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 2024:10.1038/s41589-024-01636-y. [PMID: 38831037 DOI: 10.1038/s41589-024-01636-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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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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3
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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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4
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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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5
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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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6
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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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7
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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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8
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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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9
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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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10
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Iterative polyketide biosynthesis by modular polyketide synthases in bacteria. Appl Microbiol Biotechnol 2015; 100:541-57. [PMID: 26549236 DOI: 10.1007/s00253-015-7093-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/10/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
Abstract
Modular polyketide synthases (type I PKSs) in bacteria are responsible for synthesizing a significant percentage of bioactive natural products. This group of synthases has a characteristic modular organization, and each module within a PKS carries out one cycle of polyketide chain elongation; thus each module is non-iterative in function. It was possible to predict the basic structure of a polyketide product from the module organization of the PKSs, since there generally existed a co-linearity between the number of modules and the number of chain elongations. However, more and more bacterial modular PKSs fail to conform to the canonical rules, and a particularly noteworthy group of non-canonical PKSs is the bacterial iterative type I PKSs. This review covers recent examples of iteratively used modular PKSs in bacteria. These non-canonical PKSs give rise to a large array of natural products with impressive structural diversity. The molecular mechanism behind the iterations is often unclear, presenting a new challenge to the rational engineering of these PKSs with the goal of generating new natural products. Structural elucidation of these synthase complexes and better understanding of potential PKS-PKS interactions as well as PKS-substrate recognition may provide new prospects and inspirations for the discovery and engineering of new bioactive polyketides.
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11
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Elshahawi SI, Ramelot TA, Seetharaman J, Chen J, Singh S, Yang Y, Pederson K, Kharel MK, Xiao R, Lew S, Yennamalli RM, Miller MD, Wang F, Tong L, Montelione GT, Kennedy MA, Bingman CA, Zhu H, Phillips GN, Thorson JS. Structure-guided functional characterization of enediyne self-sacrifice resistance proteins, CalU16 and CalU19. ACS Chem Biol 2014; 9:2347-58. [PMID: 25079510 PMCID: PMC4201346 DOI: 10.1021/cb500327m] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Calicheamicin γ1I (1)
is an enediyne antitumor compound produced by Micromonospora
echinospora spp. calichensis, and its biosynthetic gene cluster
has been previously reported. Despite extensive analysis and biochemical
study, several genes in the biosynthetic gene cluster of 1 remain functionally unassigned. Using a structural genomics approach
and biochemical characterization, two proteins encoded by genes from
the 1 biosynthetic gene cluster assigned as “unknowns”,
CalU16 and CalU19, were characterized. Structure analysis revealed
that they possess the STeroidogenic Acute Regulatory protein related
lipid Transfer (START) domain known mainly to bind and transport lipids
and previously identified as the structural signature of the enediyne
self-resistance protein CalC. Subsequent study revealed calU16 and calU19 to confer resistance to 1, and reminiscent of the prototype CalC, both CalU16 and CalU19 were
cleaved by 1in vitro. Through site-directed
mutagenesis and mass spectrometry, we identified the site of cleavage
in each protein and characterized their function in conferring resistance
against 1. This report emphasizes the importance of structural
genomics as a powerful tool for the functional annotation of unknown
proteins.
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Affiliation(s)
- Sherif I. Elshahawi
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Theresa A. Ramelot
- Department
of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056, United States
| | - Jayaraman Seetharaman
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry & Center for Structural Biology, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Shanteri Singh
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Yunhuang Yang
- Department
of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056, United States
| | - Kari Pederson
- Complex Carbohydrate
Research Center, Northeast Structural Genomics Consortium, University of Georgia, Athens, Georgia 30602, United States
| | - Madan K. Kharel
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Rong Xiao
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology
and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Scott Lew
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Ragothaman M. Yennamalli
- Department
of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Mitchell D. Miller
- Department
of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Fengbin Wang
- Department
of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Liang Tong
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Gaetano T. Montelione
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology
and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Department
of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Michael A. Kennedy
- Department
of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056, United States
| | - Craig A. Bingman
- Department
of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry & Center for Structural Biology, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - George N. Phillips
- Department
of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, United States
| | - Jon S. Thorson
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
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12
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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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Belecki K, Townsend CA. Biochemical determination of enzyme-bound metabolites: preferential accumulation of a programmed octaketide on the enediyne polyketide synthase CalE8. J Am Chem Soc 2013; 135:14339-48. [PMID: 24041368 DOI: 10.1021/ja406697t] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite considerable interest in the enediyne family of antitumor antibiotics, assembly of their polyketide core structures in nature remains poorly understood. Discriminating methods to access enzyme-bound intermediates are critical for elucidating unresolved polyketide and nonribosomal peptide biosynthetic pathways. Here, we describe the development of broadly applicable techniques for the mild chemical release and analysis of intermediates bound to carrier proteins (CPs), providing access to these species even in sensitive systems. These techniques were applied to CalE8, the polyketide synthase (PKS) involved in calicheamicin biosynthesis, facilitating the unambiguous identification of enzyme-bound polyketides on an enediyne PKS. Moreover, these methods enabled the preparation of fully unloaded CalE8, providing a "clean slate" for reconstituted activity and allowing us to demonstrate the preferential accumulation of a PKS-bound octaketide with evidence of programmed processing control by CalE8. This intermediate, which has the expected chain length for enediyne core construction, could previously only be indirectly inferred. These studies prove that this polyketide is an authentic product of CalE8 and may be a key precursor to the enediyne core of calicheamicin, as it is the only programmed, enzyme-bound species observed for any enediyne system to date. Our experimental advances into a generally inaccessible system illustrate the utility of these techniques for investigating CP-based biosynthetic pathways.
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Affiliation(s)
- Katherine Belecki
- Department of Chemistry, The Johns Hopkins University , Remsen 252, 3400 North Charles St., Baltimore, Maryland 21218, United States
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Microbial natural products: molecular blueprints for antitumor drugs. J Ind Microbiol Biotechnol 2013; 40:1181-210. [PMID: 23999966 DOI: 10.1007/s10295-013-1331-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 08/07/2013] [Indexed: 12/18/2022]
Abstract
Microbes from two of the three domains of life, the Prokarya, and Eukarya, continue to serve as rich sources of structurally complex chemical scaffolds that have proven to be essential for the development of anticancer therapeutics. This review describes only a handful of exemplary natural products and their derivatives as well as those that have served as elegant blueprints for the development of novel synthetic structures that are either currently in use or in clinical or preclinical trials together with some of their earlier analogs in some cases whose failure to proceed aided in the derivation of later compounds. In every case, a microbe has been either identified as the producer of secondary metabolites or speculated to be involved in the production via symbiotic associations. Finally, rapidly evolving next-generation sequencing technologies have led to the increasing availability of microbial genomes. Relevant examples of genome mining and genetic manipulation are discussed, demonstrating that we have only barely scratched the surface with regards to harnessing the potential of microbes as sources of new pharmaceutical leads/agents or biological probes.
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