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Tirkkonen H, Brown KV, Niemczura M, Faudemer Z, Brown C, Ponomareva LV, Helmy YA, Thorson JS, Nybo SE, Metsä-Ketelä M, Shaaban KA. Engineering BioBricks for Deoxysugar Biosynthesis and Generation of New Tetracenomycins. ACS OMEGA 2023; 8:21237-21253. [PMID: 37332790 PMCID: PMC10269268 DOI: 10.1021/acsomega.3c02460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/18/2023] [Indexed: 06/20/2023]
Abstract
Tetracenomycins and elloramycins are polyketide natural products produced by several actinomycetes that exhibit antibacterial and anticancer activities. They inhibit ribosomal translation by binding in the polypeptide exit channel of the large ribosomal subunit. The tetracenomycins and elloramycins are typified by a shared oxidatively modified linear decaketide core, yet they are distinguished by the extent of O-methylation and the presence of a 2',3',4'-tri-O-methyl-α-l-rhamnose appended at the 8-position of elloramycin. The transfer of the TDP-l-rhamnose donor to the 8-demethyl-tetracenomycin C aglycone acceptor is catalyzed by the promiscuous glycosyltransferase ElmGT. ElmGT exhibits remarkable flexibility toward transfer of many TDP-deoxysugar substrates to 8-demethyltetracenomycin C, including TDP-2,6-dideoxysugars, TDP-2,3,6-trideoxysugars, and methyl-branched deoxysugars in both d- and l-configurations. Previously, we developed an improved host, Streptomyces coelicolor M1146::cos16F4iE, which is a stable integrant harboring the required genes for 8-demethyltetracenomycin C biosynthesis and expression of ElmGT. In this work, we developed BioBricks gene cassettes for the metabolic engineering of deoxysugar biosynthesis in Streptomyces spp. As a proof of concept, we used the BioBricks expression platform to engineer biosynthesis for d-configured TDP-deoxysugars, including known compounds 8-O-d-glucosyl-tetracenomycin C, 8-O-d-olivosyl-tetracenomycin C, 8-O-d-mycarosyl-tetracenomycin C, and 8-O-d-digitoxosyl-tetracenomycin C. In addition, we generated four new tetracenomycins including one modified with a ketosugar, 8-O-4'-keto-d-digitoxosyl-tetracenomycin C, and three modified with 6-deoxysugars, including 8-O-d-fucosyl-tetracenomycin C, 8-O-d-allosyl-tetracenomycin C, and 8-O-d-quinovosyl-tetracenomycin C. Our work demonstrates the feasibility of BioBricks cloning, with the ability to recycle intermediate constructs, for the rapid assembly of diverse carbohydrate pathways and glycodiversification of a variety of natural products.
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Affiliation(s)
- Heli Tirkkonen
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Katelyn V. Brown
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Magdalena Niemczura
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Zélie Faudemer
- Chemistry
and Chemical Engineering Department, SIGMA
Clermont, 63170 Aubière, France
| | - Courtney Brown
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Larissa V. Ponomareva
- Center for Pharmaceutical Research and Innovation,
College
of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Yosra A. Helmy
- Department
of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Jon S. Thorson
- Center for Pharmaceutical Research and Innovation,
College
of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - S. Eric Nybo
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Mikko Metsä-Ketelä
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Khaled A. Shaaban
- Center for Pharmaceutical Research and Innovation,
College
of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
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Yue Z, Wu F, Guo F, Park J, Wang J, Zhang L, Liao D, Li W, Schärer OD, Lei X. Polycarcin V induces DNA-damage response and enables the profiling of DNA-binding proteins. Natl Sci Rev 2022; 9:nwac046. [PMID: 36601137 PMCID: PMC9798893 DOI: 10.1093/nsr/nwac046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/05/2022] [Accepted: 02/10/2022] [Indexed: 01/07/2023] Open
Abstract
To maintain genomic integrity and avoid diseases, the DNA-damage response (DDR) not only detects and repairs DNA lesions, but also contributes to the resistance to DNA-damaging chemotherapeutics. Targeting the DDR plays a significant role in drug discovery using the principle of synthetic lethality. The incomplete current knowledge of the DDR encouraged us to develop new strategies to identify and study its components and pathways. Polycarcin V, belonging to the C-aryl glycoside natural products, is a light-activatable DNA-intercalating agent that causes DNA damage by forming a covalent [2+2] cycloadduct with thymine residue under 365-450 nm of light irradiation in a DNA-sequence-independent manner. Taking advantage of the light-activatable feature and temporal control of DDR, we designed and synthesized polycarcin V-based bifunctional chemical probes, including one that cross-links DNA to DNA-binding protein to explore the DDR induced by polycarcin V and uncover novel DNA-protein interactions. Utilizing this chemical probe and activity-based protein profiling-stable isotope labeling with amino acids in cell culture, we identified 311 DNA-binding protein candidates, including known DDR factors and additional proteins that may be of interest in discovering new biology. We validated our approach by showing that our probe could specifically cross-link proteins involved in nucleotide excision repair (NER) that repair bulky DNA adducts. Our studies showed that the [2+2] cycloadduct formed by polycarcin V could indeed be repaired by NER in vivo. As a DNA-damaging agent, polycarcin V or its drug-like derivative plus blue light showed promising properties for psoriasis treatment, suggesting that it may itself hold promise for clinic applications.
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Affiliation(s)
| | | | | | - Jiyeong Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Jin Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, China
| | - Liyun Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, China
| | - Daohong Liao
- Jiangsu JITRI Molecular Engineering Inst. Co., Ltd., Suzhou 215500, China
| | - Wenyang Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, China
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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Kong L, Wang Q, Yang W, Shen J, Li Y, Zheng X, Wang L, Chu Y, Deng Z, Chooi YH, You D. Three Recently Diverging Duplicated Methyltransferases Exhibit Substrate-Dependent Regioselectivity Essential for Xantholipin Biosynthesis. ACS Chem Biol 2020; 15:2107-2115. [PMID: 32649177 DOI: 10.1021/acschembio.0c00296] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Polycyclic xanthones are characterized by highly oxygenated, angular hexacyclic frameworks and exhibit diverse biological activities. Although many of them have been isolated and chemically synthesized, the detailed biosynthetic machinery awaits discovery. Recently, xanthone construction in the xantholipin (1) pathway was shown to involve cryptic demethoxylation. This suggested a rationale for the existence of three O-methyltransferase (OMT) genes in the gene cluster, although there are only two O-methyl groups in the structure of 1. Here, in vivo and in vitro analysis have been used to show that the three paralogous OMTs, XanM1-M3, introduce individual methyl groups at specific points in the biosynthetic pathway. Each OMT can to some extent take over the role of the other OMTs, although they exhibit highly substrate-dependent regiospecificity. In addition, phylogenetic analysis suggests their evolution from a common ancestor. Four putative ancestral proteins were constructed, and one of them performed all the functions of XanM1-M3, while the others possessed more limited catalytic functions. The results suggest that a promiscuous common ancestor may have been able to catalyze all three reactions prior to gene duplication and functional divergence. The characterization of XanM1-M3 expands the enzyme inventory for polycyclic xanthone biosynthesis and suggests novel directed evolution approaches to diversifying natural product pathways.
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Affiliation(s)
- Lingxin Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Qing Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Weinan Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jufang Shen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yan Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xiaoqing Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Lu Wang
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610052, China
| | - Yiwen Chu
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610052, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yit-Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
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Enabling techniques in the search for new antibiotics: Combinatorial biosynthesis of sugar-containing antibiotics. Biochem Pharmacol 2017; 134:56-73. [DOI: 10.1016/j.bcp.2016.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/24/2016] [Indexed: 12/12/2022]
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Parajuli P, Pandey RP, Huyen Nguyen TT, Shrestha B, Yamaguchi T, Sohng JK. Biosynthesis of natural and non-natural genistein glycosides. RSC Adv 2017. [DOI: 10.1039/c6ra28145a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Biosynthesis of various genistein glycopyranoside scaffolds using versatile GTs and SOMTs. Each compound was structurally characterized and biological activity assay was carried out.
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Affiliation(s)
- Prakash Parajuli
- Department of Life Science and Biochemical Engineering
- Sun Moon University
- Tangjeong-myeon Asan-Si
- Republic of Korea
| | - Ramesh Prasad Pandey
- Department of Life Science and Biochemical Engineering
- Sun Moon University
- Tangjeong-myeon Asan-Si
- Republic of Korea
- Department of BT-Convergent Pharmaceutical Engineering
| | - Trang Thi Huyen Nguyen
- Department of Life Science and Biochemical Engineering
- Sun Moon University
- Tangjeong-myeon Asan-Si
- Republic of Korea
| | - Biplav Shrestha
- Department of Life Science and Biochemical Engineering
- Sun Moon University
- Tangjeong-myeon Asan-Si
- Republic of Korea
| | - Tokutaro Yamaguchi
- Department of Life Science and Biochemical Engineering
- Sun Moon University
- Tangjeong-myeon Asan-Si
- Republic of Korea
- Department of BT-Convergent Pharmaceutical Engineering
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering
- Sun Moon University
- Tangjeong-myeon Asan-Si
- Republic of Korea
- Department of BT-Convergent Pharmaceutical Engineering
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Kalb D, Heinekamp T, Schieferdecker S, Nett M, Brakhage AA, Hoffmeister D. An Iterative O-Methyltransferase Catalyzes 1,11-Dimethylation of Aspergillus fumigatus Fumaric Acid Amides. Chembiochem 2016; 17:1813-1817. [PMID: 27442960 DOI: 10.1002/cbic.201600293] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Indexed: 11/12/2022]
Abstract
S-adenosyl-l-methionine (SAM)-dependent methyltransfer is a common biosynthetic strategy to modify natural products. We investigated the previously uncharacterized Aspergillus fumigatus methyltransferase FtpM, which is encoded next to the bimodular fumaric acid amide synthetase FtpA. Structure elucidation of two new A. fumigatus natural products, the 1,11-dimethyl esters of fumaryl-l-tyrosine and fumaryl-l-phenylalanine, together with ftpM gene disruption suggested that FtpM catalyzes iterative methylation. Final evidence that a single enzyme repeatedly acts on fumaric acid amides came from an in vitro biochemical investigation with recombinantly produced FtpM. Size-exclusion chromatography indicated that this methyltransferase is active as a dimer. As ftpA and ftpM homologues are found clustered in other fungi, we expect our work will help to identify and annotate natural product biosynthesis genes in various species.
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Affiliation(s)
- Daniel Kalb
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Friedrich Schiller University, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Thorsten Heinekamp
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Friedrich Schiller University, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Sebastian Schieferdecker
- Research Group Secondary Metabolism of Predatory Bacteria, Leibniz Institute for Natural Product Research and Infection Biology, Friedrich Schiller University, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering, Technical University Dortmund, Emil-Figge-Strasse 66, 44227, Dortmund, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Friedrich Schiller University, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Dirk Hoffmeister
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Friedrich Schiller University, Beutenbergstrasse 11a, 07745, Jena, Germany.
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