluostatins explains how dimerization takes place, and suggests a strategy for the assembly of C–C and C–N coupled aromatic polyketide dimers. Additionally, a deacylase FlsH was identified which may help to prevent accumulation of toxic quinone methides by catalyzing hydrolysis of the acyl group. Benzofluorene-containing angucyclines, bacterial natural compounds with potential use as therapeutics/antibiotics, occur as dimers. Here, the authors elucidated the dimerization mechanism which turned out to work spontaneously, without enzymatic catalysis.
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Affiliation(s)
- Chunshuai Huang
- Key Laboratory of Tropical Marine Bio-resources and EcologyGuangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Chunfang Yang
- Key Laboratory of Tropical Marine Bio-resources and EcologyGuangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Wenjun Zhang
- Key Laboratory of Tropical Marine Bio-resources and EcologyGuangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and EcologyGuangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Bidhan Chandra De
- Key Laboratory of Tropical Marine Bio-resources and EcologyGuangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and EcologyGuangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Xiaodong Jiang
- Key Laboratory of Tropical Marine Bio-resources and EcologyGuangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Chunyan Fang
- Key Laboratory of Tropical Marine Bio-resources and EcologyGuangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and EcologyGuangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Cheng-Shan Yuan
- Key Laboratory of Tropical Marine Bio-resources and EcologyGuangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Hung-Wen Liu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy and Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and EcologyGuangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.
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29
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Harvey CJB, Tang M, Schlecht U, Horecka J, Fischer CR, Lin HC, Li J, Naughton B, Cherry J, Miranda M, Li YF, Chu AM, Hennessy JR, Vandova GA, Inglis D, Aiyar RS, Steinmetz LM, Davis RW, Medema MH, Sattely E, Khosla C, St. Onge RP, Tang Y, Hillenmeyer ME. HEx: A heterologous expression platform for the discovery of fungal natural products. SCIENCE ADVANCES 2018; 4:eaar5459. [PMID: 29651464 PMCID: PMC5895447 DOI: 10.1126/sciadv.aar5459] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/26/2018] [Indexed: 05/18/2023]
Abstract
For decades, fungi have been a source of U.S. Food and Drug Administration-approved natural products such as penicillin, cyclosporine, and the statins. Recent breakthroughs in DNA sequencing suggest that millions of fungal species exist on Earth, with each genome encoding pathways capable of generating as many as dozens of natural products. However, the majority of encoded molecules are difficult or impossible to access because the organisms are uncultivable or the genes are transcriptionally silent. To overcome this bottleneck in natural product discovery, we developed the HEx (Heterologous EXpression) synthetic biology platform for rapid, scalable expression of fungal biosynthetic genes and their encoded metabolites in Saccharomyces cerevisiae. We applied this platform to 41 fungal biosynthetic gene clusters from diverse fungal species from around the world, 22 of which produced detectable compounds. These included novel compounds with unexpected biosynthetic origins, particularly from poorly studied species. This result establishes the HEx platform for rapid discovery of natural products from any fungal species, even those that are uncultivable, and opens the door to discovery of the next generation of natural products.
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Affiliation(s)
- Colin J. B. Harvey
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Mancheng Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Ulrich Schlecht
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Joe Horecka
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Curt R. Fischer
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Stanford ChEM-H (Chemistry, Engineering and Medicine for Human Health), Stanford University, Palo Alto, CA 94304, USA
| | - Hsiao-Ching Lin
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Jian Li
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Brian Naughton
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - James Cherry
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Molly Miranda
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Yong Fuga Li
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Angela M. Chu
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - James R. Hennessy
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Gergana A. Vandova
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Diane Inglis
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Raeka S. Aiyar
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Lars M. Steinmetz
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- European Molecular Biology Laboratory Heidelberg, 69117 Heidelberg, Germany
| | - Ronald W. Davis
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
| | - Elizabeth Sattely
- Department of Chemical Engineering, Stanford University, Palo Alto, CA 94304, USA
| | - Chaitan Khosla
- Stanford ChEM-H (Chemistry, Engineering and Medicine for Human Health), Stanford University, Palo Alto, CA 94304, USA
- Department of Chemical Engineering, Stanford University, Palo Alto, CA 94304, USA
- Department of Chemistry, Stanford University, Palo Alto, CA 94304, USA
| | - Robert P. St. Onge
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Maureen E. Hillenmeyer
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
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30
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Fluostatins M-Q Featuring a 6-5-6-6 Ring Skeleton and High Oxidized A-Rings from Marine Streptomyces sp. PKU-MA00045. Mar Drugs 2018. [PMID: 29522466 PMCID: PMC5867631 DOI: 10.3390/md16030087] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aromatic polyketides from marine actinomycetes have received increasing attention due to their unusual structures and potent bioactivities. Compared to their terrestrial counterparts, marine aromatic polyketides have been less discovered and their structural and biological diversities are far from being fully investigated. In this study, we employed a PCR-based genome mining method to discover aromatic polyketides in our marine bacteria collection. Five new atypical angucyclinones, fluostatins M–Q (1–5) featuring a unique 6-5-6-6 ring skeleton, were discovered from one “positive” Streptomyces sp. PKU-MA00045. The structures of fluostatins M–Q (1–5) were elucidated based on comprehensive spectroscopic analyses and the crystallographic structure of fluostatin P (4), which contains the most oxidized A-ring, was solved by X-ray diffraction analysis with Cu Kα radiation. Compared to the published 16 fluostatin analogues, fluostatins M–Q (1–5) contained a different methoxy group attached at C-7 and hydroxy group attached at C-4, enriching the structural diversity of aromatic polyketides from marine actinomycetes. Genome sequencing of Streptomyces sp. PKU-MA00045 revealed the biosynthetic gene cluster of fluostatins M–Q (1–5), which contained different genes and gene organizations compared to known fluostatin gene clusters, facilitating the investigation of the biosynthesis of the unique 6-5-6-6 ring skeleton in all fluostatins.
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31
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Wu N, Huang H, Min T, Hu H. TAR cloning and integrated overexpression of 6-demethylchlortetracycline biosynthetic gene cluster in Streptomyces aureofaciens. Acta Biochim Biophys Sin (Shanghai) 2017; 49:1129-1134. [PMID: 29087452 DOI: 10.1093/abbs/gmx110] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Indexed: 12/28/2022] Open
Abstract
6-Demethylchlortetracycline (6-DCT), a tetracycline antibiotic produced by Streptomyces aureofaciens, is a crucial precursor employed for the semi-synthesis of tigecycline, minocycline, and amadacyclin (PTK 0796). In this study, the 6-DCT biosynthetic gene cluster (BGC) was cloned from genomic DNA of a high 6-DCT-producing strain, S. aureofaciens DM-1, using the transformation-associated recombination method. An extra copy of the 6-DCT BGC was introduced and integrated into the chromosome of S. aureofaciens DM-1. Duplication of the 6-DCT BGC resulted in a maximum increase of the 6-DCT titer by 34%.
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Affiliation(s)
- Naxin Wu
- School of Pharmacy, Department of Pharmacology, Fudan University, Shanghai, China
- Shanghai Institute of Pharmaceutical Industry, Department of Biopharmceutical, Shanghai, China
| | - He Huang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Taoling Min
- Shanghai Institute of Pharmaceutical Industry, Department of Biopharmceutical, Shanghai, China
| | - Haifeng Hu
- Shanghai Institute of Pharmaceutical Industry, Department of Biopharmceutical, Shanghai, China
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Döhlemann J, Wagner M, Happel C, Carrillo M, Sobetzko P, Erb TJ, Thanbichler M, Becker A. A Family of Single Copy repABC-Type Shuttle Vectors Stably Maintained in the Alpha-Proteobacterium Sinorhizobium meliloti. ACS Synth Biol 2017; 6:968-984. [PMID: 28264559 PMCID: PMC7610768 DOI: 10.1021/acssynbio.6b00320] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
A considerable
share of bacterial species maintains segmented genomes.
Plant symbiotic α-proteobacterial rhizobia contain up to six repABC-type replicons in addition to the primary chromosome.
These low or unit-copy replicons, classified as secondary chromosomes,
chromids, or megaplasmids, are exclusively found in α-proteobacteria.
Replication and faithful partitioning of these replicons to the daughter
cells is mediated by the repABC region. The importance
of α-rhizobial symbiotic nitrogen fixation for sustainable agriculture
and Agrobacterium-mediated plant transformation as
a tool in plant sciences has increasingly moved biological engineering
of these organisms into focus. Plasmids are ideal DNA-carrying vectors
for these engineering efforts. On the basis of repABC regions collected from α-rhizobial secondary replicons, and
origins of replication derived from traditional cloning vectors, we
devised the versatile family of pABC shuttle vectors propagating in Sinorhizobium meliloti, related members of the Rhizobiales, and Escherichia coli. A modular plasmid library
providing the elemental parts for pABC vector assembly was founded.
The standardized design of these vectors involves five basic modules:
(1) repABC cassette, (2) plasmid-derived origin of
replication, (3) RK2/RP4 mobilization site (optional), (4) antibiotic
resistance gene, and (5) multiple cloning site flanked by transcription
terminators. In S. meliloti, pABC vectors showed
high propagation stability and unit-copy number. We demonstrated stable
coexistence of three pABC vectors in addition to the two indigenous
megaplasmids in S. meliloti, suggesting combinability
of multiple compatible pABC plasmids. We further devised an in vivo cloning strategy involving Cre/lox-mediated translocation of large DNA fragments to an autonomously
replicating repABC-based vector, followed by conjugation-mediated
transfer either to compatible rhizobia or E. coli.
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Affiliation(s)
- Johannes Döhlemann
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Marcel Wagner
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Carina Happel
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Martina Carrillo
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
| | - Tobias J. Erb
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Martin Thanbichler
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
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33
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Isolation, structure elucidation and biosynthesis of benzo[b]fluorene nenestatin A from deep-sea derived Micromonospora echinospora SCSIO 04089. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.03.054] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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34
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Hill P, Heberlig GW, Boddy CN. Sampling Terrestrial Environments for Bacterial Polyketides. Molecules 2017; 22:E707. [PMID: 28468277 PMCID: PMC6154731 DOI: 10.3390/molecules22050707] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/14/2017] [Accepted: 04/18/2017] [Indexed: 12/17/2022] Open
Abstract
Bacterial polyketides are highly biologically active molecules that are frequently used as drugs, particularly as antibiotics and anticancer agents, thus the discovery of new polyketides is of major interest. Since the 1980s discovery of polyketides has slowed dramatically due in large part to the repeated rediscovery of known compounds. While recent scientific and technical advances have improved our ability to discover new polyketides, one key area has been under addressed, namely the distribution of polyketide-producing bacteria in the environment. Identifying environments where producing bacteria are abundant and diverse should improve our ability to discover (bioprospect) new polyketides. This review summarizes for the bioprospector the state-of-the-field in terrestrial microbial ecology. It provides insight into the scientific and technical challenges limiting the application of microbial ecology discoveries for bioprospecting and summarizes key developments in the field that will enable more effective bioprospecting. The major recent efforts by researchers to sample new environments for polyketide discovery is also reviewed and key emerging environments such as insect associated bacteria, desert soils, disease suppressive soils, and caves are highlighted. Finally strategies for taking and characterizing terrestrial samples to help maximize discovery efforts are proposed and the inclusion of non-actinomycetal bacteria in any terrestrial discovery strategy is recommended.
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Affiliation(s)
- Patrick Hill
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Graham W Heberlig
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Christopher N Boddy
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
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35
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Nah HJ, Pyeon HR, Kang SH, Choi SS, Kim ES. Cloning and Heterologous Expression of a Large-sized Natural Product Biosynthetic Gene Cluster in Streptomyces Species. Front Microbiol 2017; 8:394. [PMID: 28360891 PMCID: PMC5350119 DOI: 10.3389/fmicb.2017.00394] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 02/24/2017] [Indexed: 12/14/2022] Open
Abstract
Actinomycetes family including Streptomyces species have been a major source for the discovery of novel natural products (NPs) in the last several decades thanks to their structural novelty, diversity and complexity. Moreover, recent genome mining approach has provided an attractive tool to screen potentially valuable NP biosynthetic gene clusters (BGCs) present in the actinomycetes genomes. Since many of these NP BGCs are silent or cryptic in the original actinomycetes, various techniques have been employed to activate these NP BGCs. Heterologous expression of BGCs has become a useful strategy to produce, reactivate, improve, and modify the pathways of NPs present at minute quantities in the original actinomycetes isolates. However, cloning and efficient overexpression of an entire NP BGC, often as large as over 100 kb, remain challenging due to the ineffectiveness of current genetic systems in manipulating large NP BGCs. This mini review describes examples of actinomycetes NP production through BGC heterologous expression systems as well as recent strategies specialized for the large-sized NP BGCs in Streptomyces heterologous hosts.
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Affiliation(s)
- Hee-Ju Nah
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Hye-Rim Pyeon
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Seung-Hoon Kang
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Si-Sun Choi
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University Incheon, South Korea
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36
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Pan G, Gao X, Fan K, Liu J, Meng B, Gao J, Wang B, Zhang C, Han H, Ai G, Chen Y, Wu D, Liu ZJ, Yang K. Structure and Function of a C-C Bond Cleaving Oxygenase in Atypical Angucycline Biosynthesis. ACS Chem Biol 2017; 12:142-152. [PMID: 28103689 DOI: 10.1021/acschembio.6b00621] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
C-C bond ring cleaving oxygenases represent a unique family of enzymes involved in the B ring cleavage reaction only observed in atypical angucycline biosynthesis. B ring cleavage is the key reaction leading to dramatic divergence in the final structures of atypical angucyclines. Here, we present the crystal structure of AlpJ, the first structure of this family of enzymes. AlpJ has been verified as the enzyme catalyzing C-C bond cleavage in kinamycin biosynthesis. The crystal structure of the AlpJ monomer resembles the dimeric structure of ferredoxin-like proteins. The N- and C-terminal halves of AlpJ are homologous, and both contain a putative hydrophobic substrate binding pocket in the "closed" and "open" conformations, respectively. Structural comparison of AlpJ with ActVA-Orf6 and protein-ligand docking analysis suggest that the residues including Asn60, Trp64, and Trp181 are possibly involved in substrate recognition. Site-directed mutagenesis results supported our hypothesis, as mutation of these residues led to nearly a complete loss of the activity of AlpJ. Structural analysis also revealed that AlpJ possesses an intramolecular domain-domain interface, where the residues His50 and Tyr178 form a hydrogen bond that probably stabilizes the three-dimensional structure of AlpJ. Site-directed mutagenesis showed that the two residues, His50 and Tyr178, were vital for the activity of AlpJ. Our findings shed light on the structure and catalytic mechanism of the AlpJ family of oxygenases, which presumably involves two active sites that might function in a cooperative manner.
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Affiliation(s)
- Guohui Pan
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Xiaoqin Gao
- National
Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Keqiang Fan
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Junlin Liu
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, People’s Republic of China
| | - Bing Meng
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, People’s Republic of China
| | - Jinmin Gao
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Bin Wang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Chaobo Zhang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Hui Han
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Guomin Ai
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yihua Chen
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Dong Wu
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, People’s Republic of China
| | - Zhi-Jie Liu
- National
Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- Institute
of Molecular and Clinical Medicine, Kunming Medical University, Kunming 650500, China
| | - Keqian Yang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
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37
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Zhang W, Yang C, Huang C, Zhang L, Zhang H, Zhang Q, Yuan CS, Zhu Y, Zhang C. Pyrazolofluostatins A–C, Pyrazole-Fused Benzo[a]fluorenes from South China Sea-Derived Micromonospora rosaria SCSIO N160. Org Lett 2017; 19:592-595. [PMID: 28075605 DOI: 10.1021/acs.orglett.6b03745] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Wenjun Zhang
- Key
Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Chunfang Yang
- Key
Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Chunshuai Huang
- Key
Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Liping Zhang
- Key
Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Haibo Zhang
- Key
Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Qingbo Zhang
- Key
Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Cheng-shan Yuan
- Key
Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Yiguang Zhu
- Key
Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Changsheng Zhang
- Key
Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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38
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Kawamura M, Kamo S, Azuma S, Kubo K, Sasamori T, Tokitoh N, Kuramochi K, Tsubaki K. Skeletal Rearrangements of Polycyclic α-Ketols. Org Lett 2017; 19:301-303. [DOI: 10.1021/acs.orglett.6b03541] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Moe Kawamura
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Shogo Kamo
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
- Department
of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Shuhei Azuma
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Konomi Kubo
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Takahiro Sasamori
- Institute
for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Norihiro Tokitoh
- Institute
for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kouji Kuramochi
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
- Department
of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kazunori Tsubaki
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
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39
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"Cre/loxP plus BAC": a strategy for direct cloning of large DNA fragment and its applications in Photorhabdus luminescens and Agrobacterium tumefaciens. Sci Rep 2016; 6:29087. [PMID: 27364376 PMCID: PMC4929569 DOI: 10.1038/srep29087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/14/2016] [Indexed: 01/23/2023] Open
Abstract
Heterologous expression has been proven to be a valid strategy for elucidating the natural products produced by gene clusters uncovered by genome sequencing projects. Efforts have been made to efficiently clone gene clusters directly from genomic DNA and several approaches have been developed. Here, we present an alternative strategy based on the site-specific recombinase system Cre/loxP for direct cloning gene clusters. A type three secretion system (T3SS) gene cluster (~32 kb) from Photorhabdus luminescens TT01 and DNA fragment (~78 kb) containing the siderophore biosynthetic gene cluster from Agrobacterium tumefaciens C58 have been successfully cloned into pBeloBAC11 with “Cre/loxP plus BAC” strategy. Based on the fact that Cre/loxP system has successfully used for genomic engineering in a wide range of organisms, we believe that this strategy could be widely used for direct cloning of large DNA fragment.
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40
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Old dogs and new tricks in antimicrobial discovery. Curr Opin Microbiol 2016; 33:25-34. [PMID: 27262526 DOI: 10.1016/j.mib.2016.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 05/16/2016] [Accepted: 05/19/2016] [Indexed: 11/22/2022]
Abstract
The discovery of new antibiotics is crucial if we are to avoid a future in which simple infections once again lead to death. New antibiotics were traditionally discovered by analyzing extracts from cultured soil-derived microbes. However, in the last few years only a few new antibiotic classes have been identified using this method. Attempts to apply target-based screening approaches to antibiotic discovery have also proven to be unproductive. In this article, we describe how DNA sequencing and bioinformatic techniques are revolutionizing natural product discovery leading to new natural product antibiotics sourced from both cultivated and uncultivated microbes. New chemical structures are also being 'crowd sourced' from chemists around the world, and 'forgotten' antibiotics repositioned for clinical trials after chemical or biochemical modification of the original natural product. Collectively such approaches have the potential to revamp antibiotic lead discovery and re-invigorate the antibiotic pipeline.
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41
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Bond C, Tang Y, Li L. Saccharomyces cerevisiae as a tool for mining, studying and engineering fungal polyketide synthases. Fungal Genet Biol 2016; 89:52-61. [PMID: 26850128 PMCID: PMC4789138 DOI: 10.1016/j.fgb.2016.01.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/01/2016] [Accepted: 01/09/2016] [Indexed: 12/17/2022]
Abstract
Small molecule secondary metabolites produced by organisms such as plants, bacteria, and fungi form a fascinating and important group of natural products, many of which have shown promise as medicines. Fungi in particular have been important sources of natural product polyketide pharmaceuticals. While the structural complexity of these polyketides makes them interesting and useful bioactive compounds, these same features also make them difficult and expensive to prepare and scale-up using synthetic methods. Currently, nearly all commercial polyketides are prepared through fermentation or semi-synthesis. However, elucidation and engineering of polyketide pathways in the native filamentous fungi hosts are often hampered due to a lack of established genetic tools and of understanding of the regulation of fungal secondary metabolisms. Saccharomyces cerevisiae has many advantages beneficial to the study and development of polyketide pathways from filamentous fungi due to its extensive genetic toolbox and well-studied metabolism. This review highlights the benefits S. cerevisiae provides as a tool for mining, studying, and engineering fungal polyketide synthases (PKSs), as well as notable insights this versatile tool has given us into the mechanisms and products of fungal PKSs.
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Affiliation(s)
- Carly Bond
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, United States.
| | - Li Li
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States; Engineering Research Center of Industrial Microbiology (Ministry of Education), College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350108, China; State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200030, China
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42
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Liu X. Generate a bioactive natural product library by mining bacterial cytochrome P450 patterns. Synth Syst Biotechnol 2016; 1:95-108. [PMID: 29062932 PMCID: PMC5640691 DOI: 10.1016/j.synbio.2016.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 01/26/2016] [Indexed: 11/25/2022] Open
Abstract
The increased number of annotated bacterial genomes provides a vast resource for genome mining. Several bacterial natural products with epoxide groups have been identified as pre-mRNA spliceosome inhibitors and antitumor compounds through genome mining. These epoxide-containing natural products feature a common biosynthetic characteristic that cytochrome P450s (CYPs) and its patterns such as epoxidases are employed in the tailoring reactions. The tailoring enzyme patterns are essential to both biological activities and structural diversity of natural products, and can be used for enzyme pattern-based genome mining. Recent development of direct cloning, heterologous expression, manipulation of the biosynthetic pathways and the CRISPR-CAS9 system have provided molecular biology tools to turn on or pull out nascent biosynthetic gene clusters to generate a microbial natural product library. This review focuses on a library of epoxide-containing natural products and their associated CYPs, with the intention to provide strategies on diversifying the structures of CYP-catalyzed bioactive natural products. It is conceivable that a library of diversified bioactive natural products will be created by pattern-based genome mining, direct cloning and heterologous expression as well as the genomic manipulation.
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Affiliation(s)
- Xiangyang Liu
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
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43
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Abstract
Polyketides are a diverse group of natural products that form the basis of many important drugs. The engineering of the polyketide synthase (PKS) enzymes responsible for the formation of these compounds has long been considered to have great potential for producing new bioactive molecules. Recent advances in this field have contributed to the understanding of this powerful and complex enzymatic machinery, particularly with regard to domain activity and engineering, unique building block formation and incorporation, and programming rules and limitations. New developments in tools for
in vitro biochemical analysis, full-length megasynthase structural studies, and
in vivo heterologous expression will continue to improve our fundamental understanding of polyketide synthesis as well as our ability to engineer the production of polyketides.
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Affiliation(s)
- Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Joyce Liu
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
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44
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O'Mahony MM, Henneberger R, Selvin J, Kennedy J, Doohan F, Marchesi JR, Dobson ADW. Inhibition of the growth of Bacillus subtilis DSM10 by a newly discovered antibacterial protein from the soil metagenome. Bioengineered 2016; 6:89-98. [PMID: 25692994 PMCID: PMC4601227 DOI: 10.1080/21655979.2015.1018493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
A functional metagenomics based approach exploiting the microbiota of suppressive soils from an organic field site has succeeded in the identification of a clone with the ability to inhibit the growth of Bacillus subtilis DSM10. Sequencing of the fosmid identified a putative β-lactamase-like gene abgT. Transposon mutagenesis of the abgT gene resulted in a loss in ability to inhibit the growth of B. subtilis DSM10. Further analysis of the deduced amino acid sequence of AbgT revealed moderate homology to esterases, suggesting that the protein may possess hydrolytic activity. Weak lipolytic activity was detected; however the clone did not appear to produce any β-lactamase activity. Phylogenetic analysis revealed the protein is a member of the family VIII group of lipase/esterases and clusters with a number of proteins of metagenomic origin. The abgT gene was sub-cloned into a protein expression vector and when introduced into the abgT transposon mutant clones restored the ability of the clones to inhibit the growth of B. subtilis DSM10, clearly indicating that the abgT gene is involved in the antibacterial activity. While the precise role of this protein has yet to fully elucidated, it may be involved in the generation of free fatty acid with antibacterial properties. Thus functional metagenomic approaches continue to provide a significant resource for the discovery of novel functional proteins and it is clear that hydrolytic enzymes, such as AbgT, may be a potential source for the development of future antimicrobial therapies.
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Affiliation(s)
- Mark M O'Mahony
- a School of Microbiology and Marine Biotechnology Center; Environmental Research Institute; University College Cork ; Cork , Ireland
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45
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Zarins-Tutt JS, Barberi TT, Gao H, Mearns-Spragg A, Zhang L, Newman DJ, Goss RJM. Prospecting for new bacterial metabolites: a glossary of approaches for inducing, activating and upregulating the biosynthesis of bacterial cryptic or silent natural products. Nat Prod Rep 2016; 33:54-72. [DOI: 10.1039/c5np00111k] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Over the centuries, microbial secondary metabolites have played a central role in the treatment of human diseases and have revolutionised the pharmaceutical industry.
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Affiliation(s)
| | | | - Hong Gao
- School of Chemistry
- University of St Andrews
- St Andrews
- UK
| | | | - Lixin Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology
- Institute of Microbiology
- Chinese Academy of Sciences
- Beijing
- China
| | - David J. Newman
- Frederick National Laboratories for Cancer Research
- Natural Products Branch
- Frederick
- USA
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46
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Culture-independent discovery of natural products from soil metagenomes. J Ind Microbiol Biotechnol 2015; 43:129-41. [PMID: 26586404 DOI: 10.1007/s10295-015-1706-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 10/29/2015] [Indexed: 12/20/2022]
Abstract
Bacterial natural products have proven to be invaluable starting points in the development of many currently used therapeutic agents. Unfortunately, traditional culture-based methods for natural product discovery have been deemphasized by pharmaceutical companies due in large part to high rediscovery rates. Culture-independent, or "metagenomic," methods, which rely on the heterologous expression of DNA extracted directly from environmental samples (eDNA), have the potential to provide access to metabolites encoded by a large fraction of the earth's microbial biosynthetic diversity. As soil is both ubiquitous and rich in bacterial diversity, it is an appealing starting point for culture-independent natural product discovery efforts. This review provides an overview of the history of soil metagenome-driven natural product discovery studies and elaborates on the recent development of new tools for sequence-based, high-throughput profiling of environmental samples used in discovering novel natural product biosynthetic gene clusters. We conclude with several examples of these new tools being employed to facilitate the recovery of novel secondary metabolite encoding gene clusters from soil metagenomes and the subsequent heterologous expression of these clusters to produce bioactive small molecules.
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47
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Reinvigorating natural product combinatorial biosynthesis with synthetic biology. Nat Chem Biol 2015; 11:649-59. [PMID: 26284672 DOI: 10.1038/nchembio.1893] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/22/2015] [Indexed: 12/24/2022]
Abstract
Natural products continue to play a pivotal role in drug-discovery efforts and in the understanding if human health. The ability to extend nature's chemistry through combinatorial biosynthesis--altering functional groups, regiochemistry and scaffold backbones through the manipulation of biosynthetic enzymes--offers unique opportunities to create natural product analogs. Incorporating emerging synthetic biology techniques has the potential to further accelerate the refinement of combinatorial biosynthesis as a robust platform for the diversification of natural chemical drug leads. Two decades after the field originated, we discuss the current limitations, the realities and the state of the art of combinatorial biosynthesis, including the engineering of substrate specificity of biosynthetic enzymes and the development of heterologous expression systems for biosynthetic pathways. We also propose a new perspective for the combinatorial biosynthesis of natural products that could reinvigorate drug discovery by using synthetic biology in combination with synthetic chemistry.
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48
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Yang C, Huang C, Zhang W, Zhu Y, Zhang C. Heterologous Expression of Fluostatin Gene Cluster Leads to a Bioactive Heterodimer. Org Lett 2015; 17:5324-7. [PMID: 26465097 DOI: 10.1021/acs.orglett.5b02683] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chunfang Yang
- Key
Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Chunshuai Huang
- Key
Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Wenjun Zhang
- Key
Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Yiguang Zhu
- Key
Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Changsheng Zhang
- Key
Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology,
South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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49
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Elsayed SS, Trusch F, Deng H, Raab A, Prokes I, Busarakam K, Asenjo JA, Andrews BA, van West P, Bull AT, Goodfellow M, Yi Y, Ebel R, Jaspars M, Rateb ME. Chaxapeptin, a Lasso Peptide from Extremotolerant Streptomyces leeuwenhoekii Strain C58 from the Hyperarid Atacama Desert. J Org Chem 2015; 80:10252-60. [DOI: 10.1021/acs.joc.5b01878] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Somayah S. Elsayed
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Franziska Trusch
- Aberdeen
Oomycetes Laboratory, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K
| | - Hai Deng
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Andrea Raab
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Ivan Prokes
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | | | - Juan A. Asenjo
- Centre
for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Barbara A. Andrews
- Centre
for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Pieter van West
- Aberdeen
Oomycetes Laboratory, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K
| | - Alan T. Bull
- School
of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Michael Goodfellow
- School
of Biology, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
| | - Yu Yi
- Key Laboratory
of Combinatory Biosynthesis and Drug Discovery, School of Pharmaceutical
Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, P. R. China
| | - Rainer Ebel
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Marcel Jaspars
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Mostafa E. Rateb
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
- Pharmacognosy
Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 32514, Egypt
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Knaus T, Mutti FG, Humphreys LD, Turner NJ, Scrutton NS. Systematic methodology for the development of biocatalytic hydrogen-borrowing cascades: application to the synthesis of chiral α-substituted carboxylic acids from α-substituted α,β-unsaturated aldehydes. Org Biomol Chem 2015; 13:223-33. [PMID: 25372591 DOI: 10.1039/c4ob02282c] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ene-reductases (ERs) are flavin dependent enzymes that catalyze the asymmetric reduction of activated carbon-carbon double bonds. In particular, α,β-unsaturated carbonyl compounds (e.g. enals and enones) as well as nitroalkenes are rapidly reduced. Conversely, α,β-unsaturated esters are poorly accepted substrates whereas free carboxylic acids are not converted at all. The only exceptions are α,β-unsaturated diacids, diesters as well as esters bearing an electron-withdrawing group in α- or β-position. Here, we present an alternative approach that has a general applicability for directly obtaining diverse chiral α-substituted carboxylic acids. This approach combines two enzyme classes, namely ERs and aldehyde dehydrogenases (Ald-DHs), in a concurrent reductive-oxidative biocatalytic cascade. This strategy has several advantages as the starting material is an α-substituted α,β-unsaturated aldehyde, a class of compounds extremely reactive for the reduction of the alkene moiety. Furthermore no external hydride source from a sacrificial substrate (e.g. glucose, formate) is required since the hydride for the first reductive step is liberated in the second oxidative step. Such a process is defined as a hydrogen-borrowing cascade. This methodology has wide applicability as it was successfully applied to the synthesis of chiral substituted hydrocinnamic acids, aliphatic acids, heterocycles and even acetylated amino acids with elevated yield, chemo- and stereo-selectivity. A systematic methodology for optimizing the hydrogen-borrowing two-enzyme synthesis of α-chiral substituted carboxylic acids was developed. This systematic methodology has general applicability for the development of diverse hydrogen-borrowing processes that possess the highest atom efficiency and the lowest environmental impact.
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Affiliation(s)
- Tanja Knaus
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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