1
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Gui C, Kalkreuter E, Lauterbach L, Yang D, Shen B. Enediyne natural product biosynthesis unified by a diiodotetrayne intermediate. Nat Chem Biol 2024; 20:1210-1219. [PMID: 38831037 DOI: 10.1038/s41589-024-01636-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 05/08/2024] [Indexed: 06/05/2024]
Abstract
Enediyne natural products are renowned for their potent cytotoxicities but the biosynthesis of their defining 1,5-diyne-3-ene core moiety remains largely enigmatic. Since the discovery of the enediyne polyketide synthase cassette in 2002, genome sequencing has revealed thousands of distinct enediyne biosynthetic gene clusters, each harboring the conserved enediyne polyketide synthase cassette. Here we report that (1) the products of this cassette are an iodoheptaene, a diiodotetrayne and two pentaynes; (2) the diiodotetrayne represents a common biosynthetic intermediate for all known enediynes; and (3) cryptic iodination can be exploited to increase enediyne titers. These findings establish a unified biosynthetic pathway for the enediynes, set the stage to further advance enediyne core biosynthesis and enable fundamental breakthroughs in chemistry, enzymology and translational applications of enediyne natural products.
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Affiliation(s)
- Chun Gui
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, Jupiter, FL, USA
| | - Edward Kalkreuter
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, Jupiter, FL, USA
| | - Lukas Lauterbach
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, Jupiter, FL, USA
| | - Dong Yang
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, Jupiter, FL, USA
- Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, Jupiter, FL, USA
| | - Ben Shen
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, Jupiter, FL, USA.
- Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, Jupiter, FL, USA.
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, Jupiter, FL, USA.
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2
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Ma GL, Liu WQ, Huang H, Yan XF, Shen W, Visitsatthawong S, Prakinee K, Tran H, Fan X, Gao YG, Chaiyen P, Li J, Liang ZX. An Enzymatic Oxidation Cascade Converts δ-Thiolactone Anthracene to Anthraquinone in the Biosynthesis of Anthraquinone-Fused Enediynes. JACS AU 2024; 4:2925-2935. [PMID: 39211597 PMCID: PMC11350584 DOI: 10.1021/jacsau.4c00279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/31/2024] [Accepted: 07/05/2024] [Indexed: 09/04/2024]
Abstract
Anthraquinone-fused enediynes are anticancer natural products featuring a DNA-intercalating anthraquinone moiety. Despite recent insights into anthraquinone-fused enediyne (AQE) biosynthesis, the enzymatic steps involved in anthraquinone biogenesis remain to be elucidated. Through a combination of in vitro and in vivo studies, we demonstrated that a two-enzyme system, composed of a flavin adenine dinucleotide (FAD)-dependent monooxygenase (DynE13) and a cofactor-free enzyme (DynA1), catalyzes the final steps of anthraquinone formation by converting δ-thiolactone anthracene to hydroxyanthraquinone. We showed that the three oxygen atoms in the hydroxyanthraquinone originate from molecular oxygen (O2), with the sulfur atom eliminated as H2S. We further identified the key catalytic residues of DynE13 and A1 by structural and site-directed mutagenesis studies. Our data support a catalytic mechanism wherein DynE13 installs two oxygen atoms with concurrent desulfurization and decarboxylation, whereas DynA1 acts as a cofactor-free monooxygenase, installing the final oxygen atom in the hydroxyanthraquinone. These findings establish the indispensable roles of DynE13 and DynA1 in AQE biosynthesis and unveil novel enzymatic strategies for anthraquinone formation.
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Affiliation(s)
- Guang-Lei Ma
- School
of Biological Sciences, Nanyang Technological
University, Singapore 637551, Singapore
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- National
Key Laboratory of Chinese Medicine Modernization, Innovation Center
of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
| | - Wan-Qiu Liu
- School
of Physical Science and Technology, ShanghaiTech
University, Shanghai 201210, China
| | - Huawei Huang
- School
of Biological Sciences, Nanyang Technological
University, Singapore 637551, Singapore
| | - Xin-Fu Yan
- School
of Biological Sciences, Nanyang Technological
University, Singapore 637551, Singapore
| | - Wei Shen
- National
Key Laboratory of Chinese Medicine Modernization, Innovation Center
of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
| | - Surawit Visitsatthawong
- School
of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Kridsadakorn Prakinee
- School
of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Hoa Tran
- School
of Biological Sciences, Nanyang Technological
University, Singapore 637551, Singapore
| | - Xiaohui Fan
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- National
Key Laboratory of Chinese Medicine Modernization, Innovation Center
of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
| | - Yong-Gui Gao
- School
of Biological Sciences, Nanyang Technological
University, Singapore 637551, Singapore
| | - Pimchai Chaiyen
- School
of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Jian Li
- School
of Physical Science and Technology, ShanghaiTech
University, Shanghai 201210, China
| | - Zhao-Xun Liang
- School
of Biological Sciences, Nanyang Technological
University, Singapore 637551, Singapore
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3
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Han EJ, Seyedsayamdost MR. Genome mining for new enediyne antibiotics. Curr Opin Chem Biol 2024; 81:102481. [PMID: 38917732 PMCID: PMC11323183 DOI: 10.1016/j.cbpa.2024.102481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
Enediyne antibiotics epitomize nature's chemical creativity. They contain intricate molecular architectures that are coupled with potent biological activities involving double-stranded DNA scission. The recent explosion in microbial genome sequences has revealed a large reservoir of novel enediynes. However, while hundreds of enediyne biosynthetic gene clusters (BGCs) can be detected, less than two dozen natural products have been characterized to date as many clusters remain silent or sparingly expressed under standard laboratory growth conditions. This review focuses on four distinct strategies, which have recently enabled discoveries of novel enediynes: phenotypic screening from rare sources, biosynthetic manipulation, genomic signature-based PCR screening, and DNA-cleavage assays coupled with activation of silent BGCs via high-throughput elicitor screening. With an abundance of enediyne BGCs and emerging approaches for accessing them, new enediyne natural products and further insights into their biogenesis are imminent.
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Affiliation(s)
- Esther J Han
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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4
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Pal P, Wessely SML, Townsend CA. Normal and Aberrant Methyltransferase Activities Give Insights into the Final Steps of Dynemicin A Biosynthesis. J Am Chem Soc 2023; 145:12935-12947. [PMID: 37276497 PMCID: PMC10985829 DOI: 10.1021/jacs.3c04393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The naturally occurring enediynes are notable for their complex structures, potent DNA cleaving ability, and emerging usefulness in cancer chemotherapy. They can be classified into three distinct structural families, but all are thought to originate from a common linear C15-heptaene. Dynemicin A (DYN) is the paradigm member of anthraquinone-fused enediynes, one of the three main classes and exceptional among them for derivation of both its enediyne and anthraquinone portions from this same early biosynthetic building block. Evidence is growing about how two structurally dissimilar, but biosynthetically related, intermediates combine in two heterodimerization reactions to create a nitrogen-containing C30-coupled product. We report here deletions of two genes that encode biosynthetic proteins that are annotated as S-adenosylmethionine (SAM)-dependent methyltransferases. While one, DynO6, is indeed the required O-methyltransferase implicated long ago in the first studies of DYN biosynthesis, the other, DynA5, functions in an unanticipated manner in the post-heterodimerization events that complete the biosynthesis of DYN. Despite its removal from the genome of Micromonospora chersina, the ΔdynA5 strain retains the ability to synthesize DYN, albeit in reduced titers, accompanied by two unusual co-metabolites. We link the appearance of these unexpected structures to a substantial and contradictory body of other recent experimental data to advance a biogenetic rationale for the downstream steps that lead to the final formation of DYN. A sequence of product-forming transformations that is in line with new and existing experimental results is proposed and supported by a model reaction that also encompasses the formation of the crucial epoxide essential for the activation of DYN for DNA cleavage.
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Affiliation(s)
- Paramita Pal
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Serena M L Wessely
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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5
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Bhardwaj M, Cui Z, Daniel Hankore E, Moonschi FH, Saghaeiannejad Esfahani H, Kalkreuter E, Gui C, Yang D, Phillips GN, Thorson JS, Shen B, Van Lanen SG. A discrete intermediate for the biosynthesis of both the enediyne core and the anthraquinone moiety of enediyne natural products. Proc Natl Acad Sci U S A 2023; 120:e2220468120. [PMID: 36802426 PMCID: PMC9992847 DOI: 10.1073/pnas.2220468120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
The enediynes are structurally characterized by a 1,5-diyne-3-ene motif within a 9- or 10-membered enediyne core. The anthraquinone-fused enediynes (AFEs) are a subclass of 10-membered enediynes that contain an anthraquinone moiety fused to the enediyne core as exemplified by dynemicins and tiancimycins. A conserved iterative type I polyketide synthase (PKSE) is known to initiate the biosynthesis of all enediyne cores, and evidence has recently been reported to suggest that the anthraquinone moiety also originates from the PKSE product. However, the identity of the PKSE product that is converted to the enediyne core or anthraquinone moiety has not been established. Here, we report the utilization of recombinant E. coli coexpressing various combinations of genes that encode a PKSE and a thioesterase (TE) from either 9- or 10-membered enediyne biosynthetic gene clusters to chemically complement ΔPKSE mutant strains of the producers of dynemicins and tiancimycins. Additionally, 13C-labeling experiments were performed to track the fate of the PKSE/TE product in the ΔPKSE mutants. These studies reveal that 1,3,5,7,9,11,13-pentadecaheptaene is the nascent, discrete product of the PKSE/TE that is converted to the enediyne core. Furthermore, a second molecule of 1,3,5,7,9,11,13-pentadecaheptaene is demonstrated to serve as the precursor of the anthraquinone moiety. The results establish a unified biosynthetic paradigm for AFEs, solidify an unprecedented biosynthetic logic for aromatic polyketides, and have implications for the biosynthesis of not only AFEs but all enediynes.
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Affiliation(s)
- Minakshi Bhardwaj
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY40536
| | - Zheng Cui
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY40536
| | - Erome Daniel Hankore
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY40536
| | - Faruk H. Moonschi
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY40536
| | - Hoda Saghaeiannejad Esfahani
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY40536
| | - Edward Kalkreuter
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL33458
| | - Chun Gui
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL33458
| | - Dong Yang
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL33458
- Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL33458
| | | | - Jon S. Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY40536
| | - Ben Shen
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL33458
- Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL33458
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL33458
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, FL33458
| | - Steven G. Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY40536
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY40536
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6
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Hou A, Dickschat JS. Labelling studies in the biosynthesis of polyketides and non-ribosomal peptides. Nat Prod Rep 2023; 40:470-499. [PMID: 36484402 DOI: 10.1039/d2np00071g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: 2015 to 2022In this review, we discuss the recent advances in the use of isotopically labelled compounds to investigate the biosynthesis of polyketides, non-ribosomally synthesised peptides, and their hybrids. Also, we highlight the use of isotopes in the elucidation of their structures and investigation of enzyme mechanisms. The biosynthetic pathways of selected examples are presented in detail to reveal the principles of the discussed labelling experiments. The presented examples demonstrate that the application of isotopically labelled compounds is still the state of the art and can provide valuable information for the biosynthesis of natural products.
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Affiliation(s)
- Anwei Hou
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, West 7th Avenue No. 32, 300308 Tianjin, China.,Institute of Microbiology, Jiangxi Academy of Sciences, Changdong Road No. 7777, 330096 Nanchang, China
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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7
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Pal P, Alley JR, Townsend CA. Examining Heterodimerization by Aryl C-N Coupling in Dynemicin Biosynthesis. ACS Chem Biol 2023; 18:304-314. [PMID: 36696117 DOI: 10.1021/acschembio.2c00709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Distinct among the enediyne antitumor antibiotics, the dynemicin subgroup is comprised of two discrete halves, an enediyne and an anthraquinone, but each is ultimately derived from the same linear β-hydroxyhexaene precursor. The linkage of these two halves by an aryl C-N bond is examined here using a variety of experimental approaches. We demonstrate that this heterodimerization is specific for anthracenyl iodide as the corresponding bromo- and amino-substituted anthracenes do not support dynemicin biosynthesis. Furthermore, biochemical experiments and chemical model reactions support an SRN1 mechanism for the aryl C-N coupling in which electron transfer occurs to the iodoanthracene, followed by loss of an anthracenyl iodide and partition of the resulting aryl radical between C-N coupling and reduction by hydrogen abstraction. An enzyme pull-down experiment aiming to capture the protein(s) involved in the coupling reaction is described in which two proteins, Orf14 and Orf16, encoded by the dynemicin biosynthetic gene cluster, are specifically isolated. Deletion of orf14 from the genome abolished dynemicin production accompanied by a 3-fold increased accumulation of the iodoanthracene coupling partner, indicating the plausible involvement of this protein in the heterodimerization process. On the other hand, the deletion of orf16 only reduced dynemicin production to 55%, implying a noncatalytic, auxiliary role of the protein. Structural comparisons using AlphaFold imply key similarities between Orf14 and X-ray crystal structures of several proteins from enediyne BGCs believed to bind hydrophobic polyene or enediyne motifs suggest Orf14 templates aryl C-N bond formation during the central heterodimerization in dynemicin biosynthesis.
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Affiliation(s)
- Paramita Pal
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jamie R Alley
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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8
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Pan J, Tan Q, Zhu S, Yan X, Li Y, Zhuang Z, Zhu X, Duan Y, Huang Y. Discovery of pentaene polyols by the activation of an enediyne gene cluster: biosynthetic implications for 9-membered enediyne core structures. Chem Sci 2022; 13:13475-13481. [PMID: 36507168 PMCID: PMC9682884 DOI: 10.1039/d2sc04379c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/28/2022] [Indexed: 12/15/2022] Open
Abstract
The identification and characterization of enediyne polyketide synthases (PKSEs) revealed that PKSE-bound polyene is a common intermediate, while its subsequent tailoring steps to enediyne cores remain obscure. Herein, we report pentaene polyols 5-7 and cinnamic acid derivatives 8 and 9 biosynthesized from an activated enediyne biosynthetic gene cluster in Streptomyces sp. CB02130. The C-1027 pksE could partially complement production of these polyene polyols in a CB02130 mutant where the native pksE is inactivated. The yields of 5-7 were improved by increasing the cellular pool of l-Phe through either gene inactivation of a prephenate dehydrogenase WlsPDH or supplementation of l-Phe. A flexible ammonia lyase WlsC4 is responsible for biosynthesis of 8 and 9 from l-Phe. The co-localization of wlsPDH and PKSE gene cassette supports their close evolutionary relationships and an enediyne genome mining strategy using WlsPDH. These findings not only provide a facile approach to activate silent enediyne BGCs, but suggest that a polyene epoxide intermediate may be formed for construction of 9-membered enediyne macrocycles.
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Affiliation(s)
- Jian Pan
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China
| | - Qingwen Tan
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China
| | - Saibin Zhu
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China
| | - Xiaohui Yan
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China, State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese MedicineTianjinChina
| | - Yu Li
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China
| | - Zhoukang Zhuang
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China,National Engineering Research Center of Combinatorial Biosynthesis for Drug DiscoveryChangshaHunan 410205China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug DiscoveryChangshaHunan 410205China,National Engineering Research Center of Combinatorial Biosynthesis for Drug DiscoveryChangshaHunan 410205China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine, Central South UniversityChangshaHunan 410013China,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug DiscoveryChangshaHunan 410205China
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9
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Yang D, Ye F, Teijaro CN, Hwang D, Annaval T, Adhikari A, Li G, Yan X, Gui C, Rader C, Shen B. Functional Characterization of Cytochrome P450 Hydroxylase YpmL in Yangpumicin A Biosynthesis and Its Application for Anthraquinone-Fused Enediyne Structural Diversification. Org Lett 2022; 24:1219-1223. [PMID: 35084871 PMCID: PMC9594962 DOI: 10.1021/acs.orglett.2c00009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Comparative analyses of four anthraquinone-fused enediyne biosynthetic gene clusters (BGCs) identified YpmL as a cytochrome P450 enzyme unique to the yangpumicin (YPM) BGC. In vitro characterization of YpmL established it as a hydroxylase, catalyzing C-6 hydroxylation in YPM A biosynthesis. In vivo application of YpmL enabled engineered production of four new tiancimycin analogues (14-17). Evaluation of their cytotoxicity against selected human cancer cell lines shed new insights into the enediyne structure-activity relationship.
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Affiliation(s)
- Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
- Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Fei Ye
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Dobeen Hwang
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Thibault Annaval
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ajeeth Adhikari
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Gengnan Li
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Chun Gui
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
- Natural Products Discovery Center at Scripps Research, The Scripps Research Institute, Jupiter, FL 33458, USA
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10
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Xue L, Zhang L, Zhang C, Zhao X, Dang W, Wang Z, Wang C, Suo T, Yan X. Discovery of Tiancimycin Congeners from Streptomyces sp. CB03234-S. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202111018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Kosgei AJ, Miller MD, Bhardwaj M, Xu W, Thorson JS, Van Lanen SG, Phillips GN. The crystal structure of DynF from the dynemicin-biosynthesis pathway of Micromonospora chersina. Acta Crystallogr F Struct Biol Commun 2022; 78:1-7. [PMID: 34981769 PMCID: PMC8725005 DOI: 10.1107/s2053230x21012322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/21/2021] [Indexed: 11/17/2022] Open
Abstract
The crystal structure of DynF was determined to a resolution of 1.50 Å, revealing a dimeric eight-stranded β-barrel structure with palmitic acid bound in the interior. Dynemicin is an enediyne natural product from Micromonospora chersina ATCC53710. Access to the biosynthetic gene cluster of dynemicin has enabled the in vitro study of gene products within the cluster to decipher their roles in assembling this unique molecule. This paper reports the crystal structure of DynF, the gene product of one of the genes within the biosynthetic gene cluster of dynemicin. DynF is revealed to be a dimeric eight-stranded β-barrel structure with palmitic acid bound within a cavity. The presence of palmitic acid suggests that DynF may be involved in binding the precursor polyene heptaene, which is central to the synthesis of the ten-membered ring of the enediyne core.
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12
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Abstract
Covering: up to the end of July, 2021Anthraquinone-fused enediynes (AFEs) are a subfamily of enediyne natural products. Dynemicin A (DYN A), the first member of the AFE family, was discovered more than thirty years ago. Subsequently, extensive studies have been reported on the mode of action and the interactions of AFEs with DNA using DYN A as a model. However, progress in the discovery, biosynthesis and clinical development of AFEs has been limited for a long time. In the past five years, four new AFEs have been discovered and significant progress has been made in the biosynthesis of AFEs, especially on the biogenesis of the anthraquinone moiety and their tailoring steps. Moreover, the streamlined total synthesis of AFEs and their analogues boosts the preparation of AFE-based linker-drugs, thus enabling the development of AFE-based antibody-drug conjugates (ADCs). This review summarizes the discovery, mechanism of action, biosynthesis, total synthesis and preclinical studies of AFEs.
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Affiliation(s)
- Xiaohui Yan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, China.
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13
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Alvarado SK, Miller MD, Bhardwaj M, Thorson JS, Van Lanen SG, Phillips GN. Structural characterization of DynU16, a START/Bet v1-like protein involved in dynemicin biosynthesis. Acta Crystallogr F Struct Biol Commun 2021; 77:328-333. [PMID: 34605436 PMCID: PMC8488855 DOI: 10.1107/s2053230x21008943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/27/2021] [Indexed: 11/10/2022] Open
Abstract
The 1.5 Å resolution crystal structure of DynU16, a protein identified in the dynemicin-biosynthetic gene cluster, is reported. The structure adopts a di-domain helix-grip fold with a uniquely positioned open cavity connecting the domains. The elongated dimensions of the cavity appear to be compatible with the geometry of a linear polyene, suggesting the involvement of DynU16 in the upstream steps of dynemicin biosynthesis.
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Affiliation(s)
- Sarah K. Alvarado
- Department of BioSciences, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Mitchell D. Miller
- Department of BioSciences, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Minakshi Bhardwaj
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - Jon S. Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - Steven G. Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - George N. Phillips
- Department of BioSciences, Rice University, 6100 Main Street, Houston, TX 77005, USA
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, USA
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14
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Ma GL, Tran HT, Low ZJ, Candra H, Pang LM, Cheang QW, Fang M, Liang ZX. Pathway Retrofitting Yields Insights into the Biosynthesis of Anthraquinone-Fused Enediynes. J Am Chem Soc 2021; 143:11500-11509. [PMID: 34293863 DOI: 10.1021/jacs.1c03911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Anthraquinone-fused enediynes (AQEs) are renowned for their distinctive molecular architecture, reactive enediyne warhead, and potent anticancer activity. Although the first members of AQEs, i.e., dynemicins, were discovered three decades ago, how their nitrogen-containing carbon skeleton is synthesized by microbial producers remains largely a mystery. In this study, we showed that the recently discovered sungeidine pathway is a "degenerative" AQE pathway that contains upstream enzymes for AQE biosynthesis. Retrofitting the sungeidine pathway with genes from the dynemicin pathway not only restored the biosynthesis of the AQE skeleton but also produced a series of novel compounds likely as the cycloaromatized derivatives of chemically unstable biosynthetic intermediates. The results suggest a cascade of highly surprising biosynthetic steps leading to the formation of the anthraquinone moiety, the hallmark C8-C9 linkage via alkyl-aryl cross-coupling, and the characteristic epoxide functionality. The findings provide unprecedented insights into the biosynthesis of AQEs and pave the way for examining these intriguing biosynthetic enzymes.
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Affiliation(s)
- Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Hoa Thi Tran
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Zhen Jie Low
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Hartono Candra
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Qing Wei Cheang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
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15
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Annaval T, Teijaro CN, Adhikari A, Yan X, Chen JJ, Crnovcic I, Yang D, Shen B. Cytochrome P450 Hydroxylase TnmL Catalyzing Sequential Hydroxylation with an Additional Proofreading Activity in Tiancimycin Biosynthesis. ACS Chem Biol 2021; 16:1172-1178. [PMID: 34138533 DOI: 10.1021/acschembio.1c00365] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tiancimycin (TNM) A belongs to the anthraquinone-fused subfamily of enediyne natural products, and selected enediynes have been translated into clinical drugs. Previously, inactivation of tnmL in Streptomyces sp. CB03234 resulted in the accumulation of TNM B and TNM E, supporting the functional assignment of TnmL as a cytochrome P450 hydroxylase that catalyzes A-ring modification in TNM A biosynthesis. Herein, we report in vitro characterization of TnmL, revealing that (i) TnmL catalyzes two successive hydroxylations of TNM E, resulting in sequential production of TNM F and TNM C, (ii) TnmL shows a strict substrate preference, with the C-26 side chain playing a critical role in substrate binding, and (iii) TnmL demethylates the C-7 OCH3 group of TNM G, affording TNM F, thereby channeling the shunt product TNM G back into TNM A biosynthesis and representing a rare proofreading logic for natural product biosynthesis. These findings shed new insights into anthraquinone-fused enediyne biosynthesis.
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16
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Li X, Lv JM, Hu D, Abe I. Biosynthesis of alkyne-containing natural products. RSC Chem Biol 2021; 2:166-180. [PMID: 34458779 PMCID: PMC8341276 DOI: 10.1039/d0cb00190b] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 11/30/2020] [Indexed: 11/23/2022] Open
Abstract
Alkyne-containing natural products are important molecules that are widely distributed in microbes and plants. Inspired by the advantages of acetylenic products used in the fields of medicinal chemistry, organic synthesis and material science, great efforts have focused on discovering the biosynthetic enzymes and pathways for alkyne formation. Here, we summarize the biosyntheses of alkyne-containing natural products and introduce de novo biosynthetic strategies for alkyne-tagged compound production.
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Affiliation(s)
- Xinyang Li
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Jian-Ming Lv
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University Guangzhou 510632 People's Republic of China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University Guangzhou 510632 People's Republic of China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo Yayoi 1-1-1 Bunkyo-ku Tokyo 113-8657 Japan
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17
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Cohen DR, Townsend CA. C-N-Coupled Metabolites Yield Insights into Dynemicin A Biosynthesis. Chembiochem 2020; 21:2137-2142. [PMID: 32198800 PMCID: PMC7685002 DOI: 10.1002/cbic.202000177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Indexed: 11/08/2022]
Abstract
The biosynthesis of the three structural subclasses of enediyne antitumor antibiotics remains largely unknown beyond a common C16 -hexaene precursor. For the anthraquinone-fused subtype, however, an unexpected iodoanthracene γ-thiolactone was established to be a mid-pathway intermediate to dynemicin A. Having deleted a putative flavin-dependent oxidoreductase from the dynemicin biosynthetic gene cluster, we can now report four metabolites that incorporate the iodoanthracene and reveal the formation of the C-N bond linking the anthraquinone and enediyne halves emblematic of this structural subclass. The coupling of an aryl iodide and an amine is familiar from organometallic chemistry, but has little or no precedent in natural product biosynthesis. These metabolites suggest further that enediyne formation occurs early in the overall biosynthesis, and that even earlier events might convert the C16 -hexaene to a common C15 intermediate that partitions to enediyne and anthraquinone building blocks for the heterodimerization.
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Affiliation(s)
- Douglas R Cohen
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
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18
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He YQ, Chen RW, Li C, Shi SB, Cui LQ, Long LJ, Tian XP. Actinomarinicola tropica gen. nov. sp. nov., a new marine actinobacterium of the family Iamiaceae, isolated from South China Sea sediment environments. Int J Syst Evol Microbiol 2020; 70:3852-3858. [PMID: 32501198 DOI: 10.1099/ijsem.0.004251] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A novel marine actinobacterium, strain SCSIO 58843T, was isolated from the sediment sample collected from the South China Sea. Strain SCSIO 58843T was Gram-stain-positive, aerobic and rod shaped. The whole-cell hydrolysis of amino acids contained dd-DAP, alanine, glutamic acid, glycine and aspartic acid. The main menaquinone was MK-9(H8). The major fatty acids were C17 : 1 ω8c and C17 : 0. The major phospholipids were diphosphatidylglycerol (DPG), phosphatidylinositol (PI), phospatidylcholine (PC) and phosphatidylinositolmannoside (PIM). The G+C content of the genomic DNA was 72.5 %. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain SCSIO 58843T formed a new lineage in the family Iamiaceae and had the highest similarity of 93.8 % with Iamia majanohamensis DSM 19957T. Strain SCSIO 58843T can be distinguished from these known genera in the family Iamiaceae by polyphasic data analyses, and represents a novel genus and novel species, for which Actinomarinicola tropica gen. nov., sp. nov is proposed with the type strain SCSIO 58843T(=KCTC 49408T=CGMCC 1.17503T).
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Affiliation(s)
- Yuan-Qiu He
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, CAS RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Rou-Wen Chen
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, CAS RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Cun Li
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, CAS RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Song-Biao Shi
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, CAS RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Lin-Qing Cui
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, CAS RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Li-Juan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, CAS RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Xin-Peng Tian
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, CAS RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
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19
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Low ZJ, Ma GL, Tran HT, Zou Y, Xiong J, Pang L, Nuryyeva S, Ye H, Hu JF, Houk KN, Liang ZX. Sungeidines from a Non-canonical Enediyne Biosynthetic Pathway. J Am Chem Soc 2020; 142:1673-1679. [PMID: 31922407 DOI: 10.1021/jacs.9b10086] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the genome-guided discovery of sungeidines, a class of microbial secondary metabolites with unique structural features. Despite evolutionary relationships with dynemicin-type enediynes, the sungeidines are produced by a biosynthetic gene cluster (BGC) that exhibits distinct differences from known enediyne BGCs. Our studies suggest that the sungeidines are assembled from two octaketide chains that are processed differently than those of the dynemicin-type enediynes. The biosynthesis also involves a unique activating sulfotransferase that promotes a dehydration reaction. The loss of genes, including a putative epoxidase gene, is likely to be the main cause of the divergence of the sungeidine pathway from other canonical enediyne pathways. The findings disclose the surprising evolvability of enediyne pathways and set the stage for characterizing the intriguing enzymatic steps in sungeidine biosynthesis.
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Affiliation(s)
- Zhen Jie Low
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | - Guang-Lei Ma
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | - Hoa Thi Tran
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | - Yike Zou
- Department of Chemistry & Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Juan Xiong
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore.,School of Pharmacy , Fudan University , Shanghai 200433 , China
| | - Limei Pang
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | - Selbi Nuryyeva
- Department of Chemistry & Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Hong Ye
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
| | - Jin-Feng Hu
- School of Pharmacy , Fudan University , Shanghai 200433 , China
| | - K N Houk
- Department of Chemistry & Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Zhao-Xun Liang
- School of Biological Sciences , Nanyang Technological University , 637551 Singapore
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20
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Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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21
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Braesel J, Crnkovic CM, Kunstman KJ, Green SJ, Maienschein-Cline M, Orjala J, Murphy BT, Eustáquio AS. Complete Genome of Micromonospora sp. Strain B006 Reveals Biosynthetic Potential of a Lake Michigan Actinomycete. JOURNAL OF NATURAL PRODUCTS 2018; 81:2057-2068. [PMID: 30110167 PMCID: PMC6174880 DOI: 10.1021/acs.jnatprod.8b00394] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Actinomycete bacteria isolated from freshwater environments are an unexplored source of natural products. Here we report the complete genome of the Great Lakes-derived Micromonospora sp. strain B006, revealing its potential for natural product biosynthesis. The 7-megabase pair chromosome of strain B006 was sequenced using Illumina and Oxford Nanopore technologies followed by Sanger sequencing to close remaining gaps. All identified biosynthetic gene clusters (BGCs) were manually curated. Five known BGCs were identified encoding desferrioxamine, alkyl- O-dihydrogeranylmethoxyhydroquinone, a spore pigment, sioxanthin, and diazepinomicin, which is currently in phase II clinical trials to treat Phelan-McDermid syndrome and co-morbid epilepsy. We report here that strain B006 is indeed a producer of diazepinomicin and at yields higher than previously reported. Moreover, 11 of the 16 identified BGCs are orphan, eight of which were transcriptionally active under the culture condition tested. Orphan BGCs include an enediyne polyketide synthase and an uncharacteristically large, 36-module polyketide synthase-nonribosomal peptide synthetase BGC. We developed a genetics system for Micromonospora sp. B006 that will contribute to deorphaning BGCs in the future. This study is one of the few attempts to report the biosynthetic capacity of a freshwater-derived actinomycete and highlights this resource as a potential reservoir for new natural products.
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Affiliation(s)
- Jana Braesel
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Camila M. Crnkovic
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Federal District 70040-020, Brazil
| | - Kevin J. Kunstman
- DNA Services Facility, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Stefan J. Green
- DNA Services Facility, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Mark Maienschein-Cline
- Core for Research Informatics, University of Illinois at Chicago, Chicago, IL 60615, USA
| | - Jimmy Orjala
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Brian T. Murphy
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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22
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Chang CY, Yan X, Crnovcic I, Annaval T, Chang C, Nocek B, Rudolf JD, Yang D, Hindra, Babnigg G, Joachimiak A, Phillips GN, Shen B. Resistance to Enediyne Antitumor Antibiotics by Sequestration. Cell Chem Biol 2018; 25:1075-1085.e4. [PMID: 29937405 PMCID: PMC6208323 DOI: 10.1016/j.chembiol.2018.05.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/04/2018] [Accepted: 05/16/2018] [Indexed: 10/28/2022]
Abstract
The enediynes, microbial natural products with extraordinary cytotoxicities, have been translated into clinical drugs. Two self-resistance mechanisms are known in the enediyne producers-apoproteins for the nine-membered enediynes and self-sacrifice proteins for the ten-membered enediyne calicheamicin. Here we show that: (1) tnmS1, tnmS2, and tnmS3 encode tiancimycin (TNM) resistance in its producer Streptomyces sp. CB03234, (2) tnmS1, tnmS2, and tnmS3 homologs are found in all anthraquinone-fused enediyne producers, (3) TnmS1, TnmS2, and TnmS3 share a similar β barrel-like structure, bind TNMs with nanomolar KD values, and confer resistance by sequestration, and (4) TnmS1, TnmS2, and TnmS3 homologs are widespread in nature, including in the human microbiome. These findings unveil an unprecedented resistance mechanism for the enediynes. Mechanisms of self-resistance in producers serve as models to predict and combat future drug resistance in clinical settings. Enediyne-based chemotherapies should now consider the fact that the human microbiome harbors genes encoding enediyne resistance.
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Affiliation(s)
- Chin-Yuan Chang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ivana Crnovcic
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Thibault Annaval
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Changsoo Chang
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Boguslaw Nocek
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Hindra
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Gyorgy Babnigg
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL 60637, USA
| | - Andrzej Joachimiak
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL 60637, USA
| | - George N Phillips
- BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX 77251, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA; Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL 33458, USA.
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23
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Yan X, Chen JJ, Adhikari A, Teijaro CN, Ge H, Crnovcic I, Chang CY, Annaval T, Yang D, Rader C, Shen B. Comparative Studies of the Biosynthetic Gene Clusters for Anthraquinone-Fused Enediynes Shedding Light into the Tailoring Steps of Tiancimycin Biosynthesis. Org Lett 2018; 20:5918-5921. [PMID: 30212211 DOI: 10.1021/acs.orglett.8b02584] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Comparative analyses of the four known anthraquinone-fused enediynes biosynthetic gene clusters identified four genes, tnmE6, tnmH, tnmL, and tnmQ, unique to the tnm gene cluster. Larger scale fermentation of both the S. sp. CB03234 wild-type and the Δ tnmH and Δ tnmL mutant strains resulted in the characterization of 20 new tiancimycin (TNM) congeners, including five enediynes. These findings enabled a proposal for the late stage of TNM biosynthesis featuring an intermediate possibly common for all anthraquinone-fused enediynes.
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24
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Cohen DR, Townsend CA. Characterization of an Anthracene Intermediate in Dynemicin Biosynthesis. Angew Chem Int Ed Engl 2018; 57:5650-5654. [PMID: 29512267 PMCID: PMC5942901 DOI: 10.1002/anie.201802036] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Indexed: 11/08/2022]
Abstract
Despite the identification of a β-hydroxyhexaene produced by the enediyne polyketide synthases (PKSs), the post-PKS biosynthetic steps to the individual members of this antitumor and antibiotic family remain largely unknown. The massive biosynthetic gene clusters (BGCs) that direct the formation of each product caution that many steps could be required. It was recently demonstrated that the enediyne PKS in the dynemicin A BGC from Micromonospora chersina gives rise to both the anthraquinone and enediyne halves of the molecule. We now present the first evidence for a mid-pathway intermediate in dynemicin A biosynthesis, an iodoanthracene bearing a fused thiolactone, which was shown to be incorporated selectively into the final product. This unusual precursor reflects just how little is understood about these biosynthetic pathways, yet constrains the mechanisms that can act to achieve the key heterodimerization to the anthraquinone-containing subclass of enediynes.
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Affiliation(s)
- Douglas R Cohen
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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25
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Cohen DR, Townsend CA. Characterization of an Anthracene Intermediate in Dynemicin Biosynthesis. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Douglas R. Cohen
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
| | - Craig A. Townsend
- Department of Chemistry; The Johns Hopkins University; 3400 North Charles Street Baltimore MD 21218 USA
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26
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A dual role for a polyketide synthase in dynemicin enediyne and anthraquinone biosynthesis. Nat Chem 2017; 10:231-236. [PMID: 29359752 PMCID: PMC5944350 DOI: 10.1038/nchem.2876] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/21/2017] [Indexed: 11/08/2022]
Abstract
Dynemicin A is a member of a subfamily of enediyne antitumour antibiotics characterized by a 10-membered carbocycle fused to an anthraquinone, both of polyketide origin. Sequencing of the dynemicin biosynthetic gene cluster in Micromonospora chersina previously identified an enediyne polyketide synthase (PKS), but no anthraquinone PKS, suggesting gene(s) for biosynthesis of the latter were distant from the core dynemicin cluster. To identify these gene(s), we sequenced and analysed the genome of M. chersina. Sequencing produced a short list of putative PKS candidates, yet CRISPR-Cas9 mutants of each locus retained dynemicin production. Subsequently, deletion of two cytochromes P450 in the dynemicin cluster suggested that the dynemicin enediyne PKS, DynE8, may biosynthesize the anthraquinone. Together with 18O-labelling studies, we now present evidence that DynE8 produces the core scaffolds of both the enediyne and anthraquinone, and provide a working model to account for their formation from the programmed octaketide of the enediyne PKS.
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27
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Yan X, Chen JJ, Adhikari A, Yang D, Crnovcic I, Wang N, Chang CY, Rader C, Shen B. Genome Mining of Micromonospora yangpuensis DSM 45577 as a Producer of an Anthraquinone-Fused Enediyne. Org Lett 2017; 19:6192-6195. [PMID: 29086572 DOI: 10.1021/acs.orglett.7b03120] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new anthraquinone-fused enediyne, yangpumicin A (YPM A, 1), along with four Bergman cyclization congeners (YPM B-E, 2-5), was isolated from Micromonospora yangpuensis DSM 45577 after mining enediyne biosynthetic gene clusters from public actinobacterial genome databases and prioritizing the hits by an enediyne genome neighborhood network analysis for discovery. YPM A is potent against a broad spectrum of human cancer cell lines. The discovery of 1 provides new opportunities for the functionalization of enediynes to develop new conjugation chemistries for antibody-drug conjugates.
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Affiliation(s)
- Xiaohui Yan
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Jian-Jun Chen
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Ajeeth Adhikari
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Dong Yang
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Ivana Crnovcic
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Nan Wang
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Chin-Yuan Chang
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Christoph Rader
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Ben Shen
- Department of Chemistry, ‡Department of Molecular Medicine, §Natural Products Library Initiative at the Scripps Research Institute, and ∥Department of Immunology and Microbiology, The Scripps Research Institute , Jupiter, Florida 33458, United States
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28
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Waldman AJ, Ng TL, Wang P, Balskus EP. Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5784-5863. [PMID: 28375000 PMCID: PMC5534343 DOI: 10.1021/acs.chemrev.6b00621] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
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Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Tai L. Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
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29
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Abstract
The enediyne family of natural products has had a profound impact on modern chemistry, biology, and medicine, and yet only 11 enediynes have been structurally characterized to date. Here we report a genome survey of 3,400 actinomycetes, identifying 81 strains that harbor genes encoding the enediyne polyketide synthase cassettes that could be grouped into 28 distinct clades based on phylogenetic analysis. Genome sequencing of 31 representative strains confirmed that each clade harbors a distinct enediyne biosynthetic gene cluster. A genome neighborhood network allows prediction of new structural features and biosynthetic insights that could be exploited for enediyne discovery. We confirmed one clade as new C-1027 producers, with a significantly higher C-1027 titer than the original producer, and discovered a new family of enediyne natural products, the tiancimycins (TNMs), that exhibit potent cytotoxicity against a broad spectrum of cancer cell lines. Our results demonstrate the feasibility of rapid discovery of new enediynes from a large strain collection. Recent advances in microbial genomics clearly revealed that the biosynthetic potential of soil actinomycetes to produce enediynes is underappreciated. A great challenge is to develop innovative methods to discover new enediynes and produce them in sufficient quantities for chemical, biological, and clinical investigations. This work demonstrated the feasibility of rapid discovery of new enediynes from a large strain collection. The new C-1027 producers, with a significantly higher C-1027 titer than the original producer, will impact the practical supply of this important drug lead. The TNMs, with their extremely potent cytotoxicity against various cancer cells and their rapid and complete cancer cell killing characteristics, in comparison with the payloads used in FDA-approved antibody-drug conjugates (ADCs), are poised to be exploited as payload candidates for the next generation of anticancer ADCs. Follow-up studies on the other identified hits promise the discovery of new enediynes, radically expanding the chemical space for the enediyne family.
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30
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Huang T, Chang CY, Lohman JR, Rudolf JD, Kim Y, Chang C, Yang D, Ma M, Yan X, Crnovcic I, Bigelow L, Clancy S, Bingman CA, Yennamalli RM, Babnigg G, Joachimiak A, Phillips GN, Shen B. Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027. J Antibiot (Tokyo) 2016; 69:731-740. [PMID: 27406907 PMCID: PMC5083130 DOI: 10.1038/ja.2016.88] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/30/2016] [Accepted: 06/15/2016] [Indexed: 12/28/2022]
Abstract
Comparative analysis of the enediyne biosynthetic gene clusters revealed sets of conserved genes serving as outstanding candidates for the enediyne core. Here we report the crystal structures of SgcJ and its homologue NCS-Orf16, together with gene inactivation and site-directed mutagenesis studies, to gain insight into enediyne core biosynthesis. Gene inactivation in vivo establishes that SgcJ is required for C-1027 production in Streptomyces globisporus. SgcJ and NCS-Orf16 share a common structure with the nuclear transport factor 2-like superfamily of proteins, featuring a putative substrate binding or catalytic active site. Site-directed mutagenesis of the conserved residues lining this site allowed us to propose that SgcJ and its homologues may play a catalytic role in transforming the linear polyene intermediate, along with other enediyne polyketide synthase-associated enzymes, into an enzyme-sequestered enediyne core intermediate. These findings will help formulate hypotheses and design experiments to ascertain the function of SgcJ and its homologues in nine-membered enediyne core biosynthesis.
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Affiliation(s)
- Tingting Huang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Chin-Yuan Chang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Jeremy R Lohman
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL USA.,Structural Biology Center, Argonne National Laboratory, Argonne, IL, USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Changsoo Chang
- Structural Biology Center, Argonne National Laboratory, Argonne, IL, USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Ming Ma
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Ivana Crnovcic
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Lance Bigelow
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Shonda Clancy
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Gyorgy Babnigg
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL USA.,Structural Biology Center, Argonne National Laboratory, Argonne, IL, USA.,Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - George N Phillips
- BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.,Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, USA.,Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL, USA
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31
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Rudolf JD, Yan X, Shen B. Genome neighborhood network reveals insights into enediyne biosynthesis and facilitates prediction and prioritization for discovery. J Ind Microbiol Biotechnol 2016; 43:261-76. [PMID: 26318027 PMCID: PMC4753101 DOI: 10.1007/s10295-015-1671-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/09/2015] [Indexed: 01/24/2023]
Abstract
The enediynes are one of the most fascinating families of bacterial natural products given their unprecedented molecular architecture and extraordinary cytotoxicity. Enediynes are rare with only 11 structurally characterized members and four additional members isolated in their cycloaromatized form. Recent advances in DNA sequencing have resulted in an explosion of microbial genomes. A virtual survey of the GenBank and JGI genome databases revealed 87 enediyne biosynthetic gene clusters from 78 bacteria strains, implying that enediynes are more common than previously thought. Here we report the construction and analysis of an enediyne genome neighborhood network (GNN) as a high-throughput approach to analyze secondary metabolite gene clusters. Analysis of the enediyne GNN facilitated rapid gene cluster annotation, revealed genetic trends in enediyne biosynthetic gene clusters resulting in a simple prediction scheme to determine 9- versus 10-membered enediyne gene clusters, and supported a genomic-based strain prioritization method for enediyne discovery.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA.
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, 33458, USA.
- Natural Products Library Initiative, The Scripps Research Institute, Jupiter, FL, 33458, USA.
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32
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Liu X. Generate a bioactive natural product library by mining bacterial cytochrome P450 patterns. Synth Syst Biotechnol 2016; 1:95-108. [PMID: 29062932 PMCID: PMC5640691 DOI: 10.1016/j.synbio.2016.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 01/26/2016] [Indexed: 11/25/2022] Open
Abstract
The increased number of annotated bacterial genomes provides a vast resource for genome mining. Several bacterial natural products with epoxide groups have been identified as pre-mRNA spliceosome inhibitors and antitumor compounds through genome mining. These epoxide-containing natural products feature a common biosynthetic characteristic that cytochrome P450s (CYPs) and its patterns such as epoxidases are employed in the tailoring reactions. The tailoring enzyme patterns are essential to both biological activities and structural diversity of natural products, and can be used for enzyme pattern-based genome mining. Recent development of direct cloning, heterologous expression, manipulation of the biosynthetic pathways and the CRISPR-CAS9 system have provided molecular biology tools to turn on or pull out nascent biosynthetic gene clusters to generate a microbial natural product library. This review focuses on a library of epoxide-containing natural products and their associated CYPs, with the intention to provide strategies on diversifying the structures of CYP-catalyzed bioactive natural products. It is conceivable that a library of diversified bioactive natural products will be created by pattern-based genome mining, direct cloning and heterologous expression as well as the genomic manipulation.
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Affiliation(s)
- Xiangyang Liu
- UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
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33
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Shen B, Hindra, Yan X, Huang T, Ge H, Yang D, Teng Q, Rudolf JD, Lohman JR. Enediynes: Exploration of microbial genomics to discover new anticancer drug leads. Bioorg Med Chem Lett 2015; 25:9-15. [PMID: 25434000 PMCID: PMC4480864 DOI: 10.1016/j.bmcl.2014.11.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 11/05/2014] [Accepted: 11/06/2014] [Indexed: 11/19/2022]
Abstract
The enediyne natural products have been explored for their phenomenal cytotoxicity. The development of enediynes into anticancer drugs has been successfully achieved through the utilization of polymer- and antibody-drug conjugates (ADCs) as drug delivery systems. An increasing inventory of enediynes would benefit current application of ADCs in many oncology programs. Innovations in expanding the enediyne inventory should take advantage of the current knowledge of enediyne biosynthesis and post-genomics technologies. Bioinformatics analysis of microbial genomes reveals that enediynes are underexplored, in particular from Actinomycetales. This digest highlights the emerging opportunities to explore microbial genomics for the discovery of novel enediyne natural products.
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Affiliation(s)
- Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL 33458, USA; Natural Products Library Initiative, The Scripps Research Institute, Jupiter, FL 33458, USA.
| | - Hindra
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Tingting Huang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Huiming Ge
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Qihui Teng
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jeremy R Lohman
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
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34
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Chen X, Ji R, Jiang X, Yang R, Liu F, Xin Y. Iterative type I polyketide synthases involved in enediyne natural product biosynthesis. IUBMB Life 2014; 66:587-95. [PMID: 25278375 DOI: 10.1002/iub.1316] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/14/2014] [Indexed: 12/12/2022]
Abstract
Enediyne natural products are potent antibiotics structurally characterized by an enediyne core containing two acetylenic groups conjugated to a double bond in a 9- or 10-membered carbocycle. The biosynthetic gene clusters for enediynes encode a novel iterative type I polyketide synthase (PKSE), which is generally believed to initiate the biosynthetic process of enediyne cores. This review article will cover research efforts made since its discovery to elucidate the role of the PKSE in enediyne core biosynthesis. Topics covered include the unique domain architecture, identification, and characterization of turnover products, and interaction with partner thioesterase protein.
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Affiliation(s)
- Xiaolei Chen
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
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35
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Ge HM, Huang T, Rudolf JD, Lohman JR, Huang SX, Guo X, Shen B. Enediyne polyketide synthases stereoselectively reduce the β-ketoacyl intermediates to β-D-hydroxyacyl intermediates in enediyne core biosynthesis. Org Lett 2014; 16:3958-61. [PMID: 25019332 PMCID: PMC4144755 DOI: 10.1021/ol501767v] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
PKSE
biosynthesizes an enediyne core precursor from decarboxylative
condensation of eight malonyl-CoAs. The KR domain of PKSE is responsible
for iterative β-ketoreduction in each round of polyketide chain
elongation. KRs from selected PKSEs were investigated in vitro with
β-ketoacyl-SNACs as substrate mimics. Each of the KRs reduced
the β-ketoacyl-SNACs stereoselectively, all affording the corresponding
β-d-hydroxyacyl-SNACs, and the catalytic efficiencies
(kcat/KM)
of the KRs increased significantly as the chain length of the β-ketoacyl-SNAC
substrate increases.
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Affiliation(s)
- Hui-Ming Ge
- Department of Chemistry, ‡Department of Molecular Therapeutics, and §Natural Products Library Initiatives, The Scripps Research Institute , Jupiter, Florida 33458, United States
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36
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Horsman GP, Lechner A, Ohnishi Y, Moore BS, Shen B. Predictive model for epoxide hydrolase-generated stereochemistry in the biosynthesis of nine-membered enediyne antitumor antibiotics. Biochemistry 2013; 52:5217-24. [PMID: 23844627 DOI: 10.1021/bi400572a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nine-membered enediyne antitumor antibiotics C-1027, neocarzinostatin (NCS), and kedarcidin (KED) possess enediyne cores to which activity-modulating peripheral moieties are attached via (R)- or (S)-vicinal diols. We have previously shown that this stereochemical difference arises from hydrolysis of epoxide precursors by epoxide hydrolases (EHs) with different regioselectivities. The inverting EHs, such as SgcF, hydrolyze an (S)-epoxide substrate to yield an (R)-diol in C-1027 biosynthesis, whereas the retaining EHs, such as NcsF2 and KedF, hydrolyze an (S)-epoxide substrate to yield an (S)-diol in NCS and KED biosynthesis. We now report the characterization of a series of EH mutants and provide a predictive model for EH regioselectivity in the biosynthesis of the nine-membered enediyne antitumor antibiotics. A W236Y mutation in SgcF increased the retaining activity toward (S)-styrene oxide by 3-fold, and a W236Y/Q237M double mutation in SgcF, mimicking NcsF2 and KedF, resulted in a 20-fold increase in the retaining activity. To test the predictive utility of these mutations, two putative enediyne biosynthesis-associated EHs were identified by genome mining and confirmed as inverting enzymes, SpoF from Salinospora tropica CNB-440 and SgrF (SGR_625) from Streptomyces griseus IFO 13350. Finally, phylogenetic analysis of EHs revealed a familial classification according to inverting versus retaining activity. Taken together, these results provide a predictive model for vicinal diol stereochemistry in enediyne biosynthesis and set the stage for further elucidating the origins of EH regioselectivity.
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Affiliation(s)
- Geoffrey P Horsman
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
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37
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Kersten RD, Lane AL, Nett M, Richter TKS, Duggan BM, Dorrestein PC, Moore BS. Bioactivity-guided genome mining reveals the lomaiviticin biosynthetic gene cluster in Salinispora tropica. Chembiochem 2013; 14:955-62. [PMID: 23649992 DOI: 10.1002/cbic.201300147] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Indexed: 12/27/2022]
Abstract
The use of genome sequences has become routine in guiding the discovery and identification of microbial natural products and their biosynthetic pathways. In silico prediction of molecular features, such as metabolic building blocks, physico-chemical properties or biological functions, from orphan gene clusters has opened up the characterization of many new chemo- and genotypes in genome mining approaches. Here, we guided our genome mining of two predicted enediyne pathways in Salinispora tropica CNB-440 by a DNA interference bioassay to isolate DNA-targeting enediyne polyketides. An organic extract of S. tropica showed DNA-interference activity that surprisingly was not abolished in genetic mutants of the targeted enediyne pathways, ST_pks1 and spo. Instead we showed that the product of the orphan type II polyketide synthase pathway, ST_pks2, is solely responsible for the DNA-interfering activity of the parent strain. Subsequent comparative metabolic profiling revealed the lomaiviticins, glycosylated diazofluorene polyketides, as the ST_pks2 products. This study marks the first report of the 59 open reading frame lomaiviticin gene cluster (lom) and supports the biochemical logic of their dimeric construction through a pathway related to the kinamycin monomer.
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Affiliation(s)
- Roland D Kersten
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204, USA
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38
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Lohman JR, Huang SX, Horsman GP, Dilfer PE, Huang T, Chen Y, Wendt-Pienkowski E, Shen B. Cloning and sequencing of the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650 revealing new insights into biosynthesis of the enediyne family of antitumor antibiotics. MOLECULAR BIOSYSTEMS 2013; 9:478-91. [PMID: 23360970 DOI: 10.1039/c3mb25523a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enediyne natural product biosynthesis is characterized by a convergence of multiple pathways, generating unique peripheral moieties that are appended onto the distinctive enediyne core. Kedarcidin (KED) possesses two unique peripheral moieties, a (R)-2-aza-3-chloro-β-tyrosine and an iso-propoxy-bearing 2-naphthonate moiety, as well as two deoxysugars. The appendage pattern of these peripheral moieties to the enediyne core in KED differs from the other enediynes studied to date with respect to stereochemical configuration. To investigate the biosynthesis of these moieties and expand our understanding of enediyne core formation, the biosynthetic gene cluster for KED was cloned from Streptoalloteichus sp. ATCC 53650 and sequenced. Bioinformatics analysis of the ked cluster revealed the presence of the conserved genes encoding for enediyne core biosynthesis, type I and type II polyketide synthase loci likely responsible for 2-aza-l-tyrosine and 3,6,8-trihydroxy-2-naphthonate formation, and enzymes known for deoxysugar biosynthesis. Genes homologous to those responsible for the biosynthesis, activation, and coupling of the l-tyrosine-derived moieties from C-1027 and maduropeptin and of the naphthonate moiety from neocarzinostatin are present in the ked cluster, supporting 2-aza-l-tyrosine and 3,6,8-trihydroxy-2-naphthoic acid as precursors, respectively, for the (R)-2-aza-3-chloro-β-tyrosine and the 2-naphthonate moieties in KED biosynthesis.
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Affiliation(s)
- Jeremy R Lohman
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, USA
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39
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Belecki K, Townsend CA. Environmental Control of the Calicheamicin Polyketide Synthase Leads to Detection of a Programmed Octaketide and a Proposal for Enediyne Biosynthesis. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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Belecki K, Townsend CA. Environmental control of the calicheamicin polyketide synthase leads to detection of a programmed octaketide and a proposal for enediyne biosynthesis. Angew Chem Int Ed Engl 2012; 51:11316-9. [PMID: 23042574 DOI: 10.1002/anie.201206462] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Indexed: 11/09/2022]
Abstract
A light in the dark: the fermentation products of the polyketide synthase CalE8 (without its cognate thioesterase) were identified and gave some insight into the elusive early steps of calicheamicin biosynthesis. Fermentation in either the light or dark resulted in different proportions of a new octaketide and led to an updated mechanistic proposal.
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Affiliation(s)
- Katherine Belecki
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, USA
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41
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Liew CW, Nilsson M, Chen MW, Sun H, Cornvik T, Liang ZX, Lescar J. Crystal structure of the acyltransferase domain of the iterative polyketide synthase in enediyne biosynthesis. J Biol Chem 2012; 287:23203-15. [PMID: 22589546 DOI: 10.1074/jbc.m112.362210] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Biosynthesis of the enediyne natural product dynemicin in Micromonospora chersina is initiated by DynE8, a highly reducing iterative type I polyketide synthase that assembles polyketide intermediates from the acetate units derived solely from malonyl-CoA. To understand the substrate specificity and the evolutionary relationship between the acyltransferase (AT) domains of DynE8, fatty acid synthase, and modular polyketide synthases, we overexpressed a 44-kDa fragment of DynE8 (hereafter named AT(DYN10)) encompassing its entire AT domain and the adjacent linker domain. The crystal structure at 1.4 Å resolution unveils a α/β hydrolase and a ferredoxin-like subdomain with the Ser-His catalytic dyad located in the cleft between the two subdomains. The linker domain also adopts a α/β fold abutting the AT catalytic domain. Co-crystallization with malonyl-CoA yielded a malonyl-enzyme covalent complex that most likely represents the acyl-enzyme intermediate. The structure explains the preference for malonyl-CoA with a conserved arginine orienting the carboxylate group of malonate and several nonpolar residues that preclude α-alkyl malonyl-CoA binding. Co-crystallization with acetyl-CoA revealed two noncovalently bound acetates generated by the enzymatic hydrolysis of acetyl-CoA that acts as an inhibitor for DynE8. This suggests that the AT domain can upload the acyl groups from either malonyl-CoA or acetyl-CoA onto the catalytic Ser(651) residue. However, although the malonyl group can be transferred to the acyl carrier protein domain, transfer of the acetyl group to the acyl carrier protein domain is suppressed. Local structural differences may account for the different stability of the acyl-enzyme intermediates.
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Affiliation(s)
- Chong Wai Liew
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
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Thibodeaux CJ, Chang WC, Liu HW. Enzymatic chemistry of cyclopropane, epoxide, and aziridine biosynthesis. Chem Rev 2012; 112:1681-709. [PMID: 22017381 PMCID: PMC3288687 DOI: 10.1021/cr200073d] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Wei-chen Chang
- College of Pharmacy and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| | - Hung-wen Liu
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
- College of Pharmacy and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
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43
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Chang A, Singh S, Bingman CA, Thorson JS, Phillips GN. Structural characterization of CalO1: a putative orsellinic acid methyltransferase in the calicheamicin-biosynthetic pathway. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:197-203. [PMID: 21358050 PMCID: PMC3046457 DOI: 10.1107/s090744491100360x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 01/28/2011] [Indexed: 11/10/2022]
Abstract
The X-ray structure determination at 2.4 Å resolution of the putative orsellinic acid C3 O-methyltransferase (CalO1) involved in calicheamicin biosynthesis is reported. Comparison of CalO1 with a homology model of the functionally related calicheamicin orsellinic acid C2 O-methyltransferase (CalO6) implicates several residues that are likely to contribute to the regiospecificity of alkylation. Consistent with the proposed requirement of an acyl-carrier-protein-bound substrate, this structural study also reveals structural determinants within CalO1 that are anticipated to accommodate an association with an acyl carrier protein.
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Affiliation(s)
- Aram Chang
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
- Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
| | - Shanteri Singh
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, National Cooperative Drug Discovery Program, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, USA
| | - Craig A. Bingman
- Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
| | - Jon S. Thorson
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, National Cooperative Drug Discovery Program, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, USA
| | - George N. Phillips
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
- Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
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Liew CW, Sharff A, Kotaka M, Kong R, Sun H, Qureshi I, Bricogne G, Liang ZX, Lescar J. Induced-fit upon ligand binding revealed by crystal structures of the hot-dog fold thioesterase in dynemicin biosynthesis. J Mol Biol 2010; 404:291-306. [PMID: 20888341 DOI: 10.1016/j.jmb.2010.09.041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 09/16/2010] [Accepted: 09/20/2010] [Indexed: 11/27/2022]
Abstract
Dynemicins are structurally related 10-membered enediyne natural products isolated from Micromonospora chernisa with potent antitumor and antibiotic activity. The early biosynthetic steps of the enediyne moiety of dynemicins are catalyzed by an iterative polyketide synthase (DynE8) and a thioesterase (DynE7). Recent studies indicate that the function of DynE7 is to off-load the linear biosynthetic intermediate assembled on DynE8. Here, we report crystal structures of DynE7 in its free form at 2.7 Å resolution and of DynE7 in complex with the DynE8-produced all-trans pentadecen-2-one at 2.1 Å resolution. These crystal structures reveal that upon ligand binding, significant conformational changes throughout the substrate-binding tunnel result in an expanded tunnel that traverses an entire monomer of the tetrameric DynE7 protein. The enlarged inner segment of the channel binds the carbonyl-conjugated polyene mainly through hydrophobic interactions, whereas the putative catalytic residues are located in the outer segment of the channel. The crystallographic information reinforces an unusual catalytic mechanism that involves a strictly conserved arginine residue for this subfamily of hot-dog fold thioesterases, distinct from the typical mechanism for hot-dog fold thioesterases that utilizes an acidic residue for catalysis.
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Affiliation(s)
- Chong Wai Liew
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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45
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Chen X, Guo ZF, Lai PM, Sze KH, Guo Z. Identification of a Nonaketide Product for the Iterative Polyketide Synthase in Biosynthesis of the Nine-Membered Enediyne C-1027. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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46
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Chen X, Guo ZF, Lai PM, Sze KH, Guo Z. Identification of a Nonaketide Product for the Iterative Polyketide Synthase in Biosynthesis of the Nine-Membered Enediyne C-1027. Angew Chem Int Ed Engl 2010; 49:7926-8. [DOI: 10.1002/anie.201003369] [Citation(s) in RCA: 12] [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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47
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Polyketide synthase chemistry does not direct biosynthetic divergence between 9- and 10-membered enediynes. Proc Natl Acad Sci U S A 2010; 107:11331-5. [PMID: 20534556 DOI: 10.1073/pnas.1003442107] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enediynes are potent antitumor antibiotics that are classified as 9- or 10-membered according to the size of the enediyne core structure. However, almost nothing is known about enediyne core biosynthesis, and the determinants of 9- versus 10-membered enediyne core biosynthetic divergence remain elusive. Previous work identified enediyne-specific polyketide synthases (PKSEs) that can be phylogenetically distinguished as being involved in 9- versus 10-membered enediyne biosynthesis, suggesting that biosynthetic divergence might originate from differing PKSE chemistries. Recent in vitro studies have identified several compounds produced by the PKSE and associated thioesterase (TE), but condition-dependent product profiles make it difficult to ascertain a true catalytic difference between 9- and 10-membered PKSE-TE systems. Here we report that PKSE chemistry does not direct 9- versus 10-membered enediyne core biosynthetic divergence as revealed by comparing the products from three 9-membered and two 10-membered PKSE-TE systems under identical conditions using robust in vivo assays. Three independent experiments support a common catalytic function for 9- and 10-membered PKSEs by the production of a heptaene metabolite from: (i) all five cognate PKSE-TE pairs in Escherichia coli; (ii) the C-1027 and calicheamicin cognate PKSE-TEs in Streptomyces lividans K4-114; and (iii) selected native producers of both 9- and 10-membered enediynes. Furthermore, PKSEs and TEs from different 9- and 10-membered enediyne biosynthetic machineries are freely interchangeable, revealing that 9- versus 10-membered enediyne core biosynthetic divergence occurs beyond the PKSE-TE level. These findings establish a starting point for determining the origins of this biosynthetic divergence.
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48
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Cundliffe E, Demain AL. Avoidance of suicide in antibiotic-producing microbes. J Ind Microbiol Biotechnol 2010; 37:643-72. [PMID: 20446033 DOI: 10.1007/s10295-010-0721-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 03/30/2010] [Indexed: 11/29/2022]
Abstract
Many microbes synthesize potentially autotoxic antibiotics, mainly as secondary metabolites, against which they need to protect themselves. This is done in various ways, ranging from target-based strategies (i.e. modification of normal drug receptors or de novo synthesis of the latter in drug-resistant form) to the adoption of metabolic shielding and/or efflux strategies that prevent drug-target interactions. These self-defence mechanisms have been studied most intensively in antibiotic-producing prokaryotes, of which the most prolific are the actinomycetes. Only a few documented examples pertain to lower eukaryotes while higher organisms have hardly been addressed in this context. Thus, many plant alkaloids, variously described as herbivore repellents or nitrogen excretion devices, are truly antibiotics-even if toxic to humans. As just one example, bulbs of Narcissus spp. (including the King Alfred daffodil) accumulate narciclasine that binds to the larger subunit of the eukaryotic ribosome and inhibits peptide bond formation. However, ribosomes in the Amaryllidaceae have not been tested for possible resistance to narciclasine and other alkaloids. Clearly, the prevalence of suicide avoidance is likely to extend well beyond the remit of the present article.
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Affiliation(s)
- Eric Cundliffe
- Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK.
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49
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Liang ZX. Complexity and simplicity in the biosynthesis of enediyne natural products. Nat Prod Rep 2010; 27:499-528. [DOI: 10.1039/b908165h] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Belecki K, Crawford JM, Townsend CA. Production of octaketide polyenes by the calicheamicin polyketide synthase CalE8: implications for the biosynthesis of enediyne core structures. J Am Chem Soc 2009; 131:12564-6. [PMID: 19689130 DOI: 10.1021/ja904391r] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enediyne antibiotics are categorized according to the presence of either a 9- or 10-membered ring within their polyketide-derived core structures. Recent literature reports have favored the notion that biosynthetic divergence of the two structural families is determined by the enediyne polyketide synthases (PKSs) alone. We now disclose the simultaneous in vitro production of three octaketide polyenes by biosynthetic enzymes for the 10-membered enediyne calicheamicin gamma(1)(I), including the elusive beta-keto acid precursor to a previously described C15 methyl hexaenone. Alongside these two polyene products, we have additionally detected a hydrocarbon heptaene previously isolated only from 9-membered enediyne systems. The discovery of the heptaene in the calicheamicin system promotes a more convergent model for the early steps of enediyne biosynthesis. Furthermore, the synthesis of this set of octaketides by the enediyne PKS CalE8 and thioesterase CalE7 suggests, in contrast to recent biosynthetic proposals, that accessory enzymes may be necessary to initiate differentiation to 9- or 10-membered enediyne precursors, either by modulation of enediyne PKS activity or by interception and modification of polyketide chain-extension intermediates.
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Affiliation(s)
- Katherine Belecki
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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