151
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Li ZR, Li J, Gu JP, Lai JYH, Duggan BM, Zhang WP, Li ZL, Li YX, Tong RB, Xu Y, Lin DH, Moore BS, Qian PY. Divergent biosynthesis yields a cytotoxic aminomalonate-containing precolibactin. Nat Chem Biol 2016; 12:773-5. [PMID: 27547923 PMCID: PMC5030165 DOI: 10.1038/nchembio.2157] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/14/2016] [Indexed: 12/25/2022]
Abstract
Colibactin is an as-yet-uncharacterized genotoxic secondary metabolite produced by human gut bacteria. Here we report the biosynthetic discovery of two new precolibactin molecules from Escherichia coli, including precolibactin-886, which uniquely incorporates the highly sought genotoxicity-associated aminomalonate building block into its unprecedented macrocyclic structure. This work provides new insights into the biosynthetic logic and mode of action of this colorectal-cancer-linked microbial chemical.
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Affiliation(s)
- Zhong-Rui Li
- Division of Life Science and Environmental Science Programs, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
| | - Jie Li
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, United States
| | - Jin-Ping Gu
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Jennifer Y. H. Lai
- Division of Life Science and Environmental Science Programs, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
| | - Brendan M. Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, United States
| | - Wei-Peng Zhang
- Division of Life Science and Environmental Science Programs, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
| | - Zhi-Long Li
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
| | - Yong-Xin Li
- Division of Life Science and Environmental Science Programs, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
| | - Rong-Biao Tong
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource & Ecoenvironmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P. R. China
| | - Dong-Hai Lin
- High-field NMR Research Center, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, United States
| | - Pei-Yuan Qian
- Division of Life Science and Environmental Science Programs, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
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152
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Awodi UR, Ronan JL, Masschelein J, de Los Santos ELC, Challis GL. Thioester reduction and aldehyde transamination are universal steps in actinobacterial polyketide alkaloid biosynthesis. Chem Sci 2016; 8:411-415. [PMID: 28451186 PMCID: PMC5365063 DOI: 10.1039/c6sc02803a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/21/2016] [Indexed: 11/21/2022] Open
Abstract
Actinobacteria produce a variety of polyketide alkaloids with unusual structures. Recently, it was shown that a type I modular polyketide synthase (PKS) is involved in the assembly of coelimycin P1, a polyketide alkaloid produced by Streptomyces coelicolor M145. However, the mechanisms for converting the product of the PKS to coelimycin P1 remain to be elucidated. Here we show that the C-terminal thioester reductase (TR) domain of the PKS and an ω-transaminase are responsible for release of the polyketide chain as an aldehyde and its subsequent reductive amination. Bioinformatics analyses identified numerous gene clusters in actinobacterial genomes that encode modular PKSs with a C-terminal TR domain and a homolog of the ω-transaminase. These are predicted to direct the biosynthesis of both known and novel polyketide alkaloids, suggesting that reductive chain release and transamination constitutes a conserved mechanism for the biosynthesis of such metabolites.
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Affiliation(s)
- U R Awodi
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - J L Ronan
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - J Masschelein
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - E L C de Los Santos
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - G L Challis
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
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153
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Chen M, Liu J, Duan P, Li M, Liu W. Biosynthesis and molecular engineering of templated natural products. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww045] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Abstract
Bioactive small molecules that are produced by living organisms, often referred to as natural products (NPs), historically play a critical role in the context of both medicinal chemistry and chemical biology. How nature creates these chemical entities with stunning structural complexity and diversity using a limited range of simple substrates has not been fully understood. Focusing on two types of NPs that share a highly evolvable ‘template’-biosynthetic logic, we here provide specific examples to highlight the conceptual and technological leaps in NP biosynthesis and witness the area of progress since the beginning of the twenty-first century. The biosynthesis of polyketides, non-ribosomal peptides and their hybrids that share an assembly-line enzymology of modular multifunctional proteins exemplifies an extended ‘central dogma’ that correlates the genotype of catalysts with the chemotype of products; in parallel, post-translational modifications of ribosomally synthesized peptides involve a number of unusual biochemical mechanisms for molecular maturation. Understanding the biosynthetic processes of these templated NPs would largely facilitate the design, development and utilization of compatible biosynthetic machineries to address the challenge that often arises from structural complexity to the accessibility and efficiency of current chemical synthesis.
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Affiliation(s)
- Ming Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jingyu Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Panpan Duan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mulin Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Huzhou Center of Bio-Synthetic Innovation, Huzhou 313000, China
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154
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Ninomiya A, Katsuyama Y, Kuranaga T, Miyazaki M, Nogi Y, Okada S, Wakimoto T, Ohnishi Y, Matsunaga S, Takada K. Biosynthetic Gene Cluster for Surugamide A Encompasses an Unrelated Decapeptide, Surugamide F. Chembiochem 2016; 17:1709-12. [DOI: 10.1002/cbic.201600350] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Akihiro Ninomiya
- Laboratory of Aquatic Natural Products Chemistry; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Yohei Katsuyama
- Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Takefumi Kuranaga
- Graduate School of Pharmaceutical Sciences; Hokkaido University; Sapporo Hokkaido 060-0812 Japan
| | - Masayuki Miyazaki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Natsushima Yokosuka Kanagawa 237-0061 Japan
| | - Yuichi Nogi
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Natsushima Yokosuka Kanagawa 237-0061 Japan
| | - Shigeru Okada
- Laboratory of Aquatic Natural Products Chemistry; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Toshiyuki Wakimoto
- Graduate School of Pharmaceutical Sciences; Hokkaido University; Sapporo Hokkaido 060-0812 Japan
| | - Yasuo Ohnishi
- Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Kentaro Takada
- Laboratory of Aquatic Natural Products Chemistry; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
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155
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Hemmerling F, Hahn F. Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides. Beilstein J Org Chem 2016; 12:1512-50. [PMID: 27559404 PMCID: PMC4979870 DOI: 10.3762/bjoc.12.148] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/22/2016] [Indexed: 01/01/2023] Open
Abstract
This review highlights the biosynthesis of heterocycles in polyketide natural products with a focus on oxygen and nitrogen-containing heterocycles with ring sizes between 3 and 6 atoms. Heterocycles are abundant structural elements of natural products from all classes and they often contribute significantly to their biological activity. Progress in recent years has led to a much better understanding of their biosynthesis. In this context, plenty of novel enzymology has been discovered, suggesting that these pathways are an attractive target for future studies.
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Affiliation(s)
- Franziska Hemmerling
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Frank Hahn
- Institut für Organische Chemie and Zentrum für Biomolekulare Wirkstoffe, Gottfried Wilhelm Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany; Fakultät für Biologie, Chemie und Geowissenschaften, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
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156
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Wang G, Liu Z, Lin R, Li E, Mao Z, Ling J, Yang Y, Yin WB, Xie B. Biosynthesis of Antibiotic Leucinostatins in Bio-control Fungus Purpureocillium lilacinum and Their Inhibition on Phytophthora Revealed by Genome Mining. PLoS Pathog 2016; 12:e1005685. [PMID: 27416025 PMCID: PMC4946873 DOI: 10.1371/journal.ppat.1005685] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 05/18/2016] [Indexed: 12/18/2022] Open
Abstract
Purpureocillium lilacinum of Ophiocordycipitaceae is one of the most promising and commercialized agents for controlling plant parasitic nematodes, as well as other insects and plant pathogens. However, how the fungus functions at the molecular level remains unknown. Here, we sequenced two isolates (PLBJ-1 and PLFJ-1) of P. lilacinum from different places Beijing and Fujian. Genomic analysis showed high synteny of the two isolates, and the phylogenetic analysis indicated they were most related to the insect pathogen Tolypocladium inflatum. A comparison with other species revealed that this fungus was enriched in carbohydrate-active enzymes (CAZymes), proteases and pathogenesis related genes. Whole genome search revealed a rich repertoire of secondary metabolites (SMs) encoding genes. The non-ribosomal peptide synthetase LcsA, which is comprised of ten C-A-PCP modules, was identified as the core biosynthetic gene of lipopeptide leucinostatins, which was specific to P. lilacinum and T. ophioglossoides, as confirmed by phylogenetic analysis. Furthermore, gene expression level was analyzed when PLBJ-1 was grown in leucinostatin-inducing and non-inducing medium, and 20 genes involved in the biosynthesis of leucionostatins were identified. Disruption mutants allowed us to propose a putative biosynthetic pathway of leucinostatin A. Moreover, overexpression of the transcription factor lcsF increased the production (1.5-fold) of leucinostatins A and B compared to wild type. Bioassays explored a new bioactivity of leucinostatins and P. lilacinum: inhibiting the growth of Phytophthora infestans and P. capsici. These results contribute to our understanding of the biosynthetic mechanism of leucinostatins and may allow us to utilize P. lilacinum better as bio-control agent.
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Affiliation(s)
- Gang Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Zhiguo Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Runmao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, PR China
- College of Life Sciences, Beijing Normal University, Beijing, PR China
| | - Erfeng Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Zhenchuan Mao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Jian Ling
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Yuhong Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, PR China
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157
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158
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Klapper M, Götze S, Barnett R, Willing K, Stallforth P. Bacterial Alkaloids Prevent Amoebal Predation. Angew Chem Int Ed Engl 2016; 55:8944-7. [PMID: 27294402 DOI: 10.1002/anie.201603312] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Indexed: 01/20/2023]
Abstract
Bacterial defense mechanisms have evolved to protect bacteria against predation by nematodes, predatory bacteria, or amoebae. We identified novel bacterial alkaloids (pyreudiones A-D) that protect the producer, Pseudomonas fluorescens HKI0770, against amoebal predation. Isolation, structure elucidation, total synthesis, and a proposed biosynthetic pathway for these structures are presented. The generation of P. fluorescens gene-deletion mutants unable to produce pyreudiones rendered the bacterium edible to a variety of soil-dwelling amoebae.
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Affiliation(s)
- Martin Klapper
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Junior Research Group Chemistry of Microbial Communication, Jena, Germany
| | - Sebastian Götze
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Junior Research Group Chemistry of Microbial Communication, Jena, Germany
| | - Robert Barnett
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Junior Research Group Chemistry of Microbial Communication, Jena, Germany
| | - Karsten Willing
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Bio Pilot Plant, Jena, Germany
| | - Pierre Stallforth
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany. .,Junior Research Group Chemistry of Microbial Communication, Jena, Germany.
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159
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Chen XP, Shi T, Wang XL, Wang J, Chen Q, Bai L, Zhao YL. Theoretical Studies on the Mechanism of Thioesterase-Catalyzed Macrocyclization in Erythromycin Biosynthesis. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01154] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Xiong-Ping Chen
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ting Shi
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiao-Lei Wang
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jitao Wang
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Qihua Chen
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Linquan Bai
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yi-Lei Zhao
- State
Key Laboratory of Microbial Metabolism, Joint International Research
Laboratory of Metabolic and Developmental Sciences, MOE-LSC, School
of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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160
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Actinoquinolines A and B, anti-inflammatory quinoline alkaloids from a marine-derived Streptomyces sp., strain CNP975. J Antibiot (Tokyo) 2016. [DOI: 10.1038/ja.2016.56 pmid: 27220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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161
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Actinoquinolines A and B, anti-inflammatory quinoline alkaloids from a marine-derived Streptomyces sp., strain CNP975. J Antibiot (Tokyo) 2016; 69:511-4. [DOI: 10.1038/ja.2016.56] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 04/17/2016] [Accepted: 04/20/2016] [Indexed: 11/08/2022]
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162
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Liu X, Jin Y, Cui Z, Nonaka K, Baba S, Funabashi M, Yang Z, Van Lanen SG. The Role of a Nonribosomal Peptide Synthetase in l-Lysine Lactamization During Capuramycin Biosynthesis. Chembiochem 2016; 17:804-10. [PMID: 26840634 PMCID: PMC4933962 DOI: 10.1002/cbic.201500701] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Indexed: 01/10/2023]
Abstract
Capuramycins are one of several known classes of natural products that contain an l-Lys-derived l-α-amino-ɛ-caprolactam (l-ACL) unit. The α-amino group of l-ACL in a capuramycin is linked to an unsaturated hexuronic acid component through an amide bond that was previously shown to originate by an ATP-independent enzymatic route. With the aid of a combined in vivo and in vitro approach, a predicted tridomain nonribosomal peptide synthetase CapU is functionally characterized here as the ATP-dependent amide-bond-forming catalyst responsible for the biosynthesis of the remaining amide bond present in l-ACL. The results are consistent with the adenylation domain of CapU as the essential catalytic component for l-Lys activation and thioesterification of the adjacent thiolation domain. However, in contrast to expectations, lactamization does not require any additional domains or proteins and is likely a nonenzymatic event. The results set the stage for examining whether a similar NRPS-mediated mechanism is employed in the biosynthesis of other l-ACL-containing natural products and, just as intriguingly, how spontaneous lactamization is avoided in the numerous NRPS-derived peptides that contain an unmodified l-Lys residue.
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Affiliation(s)
- Xiaodong Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| | - Yuanyuan Jin
- Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medicinal Sciences & Peking Union Medical College, Beijing, China
| | - Zheng Cui
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| | - Koichi Nonaka
- Biologics Technology Research Laboratories, Daiichi Sankyo, Co. Ltd., Gunma, 370-0503, Japan
| | - Satoshi Baba
- Biologics Technology Research Laboratories, Daiichi Sankyo, Co. Ltd., Gunma, 370-0503, Japan
| | - Masanori Funabashi
- Natural Product Research Group, Discovery Science and Technology Department, Daiichi Sankyo RD Novare Co. Ltd., Tokyo, 134-8630, Japan
| | - Zhaoyong Yang
- Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medicinal Sciences & Peking Union Medical College, Beijing, China
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA.
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163
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Pearson LA, Dittmann E, Mazmouz R, Ongley SE, D'Agostino PM, Neilan BA. The genetics, biosynthesis and regulation of toxic specialized metabolites of cyanobacteria. HARMFUL ALGAE 2016; 54:98-111. [PMID: 28073484 DOI: 10.1016/j.hal.2015.11.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 11/06/2015] [Indexed: 05/28/2023]
Abstract
The production of toxic metabolites by cyanobacterial blooms represents a significant threat to the health of humans and ecosystems worldwide. Here we summarize the current state of the knowledge regarding the genetics, biosynthesis and regulation of well-characterized cyanotoxins, including the microcystins, nodularin, cylindrospermopsin, saxitoxins and anatoxins, as well as the lesser-known marine toxins (e.g. lyngbyatoxin, aplysiatoxin, jamaicamides, barbamide, curacin, hectochlorin and apratoxins).
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Affiliation(s)
- Leanne A Pearson
- Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, NSW, Australia
| | - Elke Dittmann
- Institut für Biochemie und Biologie, Mikrobiologie, Universität Potsdam, Potsdam-Golm 14476, Germany
| | - Rabia Mazmouz
- Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, NSW, Australia
| | - Sarah E Ongley
- Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, NSW, Australia
| | - Paul M D'Agostino
- Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, NSW, Australia
| | - Brett A Neilan
- Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, NSW, Australia.
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164
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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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165
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Structural insights into the regulation of NADPH binding to reductase domains of nonribosomal peptide synthetases: A concerted loop movement model. J Struct Biol 2016; 194:368-74. [PMID: 26993465 DOI: 10.1016/j.jsb.2016.03.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 03/15/2016] [Accepted: 03/15/2016] [Indexed: 11/22/2022]
Abstract
The termination module of nonribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) offloads the final product as an acid (occasionally also accompanied by cyclization) upon hydrolysis by employing thioesterase domains (TE-domains). Reductase domains (R-domains) of short-chain dehydrogenase/reductase (SDR) family offer an alternative offloading mechanism by reducing 4'-phosphopantetheine (4'-PPant) arm-tethered peptidyl chain, a thioester, to an aldehyde or an alcohol. Recent studies have highlighted their functional importance, for instance in the glycopeptidolipid (GPL) biosynthesis of Mycobacterium smegmatis, where the resulting alcoholic group is the site for subsequent modifications such as glycosylations. The mechanistic understanding of how these R-domains function in the context of multi-modular NRPS and PKS is poorly understood. In this study, conformational differences in functionally important loops, not reported previously, were identified in a new crystal form of R-domain which may be relevant to functioning in the context of assembly-line NRPS and PKS enzymology. Here, we propose a concerted loop movement model that allows gating of cofactor binding to these enzymes, enabling the release of the final product only after the substrate has reached the active site during biosynthesis, and therefore distinct from a canonical single domain SDR family of enzymes.
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166
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Argyropoulos P, Bergeret F, Pardin C, Reimer JM, Pinto A, Boddy CN, Schmeing TM. Towards a characterization of the structural determinants of specificity in the macrocyclizing thioesterase for deoxyerythronolide B biosynthesis. Biochim Biophys Acta Gen Subj 2016; 1860:486-97. [DOI: 10.1016/j.bbagen.2015.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/13/2015] [Accepted: 11/20/2015] [Indexed: 12/12/2022]
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167
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Chiang YM, Ahuja M, Oakley CE, Entwistle R, Asokan A, Zutz C, Wang CCC, Oakley BR. Development of Genetic Dereplication Strains in Aspergillus nidulans Results in the Discovery of Aspercryptin. Angew Chem Int Ed Engl 2016; 55:1662-5. [PMID: 26563584 PMCID: PMC4724294 DOI: 10.1002/anie.201507097] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/04/2015] [Indexed: 11/07/2022]
Abstract
To reduce the secondary metabolite background in Aspergillus nidulans and minimize the rediscovery of compounds and pathway intermediates, we created a "genetic dereplication" strain in which we deleted eight of the most highly expressed secondary metabolite gene clusters (more than 244,000 base pairs deleted in total). This strain allowed us to discover a novel compound that we designate aspercryptin and to propose a biosynthetic pathway for the compound. Interestingly, aspercryptin is formed from compounds produced by two separate gene clusters, one of which makes the well-known product cichorine. This raises the exciting possibility that fungi use differential regulation of expression of secondary metabolite gene clusters to increase the diversity of metabolites they produce.
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Affiliation(s)
- Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan, 71710, Taiwan
| | - Manmeet Ahuja
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
- Industrial Biotechnology Division, Reliance Technology Group, Reliance Industries Limited, Reliance Corporate Park, Thane Belapur Road, Ghansoli, Navi, Mumbai, 400701, India
| | - C Elizabeth Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Ruth Entwistle
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Anabanadam Asokan
- Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66045, USA
| | - Christoph Zutz
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA.
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168
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Studt L, Janevska S, Niehaus EM, Burkhardt I, Arndt B, Sieber CMK, Humpf HU, Dickschat JS, Tudzynski B. Two separate key enzymes and two pathway-specific transcription factors are involved in fusaric acid biosynthesis in Fusarium fujikuroi. Environ Microbiol 2016; 18:936-56. [PMID: 26662839 DOI: 10.1111/1462-2920.13150] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/18/2015] [Accepted: 11/23/2015] [Indexed: 01/03/2023]
Abstract
Fusaric acid (FSA) is a mycotoxin produced by several fusaria, including the rice pathogen Fusarium fujikuroi. Genes involved in FSA biosynthesis were previously identified as a cluster containing a polyketide synthase (PKS)-encoding (FUB1) and four additional genes (FUB2-FUB5). However, the biosynthetic steps leading to FSA as well as the origin of the nitrogen atom, which is incorporated into the polyketide backbone, remained unknown. In this study, seven additional cluster genes (FUB6-FUB12) were identified via manipulation of the global regulator FfSge1. The extended FUB gene cluster encodes two Zn(II)2 Cys6 transcription factors: Fub10 positively regulates expression of all FUB genes, whereas Fub12 is involved in the formation of the two FSA derivatives, i.e. dehydrofusaric acid and fusarinolic acid, serving as a detoxification mechanism. The major facilitator superfamily transporter Fub11 functions in the export of FSA out of the cell and is essential when FSA levels become critical. Next to Fub1, a second key enzyme was identified, the non-canonical non-ribosomal peptide synthetase Fub8. Chemical analyses of generated mutant strains allowed for the identification of a triketide as PKS product and the proposition of an FSA biosynthetic pathway, thereby unravelling the unique formation of a hybrid metabolite consisting of this triketide and an amino acid moiety.
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Affiliation(s)
- Lena Studt
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-University, Schlossplatz 8, 48143, Münster, Germany
| | - Slavica Janevska
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-University, Schlossplatz 8, 48143, Münster, Germany
| | - Eva-Maria Niehaus
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-University, Schlossplatz 8, 48143, Münster, Germany
| | - Immo Burkhardt
- Kekulé Institute for Organic Chemistry and Biochemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53121, Bonn, Germany
| | - Birgit Arndt
- Institute of Food Chemistry, Westfälische Wilhelms-University, Corrensstr. 45, 48149, Münster, Germany
| | - Christian M K Sieber
- Lawrence Berkeley National Lab, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, Westfälische Wilhelms-University, Corrensstr. 45, 48149, Münster, Germany
| | - Jeroen S Dickschat
- Kekulé Institute for Organic Chemistry and Biochemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53121, Bonn, Germany
| | - Bettina Tudzynski
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-University, Schlossplatz 8, 48143, Münster, Germany
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169
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Horsman ME, Hari TPA, Boddy CN. Polyketide synthase and non-ribosomal peptide synthetase thioesterase selectivity: logic gate or a victim of fate? Nat Prod Rep 2016; 33:183-202. [DOI: 10.1039/c4np00148f] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thioesterases (TEs) are product offloading enzymes from FAS, PKS, and NRPS complexes. We review the diversity, structure, and mechanism of PKS and NRPS TEs and analyze TE loading and release steps as possible logic gates with a view to predicting TE function in new pathways.
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Affiliation(s)
- Mark E. Horsman
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
| | - Taylor P. A. Hari
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
| | - Christopher N. Boddy
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
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170
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Chiang YM, Ahuja M, Oakley CE, Entwistle R, Asokan A, Zutz C, Wang CCC, Oakley BR. Development of Genetic Dereplication Strains in Aspergillus nidulans
Results in the Discovery of Aspercryptin. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507097] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy; University of Southern California; Los Angeles CA 90089 USA
- Department of Pharmacy; Chia Nan University of Pharmacy and Science; Tainan 71710 Taiwan
| | - Manmeet Ahuja
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
- Industrial Biotechnology Division, Reliance Technology Group; Reliance Industries Limited, Reliance Corporate Park; Thane Belapur Road, Ghansoli, Navi Mumbai 400701 India
| | - C. Elizabeth Oakley
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
| | - Ruth Entwistle
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
| | - Anabanadam Asokan
- Del Shankel Structural Biology Center; University of Kansas; Lawrence KS 66045 USA
| | - Christoph Zutz
- Institute for Milk Hygiene; University of Veterinary Medicine Vienna; Vienna 1210 Austria
| | - Clay C. C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy; University of Southern California; Los Angeles CA 90089 USA
- Department of Chemistry; University of Southern California; Los Angeles CA 90089 USA
| | - Berl R. Oakley
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
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171
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Fujii R, Matsu Y, Minami A, Nagamine S, Takeuchi I, Gomi K, Oikawa H. Biosynthetic Study on Antihypercholesterolemic Agent Phomoidride: General Biogenesis of Fungal Dimeric Anhydrides. Org Lett 2015; 17:5658-61. [DOI: 10.1021/acs.orglett.5b02934] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryuya Fujii
- Division
of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yusuke Matsu
- Division
of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Atsushi Minami
- Division
of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Shota Nagamine
- Division
of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Ichiro Takeuchi
- Division
of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Katsuya Gomi
- Graduate
School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan
| | - Hideaki Oikawa
- Division
of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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172
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Metabolic engineering of Escherichia coli for the biosynthesis of 2-pyrrolidone. Metab Eng Commun 2015; 3:1-7. [PMID: 29468109 PMCID: PMC5779725 DOI: 10.1016/j.meteno.2015.11.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 10/25/2015] [Accepted: 11/03/2015] [Indexed: 11/23/2022] Open
Abstract
2-Pyrrolidone is a valuable bulk chemical with myriad applications as a solvent, polymer precursor and active pharmaceutical intermediate. A novel 2-pyrrolidone synthase, ORF27, from Streptomyces aizunensis was identified to catalyze the ring closing dehydration of γ-aminobutyrate. ORF27's tendency to aggregate was resolved by expression at low temperature and fusion to the maltose binding protein (MBP). Recombinant Escherichia coli was metabolically engineered for the production of 2-pyrrolidone from glutamate by expressing both the genes encoding GadB, a glutamate decarboxylase, and ORF27. Incorporation of a GadB mutant lacking H465 and T466, GadB_ΔHT, improved the efficiency of one-pot 2-pyrrolidone biosynthesis in vivo. When the recombinant E. coli strain expressing the E. coli GadB_ΔHT mutant and the ORF27-MBP fusion was cultured in ZYM-5052 medium containing 9 g/L of l-glutamate, 7.7 g/L of l-glutamate was converted to 1.1 g/L of 2-pyrrolidone within 31 h, achieving 25% molar yield from the consumed substrate. ORF27 from Streptomyces aizunensis catalyzes formation of 2-pyrrolidone from γ-aminobutyrate. Recombinant Escherichia coli with GadB and ORF27 produces 2-pyrrolidone from glutamate. Engineered strain capable of producing 1.1 g/L of 2-pyrrolidone from 9 g/L of glutamate within 31 h.
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173
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Directed evolution of the tryptophan synthase β-subunit for stand-alone function recapitulates allosteric activation. Proc Natl Acad Sci U S A 2015; 112:14599-604. [PMID: 26553994 DOI: 10.1073/pnas.1516401112] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymes in heteromeric, allosterically regulated complexes catalyze a rich array of chemical reactions. Separating the subunits of such complexes, however, often severely attenuates their catalytic activities, because they can no longer be activated by their protein partners. We used directed evolution to explore allosteric regulation as a source of latent catalytic potential using the β-subunit of tryptophan synthase from Pyrococcus furiosus (PfTrpB). As part of its native αββα complex, TrpB efficiently produces tryptophan and tryptophan analogs; activity drops considerably when it is used as a stand-alone catalyst without the α-subunit. Kinetic, spectroscopic, and X-ray crystallographic data show that this lost activity can be recovered by mutations that reproduce the effects of complexation with the α-subunit. The engineered PfTrpB is a powerful platform for production of Trp analogs and for further directed evolution to expand substrate and reaction scope.
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174
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Sharma R, Xia X, Cano LM, Evangelisti E, Kemen E, Judelson H, Oome S, Sambles C, van den Hoogen DJ, Kitner M, Klein J, Meijer HJG, Spring O, Win J, Zipper R, Bode HB, Govers F, Kamoun S, Schornack S, Studholme DJ, Van den Ackerveken G, Thines M. Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora. BMC Genomics 2015; 16:741. [PMID: 26438312 PMCID: PMC4594904 DOI: 10.1186/s12864-015-1904-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/27/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from Hyaloperonospora arabidopsidis. Further genomic resources for downy mildews are required to study their evolution, including pathogenicity effector proteins, such as RxLR effectors. Plasmopara halstedii is a devastating pathogen of sunflower and a potential pathosystem model to study downy mildews, as several Avr-genes and R-genes have been predicted and unlike Arabidopsis downy mildew, large quantities of almost contamination-free material can be obtained easily. RESULTS Here a high-quality draft genome of Plasmopara halstedii is reported and analysed with respect to various aspects, including genome organisation, secondary metabolism, effector proteins and comparative genomics with other sequenced oomycetes. Interestingly, the present analyses revealed further variation of the RxLR motif, suggesting an important role of the conservation of the dEER-motif. Orthology analyses revealed the conservation of 28 RxLR-like core effectors among Phytophthora species. Only six putative RxLR-like effectors were shared by the two sequenced downy mildews, highlighting the fast and largely independent evolution of two of the three major downy mildew lineages. This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic. CONCLUSIONS The genome resource will be useful for developing markers for monitoring the pathogen population and might provide the basis for new approaches to fight Phytophthora and downy mildew pathogens by targeting core pathogenicity effectors.
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Affiliation(s)
- Rahul Sharma
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany. .,Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany.
| | - Xiaojuan Xia
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany.
| | - Liliana M Cano
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK. .,Present address: Department of Plant Pathology, North Carolina State University Raleigh, Raleigh, NC, 27695, USA.
| | | | - Eric Kemen
- Max Planck Institute for Plant Breeding Research, Carl von Linne´ Weg 10, Cologne, 50829, Germany.
| | - Howard Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA.
| | - Stan Oome
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands.
| | - Christine Sambles
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
| | - D Johan van den Hoogen
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, NL-6708PB, Wageningen, The Netherlands.
| | - Miloslav Kitner
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 11, 78371, Olomouc, Czech Republic.
| | - Joël Klein
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands.
| | - Harold J G Meijer
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, NL-6708PB, Wageningen, The Netherlands.
| | - Otmar Spring
- University of Hohenheim, Institute of Botany 210, D-70593, Stuttgart, Germany.
| | - Joe Win
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Reinhard Zipper
- University of Hohenheim, Institute of Botany 210, D-70593, Stuttgart, Germany.
| | - Helge B Bode
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, NL-6708PB, Wageningen, The Netherlands.
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
| | | | - David J Studholme
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
| | - Guido Van den Ackerveken
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands.
| | - Marco Thines
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany. .,Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Integrative Fungal Research (IPF), Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325, Frankfurt am Main, Germany.
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175
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Yamamoto T, Tsunematsu Y, Noguchi H, Hotta K, Watanabe K. Elucidation of Pyranonigrin Biosynthetic Pathway Reveals a Mode of Tetramic Acid, Fused γ-Pyrone, and exo-Methylene Formation. Org Lett 2015; 17:4992-5. [DOI: 10.1021/acs.orglett.5b02435] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tsuyoshi Yamamoto
- Department
of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Yuta Tsunematsu
- Department
of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Hiroshi Noguchi
- Department
of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kinya Hotta
- School
of Biosciences, The University of Nottingham Malaysia Campus, Semenyih, Selangor Darul Ehsan 43500, Malaysia
| | - Kenji Watanabe
- Department
of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
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176
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Conserved biosynthetic pathways for phosalacine, bialaphos and newly discovered phosphonic acid natural products. J Antibiot (Tokyo) 2015; 69:15-25. [PMID: 26328935 PMCID: PMC4731264 DOI: 10.1038/ja.2015.77] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/14/2015] [Accepted: 06/15/2015] [Indexed: 12/03/2022]
Abstract
Natural products containing phosphonic or phosphinic acid functionalities often display potent biological activities with applications in medicine and agriculture. The herbicide phosphinothricin-tripeptide (PTT) was the first phosphinate natural product discovered, yet despite numerous studies, questions remain surrounding key transformations required for its biosynthesis. In particular, the enzymology required to convert phosphonoformate to carboxyphosphonoenolpyruvate and the mechanisms underlying phosphorus-methylation remain poorly understood. In addition, the model for NRPS assembly of the intact tripeptide product has undergone numerous revisions that have yet to be experimentally tested. To further investigate the biosynthesis of this unusual natural product, we completely sequenced the PTT biosynthetic locus from Streptomyces hygroscopicus and compared it to the orthologous cluster from Streptomyces viridochromogenes. We also sequenced and analysed the closely related phosalacine (PAL) biosynthetic locus from Kitasatospora phosalacinea. Using data drawn from the comparative analysis of the PTT and PAL pathways, we also evaluate three related recently discovered phosphonate biosynthetic loci from Streptomyces sviceus, Streptomyces sp. WM6386 and Frankia alni. Our observations address long-standing biosynthetic questions related to PTT and PAL production and suggest that additional members of this pharmacologically important class await discovery.
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177
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Rui Z, Huang W, Xu F, Han M, Liu X, Lin S, Zhang W. Sparsomycin Biosynthesis Highlights Unusual Module Architecture and Processing Mechanism in Non-ribosomal Peptide Synthetase. ACS Chem Biol 2015; 10:1765-9. [PMID: 26046698 DOI: 10.1021/acschembio.5b00284] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sparsomycin is a model protein synthesis inhibitor that blocks peptide bond formation by binding to the large ribosome subunit. It is a unique dipeptidyl alcohol, consisting of a uracil acrylic acid moiety and a monooxo-dithioacetal group. To elucidate the biosynthetic logic of sparsomycin, a biosynthetic gene cluster for sparsomycin was identified from the producer Streptomyces sparsogenes by genome mining, targeted gene mutations, and heterologous expression. Both the genetic and enzymatic studies revealed a minimum set of non-ribosomal peptide synthetases needed for generating the dipeptidyl alcohol scaffold of sparsomycin, featuring unusual mechanisms in dipeptidyl assembly and off-loading.
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Affiliation(s)
- Zhe Rui
- Department
of Chemical and Biomolecular Engineering, University of California, 201 Gilman Hall, MC 1462, Berkeley, California 94720, United States
| | - Wei Huang
- Department
of Chemical and Biomolecular Engineering, University of California, 201 Gilman Hall, MC 1462, Berkeley, California 94720, United States
| | - Fei Xu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Mo Han
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xinyu Liu
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Wenjun Zhang
- Department
of Chemical and Biomolecular Engineering, University of California, 201 Gilman Hall, MC 1462, Berkeley, California 94720, United States
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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178
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Vitroprocines, new antibiotics against Acinetobacter baumannii, discovered from marine Vibrio sp. QWI-06 using mass-spectrometry-based metabolomics approach. Sci Rep 2015; 5:12856. [PMID: 26238555 PMCID: PMC4523872 DOI: 10.1038/srep12856] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/08/2015] [Indexed: 01/09/2023] Open
Abstract
A robust and convenient research strategy integrating state-of-the-art analytical techniques is needed to efficiently discover novel compounds from marine microbial resources. In this study, we identified a series of amino-polyketide derivatives, vitroprocines A-J, from the marine bacterium Vibrio sp. QWI-06 by an integrated approach using imaging mass spectroscopy and molecular networking, as well as conventional bioactivity-guided fractionation and isolation. The structure-activity relationship of vitroprocines against Acinetobacter baumannii is proposed. In addition, feeding experiments with 13C-labeled precursors indicated that a pyridoxal 5′-phosphate-dependent mechanism is involved in the biosynthesis of vitroprocines. Elucidation of amino-polyketide derivatives from a species of marine bacteria for the first time demonstrates the potential of this integrated metabolomics approach to uncover marine bacterial biodiversity.
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179
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Liu L, Zhang J, Chen C, Teng J, Wang C, Luo D. Structure and biosynthesis of fumosorinone, a new protein tyrosine phosphatase 1B inhibitor firstly isolated from the entomogenous fungus Isaria fumosorosea. Fungal Genet Biol 2015; 81:191-200. [DOI: 10.1016/j.fgb.2015.03.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 03/26/2015] [Accepted: 03/30/2015] [Indexed: 11/24/2022]
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180
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Matilla MA, Leeper FJ, Salmond GPC. Biosynthesis of the antifungal haterumalide, oocydin A, in Serratia, and its regulation by quorum sensing, RpoS and Hfq. Environ Microbiol 2015; 17:2993-3008. [PMID: 25753587 PMCID: PMC4552970 DOI: 10.1111/1462-2920.12839] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 02/02/2023]
Abstract
Polyketides represent an important class of bioactive natural products with a broad range of biological activities. We identified recently a large trans-acyltransferase (AT) polyketide synthase gene cluster responsible for the biosynthesis of the antifungal, anti-oomycete and antitumor haterumalide, oocydin A (ooc). Using genome sequencing and comparative genomics, we show that the ooc gene cluster is widespread within biocontrol and phytopathogenic strains of the enterobacteria, Serratia and Dickeya. The analysis of in frame deletion mutants confirmed the role of a hydroxymethylglutaryl-coenzyme A synthase cassette, three flavin-dependent tailoring enzymes, a free-standing acyl carrier protein and two hypothetical proteins in oocydin A biosynthesis. The requirement of the three trans-acting AT domains for the biosynthesis of the macrolide was also demonstrated. Expression of the ooc gene cluster was shown to be positively regulated by an N-acyl-L-homoserine lactone-based quorum sensing system, but operating in a strain-dependent manner. At a post-transcriptional level, the RNA chaperone, Hfq, plays a key role in oocydin A biosynthesis. The Hfq-dependent regulation is partially mediated by the stationary phase sigma factor, RpoS, which was also shown to positively regulate the synthesis of the macrolide. Our results reveal differential regulation of the divergently transcribed ooc transcriptional units, highlighting the complexity of oocydin A production.
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Affiliation(s)
- Miguel A Matilla
- Department of Biochemistry, University of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK
| | - Finian J Leeper
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW, UK
| | - George P C Salmond
- Department of Biochemistry, University of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK,*For correspondence. E-mail ; Tel. +44 (0)1223 333650; Fax +44 (0)1223 766108
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181
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Barajas JF, Phelan RM, Schaub AJ, Kliewer JT, Kelly PJ, Jackson DR, Luo R, Keasling JD, Tsai SC. Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols. ACTA ACUST UNITED AC 2015; 22:1018-29. [PMID: 26235055 DOI: 10.1016/j.chembiol.2015.06.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/05/2015] [Accepted: 06/22/2015] [Indexed: 01/22/2023]
Abstract
The terminal reductase (R) domain from the non-ribosomal peptide synthetase (NRPS) module MxaA in Stigmatella aurantiaca Sga15 catalyzes a non-processive four-electron reduction to produce the myxalamide family of secondary metabolites. Despite widespread use in nature, a lack of structural and mechanistic information concerning reductive release from polyketide synthase (PKS) and NRPS assembly lines principally limits our ability to redesign R domains with altered or improved activity. Here we report crystal structures for MxaA R, both in the absence and, for the first time, in the presence of the NADPH cofactor. Molecular dynamics simulations were employed to provide a deeper understanding of this domain and further identify residues critical for structural integrity, substrate binding, and catalysis. Aggregate computational and structural findings provided a basis for mechanistic investigations and, in the process, delivered a rationally altered variant with improved activity toward highly reduced substrates.
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Affiliation(s)
- Jesus F Barajas
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Ryan M Phelan
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94270, USA
| | - Andrew J Schaub
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Jaclyn T Kliewer
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Peter J Kelly
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - David R Jackson
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Jay D Keasling
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94270, USA; Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.
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182
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Huang S, Tabudravu J, Elsayed SS, Travert J, Peace D, Tong MH, Kyeremeh K, Kelly SM, Trembleau L, Ebel R, Jaspars M, Yu Y, Deng H. Discovery of a Single Monooxygenase that Catalyzes Carbamate Formation and Ring Contraction in the Biosynthesis of the Legonmycins. Angew Chem Int Ed Engl 2015. [PMID: 26206556 DOI: 10.1002/anie.201502902] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Pyrrolizidine alkaloids (PAs) are a group of natural products with important biological activities. The discovery and characterization of the multifunctional FAD-dependent enzyme LgnC is now described. The enzyme is shown to convert indolizidine intermediates into pyrrolizidines through an unusual ring expansion/contraction mechanism, and catalyze the biosynthesis of new bacterial PAs, the so-called legonmycins. By genome-driven analysis, heterologous expression, and gene inactivation, the legonmycins were also shown to originate from non-ribosomal peptide synthetases (NRPSs). The biosynthetic origin of bacterial PAs has thus been disclosed for the first time.
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Affiliation(s)
- Sheng Huang
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071 (P.R. China)
| | - Jioji Tabudravu
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | | | - Jeanne Travert
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | - Doe Peace
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | - Ming Him Tong
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | - Kwaku Kyeremeh
- Department of Chemistry, University of Ghana, P.O. Box LG56, Legon-Accra (Ghana)
| | - Sharon M Kelly
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ (UK)
| | | | - Rainer Ebel
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | - Marcel Jaspars
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071 (P.R. China).
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen (UK).
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183
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Huang S, Tabudravu J, Elsayed SS, Travert J, Peace D, Tong MH, Kyeremeh K, Kelly SM, Trembleau L, Ebel R, Jaspars M, Yu Y, Deng H. Discovery of a Single Monooxygenase that Catalyzes Carbamate Formation and Ring Contraction in the Biosynthesis of the Legonmycins. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502902] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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184
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Unusual Biosynthesis and Structure of Locillomycins from Bacillus subtilis 916. Appl Environ Microbiol 2015; 81:6601-9. [PMID: 26162886 DOI: 10.1128/aem.01639-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 07/08/2015] [Indexed: 12/19/2022] Open
Abstract
Three families of Bacillus cyclic lipopeptides--surfactins, iturins, and fengycins--have well-recognized potential uses in biotechnology and biopharmaceutical applications. This study outlines the isolation and characterization of locillomycins, a novel family of cyclic lipopeptides produced by Bacillus subtilis 916. Elucidation of the locillomycin structure revealed several molecular features not observed in other Bacillus lipopeptides, including a unique nonapeptide sequence and macrocyclization. Locillomycins are active against bacteria and viruses. Biochemical analysis and gene deletion studies have supported the assignment of a 38-kb gene cluster as the locillomycin biosynthetic gene cluster. Interestingly, this gene cluster encodes 4 proteins (LocA, LocB, LocC, and LocD) that form a hexamodular nonribosomal peptide synthetase to biosynthesize cyclic nonapeptides. Genome analysis and the chemical structures of the end products indicated that the biosynthetic pathway exhibits two distinct features: (i) a nonlinear hexamodular assembly line, with three modules in the middle utilized twice and the first and last two modules used only once and (ii) several domains that are skipped or optionally selected.
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185
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Keller L, Plaza A, Dubiella C, Groll M, Kaiser M, Müller R. Macyranones: Structure, Biosynthesis, and Binding Mode of an Unprecedented Epoxyketone that Targets the 20S Proteasome. J Am Chem Soc 2015; 137:8121-30. [PMID: 26050527 DOI: 10.1021/jacs.5b03833] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In our screening efforts to identify unique scaffolds from myxobacteria for the drug discovery process, we used LC-SPE-NMR-MS techniques to isolate six linear peptides, termed macyranone A-F, from Cystobacter fuscus MCy9118. The macyranones are characterized by a rare 2-methylmalonamide moiety and an α-amino ketone fragment including an α',β'-epoxyketone in macyranone A. Gene disruption experiments confirmed the biosynthetic gene cluster of the macyranones as PKS/NRPS hybrid. Detailed in silico and phylogenetic analysis unraveled that the biosynthesis involves two conspicuous amide bond formations accomplished by an amidotransferase and a unique condensation domain. The gene cluster provides further insights into the formation of the powerful epoxyketone residue involving an acyl-CoA dehydrogenase and an unconventional free-standing thioesterase. Macyranone A was found to inhibit the chymotrypsin-like activity of the yeast 20S proteasome with an IC50 of 5.9 nM and the human constitutive proteasome and immunoproteasome with IC50 values of 21 and 15 nM, respectively. The β5 subunit of the 20S proteasome was characterized as target by X-ray crystallography revealing an irreversible binding mode similar to the natural product epoxomicin. The presence of the methylmalonamide residue facilitates the stabilization of macyranone A with the active β5 subunit of the proteasome. Macyranone A exhibits a potent inhibitory effect against the parasites Trypanosoma brucei rhodesiense and Leishmania donovani with IC50 values of 1.55 and 0.22 μM, respectively.
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Affiliation(s)
- Lena Keller
- †Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.,∥German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig 38124, Germany
| | - Alberto Plaza
- †Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.,∥German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig 38124, Germany
| | - Christian Dubiella
- ⊥Center for Integrated Protein Science Munich (CIPSM), Department für Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Michael Groll
- ⊥Center for Integrated Protein Science Munich (CIPSM), Department für Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Marcel Kaiser
- §Swiss Tropical and Public Health Institute (Swiss TPH), Socinstraße 57, CH-4002 Basel, Switzerland.,‡University of Basel, Petersplatz 1, CH-4003 Basel, Switzerland
| | - Rolf Müller
- †Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.,∥German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig 38124, Germany
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186
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Zhou Y, Prediger P, Dias LC, Murphy AC, Leadlay PF. Macrodiolide formation by the thioesterase of a modular polyketide synthase. Angew Chem Int Ed Engl 2015; 54:5232-5. [PMID: 25753953 PMCID: PMC4471547 DOI: 10.1002/anie.201500401] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/04/2015] [Indexed: 11/10/2022]
Abstract
Elaiophylin is an unusual C2 -symmetric antibiotic macrodiolide produced on a bacterial modular polyketide synthase assembly line. To probe the mechanism and selectivity of diolide formation, we sought to reconstitute ring formation in vitro by using a non-natural substrate. Incubation of recombinant elaiophylin thioesterase/cyclase with a synthetic pentaketide analogue of the presumed monomeric polyketide precursor of elaiophylin, specifically its N-acetylcysteamine thioester, produced a novel 16-membered C2 -symmetric macrodiolide. A linear dimeric thioester is an intermediate in ring formation, which indicates iterative use of the thioesterase active site in ligation and subsequent cyclization. Furthermore, the elaiophylin thioesterase acts on a mixture of pentaketide and tetraketide thioesters to give both the symmetric decaketide diolide and the novel asymmetric hybrid nonaketide diolide. Such thioesterases have potential as tools for the in vitro construction of novel diolides.
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Affiliation(s)
- Yongjun Zhou
- Department of Biochemistry, University of Cambridge80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Patrícia Prediger
- Institute of Chemistry, State University of Campinas, UNICAMPC.P. 6154, CEP 13084-971, Campinas SP (Brazil)
| | - Luiz Carlos Dias
- Institute of Chemistry, State University of Campinas, UNICAMPC.P. 6154, CEP 13084-971, Campinas SP (Brazil)
| | - Annabel C Murphy
- Department of Biochemistry, University of Cambridge80 Tennis Court Road, Cambridge CB2 1GA (UK)
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge80 Tennis Court Road, Cambridge CB2 1GA (UK)
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187
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Nakamura H, Wang JX, Balskus EP. Assembly line termination in cylindrocyclophane biosynthesis: discovery of an editing type II thioesterase domain in a type I polyketide synthase. Chem Sci 2015; 6:3816-3822. [PMID: 29218151 PMCID: PMC5707447 DOI: 10.1039/c4sc03132f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 04/11/2015] [Indexed: 01/18/2023] Open
Abstract
Investigation of cylindrocyclophane biosynthesis reveals a C-terminal thioesterase domain involved in PKS assembly line editing, not termination.
The termination step is an important source of structural diversity in polyketide biosynthesis. Most type I polyketide synthase (PKS) assembly lines are terminated by a thioesterase (TE) domain located at the C-terminus of the final module, while other PKS assembly lines lack a terminal TE domain and are instead terminated by a separate enzyme in trans. In cylindrocyclophane biosynthesis, the type I modular PKS assembly line is terminated by a freestanding type III PKS (CylI). Unexpectedly, the final module of the type I PKS (CylH) also possesses a C-terminal TE domain. Unlike typical type I PKSs, the CylH TE domain does not influence assembly line termination by CylI in vitro. Instead, this domain phylogenetically resembles a type II TE and possesses activity consistent with an editing function. This finding may shed light on the evolution of unusual PKS termination logic. In addition, the presence of related type II TE domains in many cryptic type I PKS and nonribosomal peptide synthetase (NRPS) assembly lines has implications for pathway annotation, product prediction, and engineering.
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Affiliation(s)
- H Nakamura
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , USA .
| | - J X Wang
- Small Molecule Mass Spectrometry Facility , FAS Division of Science , Cambridge , Massachusetts 02138 , USA
| | - E P Balskus
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , USA .
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188
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Gressler M, Hortschansky P, Geib E, Brock M. A new high-performance heterologous fungal expression system based on regulatory elements from the Aspergillus terreus terrein gene cluster. Front Microbiol 2015; 6:184. [PMID: 25852654 PMCID: PMC4360782 DOI: 10.3389/fmicb.2015.00184] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/19/2015] [Indexed: 11/13/2022] Open
Abstract
Recently, the Aspergillus terreus terrein gene cluster was identified and selected for development of a new heterologous expression system. The cluster encodes the specific transcription factor TerR that is indispensable for terrein cluster induction. To identify TerR binding sites, different recombinant versions of the TerR DNA-binding domain were analyzed for specific motif recognition. The high affinity consensus motif TCGGHHWYHCGGH was identified from genes required for terrein production and binding site mutations confirmed their essential contribution to gene expression in A. terreus. A combination of TerR with its terA target promoter was tested as recombinant expression system in the heterologous host Aspergillus niger. TerR mediated target promoter activation was directly dependent on its transcription level. Therefore, terR was expressed under control of the regulatable amylase promoter PamyB and the resulting activation of the terA target promoter was compared with activation levels obtained from direct expression of reporters from the strong gpdA control promoter. Here, the coupled system outcompeted the direct expression system. When the coupled system was used for heterologous polyketide synthase expression high metabolite levels were produced. Additionally, expression of the Aspergillus nidulans polyketide synthase gene orsA revealed lecanoric acid rather than orsellinic acid as major polyketide synthase product. Domain swapping experiments assigned this depside formation from orsellinic acid to the OrsA thioesterase domain. These experiments confirm the suitability of the expression system especially for high-level metabolite production in heterologous hosts.
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Affiliation(s)
- Markus Gressler
- Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute Jena, Germany
| | - Peter Hortschansky
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute Jena, Germany
| | - Elena Geib
- Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute Jena, Germany
| | - Matthias Brock
- Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute Jena, Germany ; Institute for Microbiology, Friedrich Schiller University Jena, Germany
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189
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Zhou Y, Prediger P, Dias LC, Murphy AC, Leadlay PF. Macrodiolide Formation by the Thioesterase of a Modular Polyketide Synthase. ACTA ACUST UNITED AC 2015; 127:5321-5324. [PMID: 26300568 PMCID: PMC4535664 DOI: 10.1002/ange.201500401] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/04/2015] [Indexed: 01/24/2023]
Abstract
Elaiophylin is an unusual C2-symmetric antibiotic macrodiolide produced on a bacterial modular polyketide synthase assembly line. To probe the mechanism and selectivity of diolide formation, we sought to reconstitute ring formation in vitro by using a non-natural substrate. Incubation of recombinant elaiophylin thioesterase/cyclase with a synthetic pentaketide analogue of the presumed monomeric polyketide precursor of elaiophylin, specifically its N-acetylcysteamine thioester, produced a novel 16-membered C2-symmetric macrodiolide. A linear dimeric thioester is an intermediate in ring formation, which indicates iterative use of the thioesterase active site in ligation and subsequent cyclization. Furthermore, the elaiophylin thioesterase acts on a mixture of pentaketide and tetraketide thioesters to give both the symmetric decaketide diolide and the novel asymmetric hybrid nonaketide diolide. Such thioesterases have potential as tools for the in vitro construction of novel diolides.
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Affiliation(s)
- Yongjun Zhou
- Department of Biochemistry, University of Cambridge 80 Tennis Court Road, Cambridge CB2 1GA (UK) E-mail:
| | - Patrícia Prediger
- Institute of Chemistry, State University of Campinas UNICAMP, C.P. 6154, CEP 13084-971, Campinas SP (Brazil)
| | - Luiz Carlos Dias
- Institute of Chemistry, State University of Campinas UNICAMP, C.P. 6154, CEP 13084-971, Campinas SP (Brazil)
| | - Annabel C Murphy
- Department of Biochemistry, University of Cambridge 80 Tennis Court Road, Cambridge CB2 1GA (UK) E-mail:
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge 80 Tennis Court Road, Cambridge CB2 1GA (UK) E-mail:
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190
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Liu C, Zhu J, Li Y, Zhang J, Lu C, Wang H, Shen Y. In Vitro Reconstitution of a PKS Pathway for the Biosynthesis of Galbonolides inStreptomycessp. LZ35. Chembiochem 2015; 16:998-1007. [DOI: 10.1002/cbic.201500017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Indexed: 01/13/2023]
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191
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Anyaogu DC, Mortensen UH. Heterologous production of fungal secondary metabolites in Aspergilli. Front Microbiol 2015; 6:77. [PMID: 25713568 PMCID: PMC4322707 DOI: 10.3389/fmicb.2015.00077] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 01/21/2015] [Indexed: 12/24/2022] Open
Abstract
Fungal natural products comprise a wide range of compounds. Some are medically attractive as drugs and drug leads, some are used as food additives, while others are harmful mycotoxins. In recent years the genome sequence of several fungi has become available providing genetic information of a large number of putative biosynthetic pathways. However, compound discovery is difficult as the genes required for the production of the compounds often are silent or barely expressed under laboratory conditions. Furthermore, the lack of available tools for genetic manipulation of most fungal species hinders pathway discovery. Heterologous expression of the biosynthetic pathway in model systems or cell factories facilitates product discovery, elucidation, and production. This review summarizes the recent strategies for heterologous expression of fungal biosynthetic pathways in Aspergilli.
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Affiliation(s)
- Diana Chinyere Anyaogu
- Section for Eukaryotic Biotechnology, Department of Systems Biology, Technical University of Denmark Kongens Lyngby, Denmark
| | - Uffe Hasbro Mortensen
- Section for Eukaryotic Biotechnology, Department of Systems Biology, Technical University of Denmark Kongens Lyngby, Denmark
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192
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Complete genome sequence and transcriptomics analyses reveal pigment biosynthesis and regulatory mechanisms in an industrial strain, Monascus purpureus YY-1. Sci Rep 2015; 5:8331. [PMID: 25660389 PMCID: PMC4321180 DOI: 10.1038/srep08331] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 01/19/2015] [Indexed: 12/20/2022] Open
Abstract
Monascus has been used to produce natural colorants and food supplements for more than one thousand years, and approximately more than one billion people eat Monascus-fermented products during their daily life. In this study, using next-generation sequencing and optical mapping approaches, a 24.1-Mb complete genome of an industrial strain, Monascus purpureus YY-1, was obtained. This genome consists of eight chromosomes and 7,491 genes. Phylogenetic analysis at the genome level provides convincing evidence for the evolutionary position of M. purpureus. We provide the first comprehensive prediction of the biosynthetic pathway for Monascus pigment. Comparative genomic analyses show that the genome of M. purpureus is 13.6–40% smaller than those of closely related filamentous fungi and has undergone significant gene losses, most of which likely occurred during its specialized adaptation to starch-based foods. Comparative transcriptome analysis reveals that carbon starvation stress, resulting from the use of relatively low-quality carbon sources, contributes to the high yield of pigments by repressing central carbon metabolism and augmenting the acetyl-CoA pool. Our work provides important insights into the evolution of this economically important fungus and lays a foundation for future genetic manipulation and engineering of this strain.
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193
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The Kolumbo submarine volcano of Santorini island is a large pool of bacterial strains with antimicrobial activity. Arch Microbiol 2015; 197:539-52. [PMID: 25627249 DOI: 10.1007/s00203-015-1086-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/13/2015] [Accepted: 01/16/2015] [Indexed: 10/24/2022]
Abstract
Microbes in hydrothermal vents with their unique secondary metabolism may represent an untapped potential source of new natural products. In this study, samples were collected from the hydrothermal field of Kolumbo submarine volcano in the Aegean Sea, in order to isolate bacteria with antimicrobial activity. Eight hundred and thirty-two aerobic heterotrophic bacteria were isolated and then differentiated through BOX-PCR analysis at the strain level into 230 genomic fingerprints, which were screened against 13 different type strains (pathogenic and nonpathogenic) of Gram-positive, Gram-negative bacteria and fungi. Forty-two out of 176 bioactive-producing genotypes (76 %) exhibited antimicrobial activity against at least four different type strains and were selected for 16S rDNA sequencing and screening for nonribosomal peptide (NRPS) and polyketide (PKS) synthases genes. The isolates were assigned to genus Bacillus and Proteobacteria, and 20 strains harbored either NRPS, PKS type I or both genes. This is the first report on the diversity of culturable mesophilic bacteria associated with antimicrobial activity from Kolumbo area; the extremely high proportion of antimicrobial-producing strains suggested that this unique environment may represent a potential reservoir of novel bioactive compounds.
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194
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Tsakos M, Schaffert ES, Clement LL, Villadsen NL, Poulsen TB. Ester coupling reactions – an enduring challenge in the chemical synthesis of bioactive natural products. Nat Prod Rep 2015; 32:605-32. [DOI: 10.1039/c4np00106k] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this review we investigate the use of complex ester fragment couplings within natural product total syntheses. Using examples from the literature up to 2014 we illustrate the state-of-the-art as well as the challenges within this area of organic synthesis.
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Affiliation(s)
- Michail Tsakos
- Chemical Biology Laboratory
- Department of Chemistry
- Aarhus University
- Aarhus C
- Denmark
| | - Eva S. Schaffert
- Chemical Biology Laboratory
- Department of Chemistry
- Aarhus University
- Aarhus C
- Denmark
| | - Lise L. Clement
- Chemical Biology Laboratory
- Department of Chemistry
- Aarhus University
- Aarhus C
- Denmark
| | - Nikolaj L. Villadsen
- Chemical Biology Laboratory
- Department of Chemistry
- Aarhus University
- Aarhus C
- Denmark
| | - Thomas B. Poulsen
- Chemical Biology Laboratory
- Department of Chemistry
- Aarhus University
- Aarhus C
- Denmark
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195
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Liu Q, Wu K, Cheng Y, Lu L, Xiao E, Zhang Y, Deng Z, Liu T. Engineering an iterative polyketide pathway in Escherichia coli results in single-form alkene and alkane overproduction. Metab Eng 2014; 28:82-90. [PMID: 25536488 DOI: 10.1016/j.ymben.2014.12.004] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 12/07/2014] [Accepted: 12/12/2014] [Indexed: 11/28/2022]
Abstract
Alkanes and alkenes are ideal biofuels, due to their high energy content and ability to be safely transported. To date, fatty acid-derived pathways for alkane and alkene bioproduction have been thoroughly explored. In this study, we engineered the pathway of the iterative Type I polyketide synthase (PKS) SgcE with the cognate thioesterase (TE) SgcE10 in Escherichia coli, with the goal of overproducing pentadecaheptaene (PDH) followed by its hydrogenation to pentadecane (PD). Based on initial in vitro titration assays, we learned that PDH production is strongly dependent on the SgcE10:SgcE ratio. Thus, we engineered a high-yield E. coli strain by fine-tuning SgcE10 expression via synthetic promoters. We analyzed engineered E. coli strains using a modified multiple reactions monitoring mass spectrometry (MRM-MS)-based targeted proteomic approach, using a chimeric SgcE10 and SgcE fusion construct to gain insight into expression levels of the two proteins. Lastly, through fed-batch fermentation followed by flow chemical hydrogenation, we obtained a PD yield of nearly 140mg/L in single-alkane form. Thus, we not only employed a metabolic engineering approach to the iterative polyketide pathway, we highlighted the potential of PKS shunt products to play a role in the production of single-form and high-value chemicals.
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Affiliation(s)
- Qian Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Kaiyue Wu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; J1 Biotech, Co. Ltd., Wuhan 430075, China
| | - Yongbo Cheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Lei Lu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Erting Xiao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Yuchen Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China.
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196
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Masschelein J, Clauwers C, Awodi UR, Stalmans K, Vermaelen W, Lescrinier E, Aertsen A, Michiels C, Challis GL, Lavigne R. A combination of polyunsaturated fatty acid, nonribosomal peptide and polyketide biosynthetic machinery is used to assemble the zeamine antibiotics. Chem Sci 2014; 6:923-929. [PMID: 29560178 PMCID: PMC5811116 DOI: 10.1039/c4sc01927j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 10/15/2014] [Indexed: 11/21/2022] Open
Abstract
The zeamines are a unique group of antibiotics produced by Serratia plymuthica RVH1 that contain variable hybrid peptide-polyketide moieties connected to a common pentaamino-hydroxyalkyl chain. They exhibit potent activity against a broad spectrum of Gram-positive and Gram-negative bacteria. Here we report a combination of targeted gene deletions, high resolution LC-MS(/MS) analyses, in vitro biochemical assays and feeding studies that define the functions of several key zeamine biosynthetic enzymes. The pentaamino-hydroxyalkyl chain is assembled by an iterative multienzyme complex (Zmn10-13) that bears a close resemblance to polyunsaturated fatty acid synthases. Zmn14 was shown to function as an NADH-dependent thioester reductase and is proposed to release a tetraamino-hydroxyalkyl thioester from the acyl carrier protein domain of Zmn10 as an aldehyde. Despite the intrinsic ability of Zmn14 to catalyze further reduction of aldehydes to alcohols, the initially-formed aldehyde intermediate is proposed to undergo preferential transamination to produce zeamine II. In a parallel pathway, hexapeptide-monoketide and hexapeptide-diketide thioesters are generated by a hybrid nonribosomal peptide synthetase-polyketide synthase multienzyme complex (Zmn16-18) and subsequently conjugated to zeamine II by a stand-alone condensing enzyme (Zmn19). Structures for the resulting prezeamines were elucidated using a combination of high resolution LC-MS/MS and 1- and 2-D NMR spectroscopic analyses. The prezeamines are hypothesized to be precursors of the previously-identified zeamines, which are generated by the action of Zmn22, an acylpeptide hydrolase that specifically cleaves the N-terminal pentapeptide of the prezeamines in a post-assembly processing step. Thus, the zeamine antibiotics are assembled by a unique combination of nonribosomal peptide synthetase, type I modular polyketide synthase and polyunsaturated fatty acid synthase-like biosynthetic machinery.
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Affiliation(s)
- Joleen Masschelein
- Laboratory of Gene Technology , KU Leuven , Kasteelpark Arenberg 21-box 2462 , B-3001 Heverlee , Belgium . ; ; Tel: +32 (0) 16 37 95 24.,Laboratory of Food Microbiology , KU Leuven , Kasteelpark Arenberg 22 , B-3001 Heverlee , Belgium
| | - Charlien Clauwers
- Laboratory of Gene Technology , KU Leuven , Kasteelpark Arenberg 21-box 2462 , B-3001 Heverlee , Belgium . ; ; Tel: +32 (0) 16 37 95 24.,Laboratory of Food Microbiology , KU Leuven , Kasteelpark Arenberg 22 , B-3001 Heverlee , Belgium
| | - Ufedo R Awodi
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , UK . ; ; Tel: +44 (0) 2476 574024
| | - Karen Stalmans
- Laboratory of Gene Technology , KU Leuven , Kasteelpark Arenberg 21-box 2462 , B-3001 Heverlee , Belgium . ; ; Tel: +32 (0) 16 37 95 24
| | - Wesley Vermaelen
- Laboratory of Gene Technology , KU Leuven , Kasteelpark Arenberg 21-box 2462 , B-3001 Heverlee , Belgium . ; ; Tel: +32 (0) 16 37 95 24
| | - Eveline Lescrinier
- Laboratory of Medicinal Chemistry , Rega Institute for Medical Research , KU Leuven , Minderbroedersstraat 10 , B-3000 Leuven , Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology , KU Leuven , Kasteelpark Arenberg 22 , B-3001 Heverlee , Belgium
| | - Chris Michiels
- Laboratory of Food Microbiology , KU Leuven , Kasteelpark Arenberg 22 , B-3001 Heverlee , Belgium
| | - Gregory L Challis
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , UK . ; ; Tel: +44 (0) 2476 574024
| | - Rob Lavigne
- Laboratory of Gene Technology , KU Leuven , Kasteelpark Arenberg 21-box 2462 , B-3001 Heverlee , Belgium . ; ; Tel: +32 (0) 16 37 95 24
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197
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Haque AS, Patel KD, Deshmukh MV, Chhabra A, Gokhale RS, Sankaranarayanan R. Delineating the reaction mechanism of reductase domains of Nonribosomal Peptide Synthetases from mycobacteria. J Struct Biol 2014; 187:207-214. [PMID: 25108240 DOI: 10.1016/j.jsb.2014.07.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/15/2014] [Accepted: 07/30/2014] [Indexed: 10/24/2022]
Abstract
Substrate binding to enzymes often follows a precise order where catalysis is accomplished through programmed conformational changes. Short-chain dehydrogenase/reductase (SDR) enzymes follow sequential order 'bi-bi' reaction kinetics. The mechanistic study of a SDR homolog, reductase (R) domain, from multifunctional enzymes, e.g. Nonribosomal Peptide Synthetases (NRPSs) and Polyketide Synthases (PKSs) has revealed that it reductively releases 4'-phosphopantetheinyl arm-tethered peptidyl product. We report that the R-domains of NRPSs from Mycobacterium tuberculosis (RNRP) and Mycobacterium smegmatis (RGPL) do not strictly adhere to the obligatory mode of catalysis performed by SDRs, but instead can carry out reductive catalysis of substrate following random bi-bi reaction mechanism as deciphered by NMR and SAXS studies. The crucial conformational change associated with NADPH binding necessary to achieve catalytically competent conformation is also delineated by SAXS studies. Using ITC, we have demonstrated that mutation of catalytic tyrosine to phenylalanine in R-domains results in 3-4-fold decrease in affinity for NADPH and attribute this phenomenon to loss of the noncovalent cation-π interactions present between the tyrosine and nicotinamide ring. We propose that the adaptation to an alternative theme of bi-bi catalytic mechanism enables the R-domains to process the substrates transferred by upstream domains and maintain assembly-line enzymology.
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Affiliation(s)
- Asfarul S Haque
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Ketan D Patel
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Mandar V Deshmukh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Arush Chhabra
- National Institute of Immunology, New Delhi 110067, India
| | - Rajesh S Gokhale
- National Institute of Immunology, New Delhi 110067, India; CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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198
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Spliceostatin hemiketal biosynthesis in Burkholderia spp. is catalyzed by an iron/α-ketoglutarate-dependent dioxygenase. Proc Natl Acad Sci U S A 2014; 111:E3376-85. [PMID: 25097259 DOI: 10.1073/pnas.1408300111] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Spliceostatins are potent spliceosome inhibitors biosynthesized by a hybrid nonribosomal peptide synthetase-polyketide synthase (NRPS-PKS) system of the trans-acyl transferase (AT) type. Burkholderia sp. FERM BP-3421 produces hemiketal spliceostatins, such as FR901464, as well as analogs containing a terminal carboxylic acid. We provide genetic and biochemical evidence for hemiketal biosynthesis by oxidative decarboxylation rather than the previously hypothesized Baeyer-Villiger oxidative release postulated to be catalyzed by a flavin-dependent monooxygenase (FMO) activity internal to the last module of the PKS. Inactivation of Fe(II)/α-ketoglutarate-dependent dioxygenase gene fr9P led to loss of hemiketal congeners, whereas the mutant was still able to produce all major carboxylic acid-type compounds. FMO mutants, on the other hand, produced both hemiketal and carboxylic acid analogs containing an exocyclic methylene instead of an epoxide, indicating that the FMO is involved in epoxidation rather than Baeyer-Villiger oxidation. Moreover, recombinant Fr9P enzyme was shown to catalyze hydroxylation to form β-hydroxy acids, which upon decarboxylation led to hemiketal FR901464. Finally, a third oxygenase activity encoded in the biosynthetic gene cluster, the cytochrome P450 monooxygenase Fr9R, was assigned as a 4-hydroxylase based on gene inactivation results. Identification and deletion of the gene involved in hemiketal formation allowed us to generate a strain--the dioxygenase fr9P(-) mutant--that accumulates only the carboxylic acid-type spliceostatins, which are as potent as the hemiketal analogs, when derivatized to increase cell permeability, but are chemically more stable.
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199
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Wang YY, Ran XX, Chen WB, Liu SP, Zhang XS, Guo YY, Jiang XH, Jiang H, Li YQ. Characterization of type II thioesterases involved in natamycin biosynthesis in Streptomyces chattanoogensis L10. FEBS Lett 2014; 588:3259-64. [PMID: 25064840 DOI: 10.1016/j.febslet.2014.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 07/11/2014] [Accepted: 07/11/2014] [Indexed: 01/11/2023]
Abstract
The known functions of type II thioesterases (TEIIs) in type I polyketide synthases (PKSs) include selecting of starter acyl units, removal of aberrant extender acyl units, releasing of final products, and dehydration of polyketide intermediates. In this study, we characterized two TEIIs (ScnI and PKSIaTEII) from Streptomyces chattanoogensis L10. Deletion of scnI in S. chattanoogensis L10 decreased the natamycin production by about 43%. Both ScnI and PKSIaTEII could remove acyl units from the acyl carrier proteins (ACPs) involved in the natamycin biosynthesis. Our results show that the TEII could play important roles in both the initiation step and the elongation steps of a polyketide biosynthesis; the intracellular TEIIs involved in different biosynthetic pathways could complement each other.
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Affiliation(s)
- Yue-Yue Wang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xin-Xin Ran
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Wei-Bin Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shui-Ping Liu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiao-Sheng Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuan-Yang Guo
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xin-Hang Jiang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Jiang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China,; Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, Zhejiang 310058, China.
| | - Yong-Quan Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China,; Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, Zhejiang 310058, China.
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200
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Li Y, Chen H, Ding Y, Xie Y, Wang H, Cerny RL, Shen Y, Du L. Iterative assembly of two separate polyketide chains by the same single-module bacterial polyketide synthase in the biosynthesis of HSAF. Angew Chem Int Ed Engl 2014; 53:7524-7530. [PMID: 24890524 PMCID: PMC4107061 DOI: 10.1002/anie.201403500] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Indexed: 12/29/2022]
Abstract
Antifungal HSAF (heat-stable antifungal factor, dihydromaltophilin) is a polycyclic tetramate macrolactam from the biocontrol agent Lysobacter enzymogenes. Its biosynthetic gene cluster contains only a single-module polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS), although two separate hexaketide chains are required to assemble the skeleton. To address the unusual biosynthetic mechanism, we expressed the biosynthetic genes in two "clean" strains of Streptomyces and showed the production of HSAF analogues and a polyene tetramate intermediate. We then expressed the PKS module in Escherichia coli and purified the enzyme. Upon incubation of the enzyme with acyl-coenzyme A and reduced nicotinamide adenine dinucleotide phosphate (NADPH), a polyene was detected in the tryptic acyl carrier protein (ACP). Finally, we incubated the polyene-PKS with the NRPS module in the presence of ornithine and adenosine triphosphate (ATP), and we detected the same polyene tetramate as that in Streptomyces transformed with the PKS-NRPS alone. Together, our results provide evidence for an unusual iterative biosynthetic mechanism for bacterial polyketide-peptide natural products.
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Affiliation(s)
- Yaoyao Li
- Key Laboratory of Chemical Biology, School of Pharmaceutical Sciences, Shandong University, Jinan 250100, China
| | - Haotong Chen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Yanjiao Ding
- Key Laboratory of Chemical Biology, School of Pharmaceutical Sciences, Shandong University, Jinan 250100, China
| | - Yunxuan Xie
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Haoxin Wang
- Key Laboratory of Chemical Biology, School of Pharmaceutical Sciences, Shandong University, Jinan 250100, China; State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Ronald L. Cerny
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Yuemao Shen
- Key Laboratory of Chemical Biology, School of Pharmaceutical Sciences, Shandong University, Jinan 250100, China; State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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