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Lauterbach L, Rinkel J, Dickschat JS. Two Bacterial Diterpene Synthases from Allokutzneria albata Produce Bonnadiene, Phomopsene, and Allokutznerene. Angew Chem Int Ed Engl 2018; 57:8280-8283. [PMID: 29758116 DOI: 10.1002/anie.201803800] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Indexed: 11/08/2022]
Abstract
Two diterpene synthases from Allokutzneria albata were studied for their products, resulting in the identification of the new compound bonnadiene from the first enzyme. Although phylogenetically unrelated to fungal phomopsene synthase, the second enzyme produced a mixture of phomopsene and a biosynthetically linked new compound, allokutznerene, as well as spiroviolene. Both enzymes were subjected to in-depth mechanistic studies involving isotopic labelling experiments, metal-cofactor variation, and site-directed mutagenesis. Oxidation products of phomopsene and allokutznerene are also discussed.
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Affiliation(s)
- Lukas Lauterbach
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Jan Rinkel
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
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High-Yield Production of Herbicidal Thaxtomins and Thaxtomin Analogs in a Nonpathogenic Streptomyces Strain. Appl Environ Microbiol 2018; 84:AEM.00164-18. [PMID: 29602787 DOI: 10.1128/aem.00164-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/27/2018] [Indexed: 12/13/2022] Open
Abstract
Thaxtomins are virulence factors of most plant-pathogenic Streptomyces strains. Due to their potent herbicidal activity, attractive environmental compatibility, and inherent biodegradability, thaxtomins are key active ingredients of bioherbicides approved by the U.S. Environmental Protection Agency. However, the low yield of thaxtomins in native Streptomyces producers limits their wide agricultural applications. Here, we describe the high-yield production of thaxtomins in a heterologous host. The thaxtomin gene cluster from S. scabiei 87.22 was cloned and expressed in S. albus J1074 after chromosomal integration. The production of thaxtomins and nitrotryptophan analogs was observed using liquid chromatography-mass spectrometry (LC-MS) analysis. When the engineered S. albus J1074 was cultured in the minimal medium Thx defined medium supplemented with 1% cellobiose (TDMc), the yield of the most abundant and herbicidal analog, thaxtomin A, was 10 times higher than that in S. scabiei 87.22, and optimization of the medium resulted in the highest yield of thaxtomin analogs at about 222 mg/liter. Further engineering of the thaxtomin biosynthetic gene cluster through gene deletion led to the production of multiple biosynthetic intermediates important to the chemical synthesis of new analogs. Additionally, the versatility of the thaxtomin biosynthetic system in S. albus J1074 was capitalized on to produce one unnatural fluorinated analog, 5-fluoro-thaxtomin A (5-F-thaxtomin A), whose structure was elucidated by a combination of MS and one-dimensional (1D) and 2D nuclear magnetic resonance (NMR) analyses. Natural and unnatural thaxtomins demonstrated potent herbicidal activity in radish seedling assays. These results indicated that S. albus J1074 has the potential to produce thaxtomins and analogs thereof with high yield, fostering their agricultural applications.IMPORTANCE Thaxtomins are agriculturally valuable herbicidal natural products, but the productivity of native producers is limiting. Heterologous expression of the thaxtomin gene cluster in S. albus J1074 resulted in the highest yield of thaxtomins ever reported, representing a significant leap forward in its wide agricultural use. Furthermore, current synthetic routes to thaxtomins and analogs are lengthy, and two thaxtomin biosynthetic intermediates produced at high yields in this work can provide precursors and building blocks to advanced synthetic routes. Importantly, the production of 5-F-thaxtomin A in engineered S. albus J1074 demonstrated a viable alternative to chemical methods in the synthesis of new thaxtomin analogs. Moreover, our work presents an attractive synthetic biology strategy to improve the supply of herbicidal thaxtomins, likely finding general applications in the discovery and production of many other bioactive natural products.
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Yang Y, Zhang Y, Zhang S, Chen Q, Ma K, Bao L, Tao Y, Yin W, Wang G, Liu H. Identification and Characterization of a Membrane-Bound Sesterterpene Cyclase from Streptomyces somaliensis. JOURNAL OF NATURAL PRODUCTS 2018; 81:1089-1092. [PMID: 29553734 DOI: 10.1021/acs.jnatprod.7b01033] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Sesterterpenes are usually found in plants and fungi, but are rare in bacteria. Here, we present the identification of StsC from Streptomyces somaliensis, a member of the UbiA superfamily, as a membrane-bound sesterterpene cyclase in bacteria. The cyclized products for StsC, somaliensenes A (1) and B (2), were identified by expressing the corresponding gene in an engineered Escherichia coli strain. The structures of 1 and 2 were determined by analysis of the NMR and MS spectroscopic data.
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Affiliation(s)
- Yanlong Yang
- State Key Laboratory of Mycology , Institute of Microbiology, Chinese Academy of Sciences , Beijing , 100101 , People's Republic of China
| | - Yuting Zhang
- State Key Laboratory of Mycology , Institute of Microbiology, Chinese Academy of Sciences , Beijing , 100101 , People's Republic of China
- Savaid Medical School , University of Chinese Academy of Sciences , Beijing , 100049 , People's Republic of China
| | - Shasha Zhang
- Chinese Academy of Science, Key Laboratory of Microbial Physiology and Metabolic Engineering , Institute of Microbiology, Chinese Academy of Sciences , Beijing , 100101 , People's Republic of China
| | - Qingwen Chen
- State Key Laboratory of Plant Genomics , Institute of Genetics and Developmental Biology, Chinese Academy of Sciences , Beijing , 100101 , People's Republic of China
| | - Ke Ma
- State Key Laboratory of Mycology , Institute of Microbiology, Chinese Academy of Sciences , Beijing , 100101 , People's Republic of China
- Savaid Medical School , University of Chinese Academy of Sciences , Beijing , 100049 , People's Republic of China
| | - Li Bao
- State Key Laboratory of Mycology , Institute of Microbiology, Chinese Academy of Sciences , Beijing , 100101 , People's Republic of China
- Savaid Medical School , University of Chinese Academy of Sciences , Beijing , 100049 , People's Republic of China
| | - Yong Tao
- Chinese Academy of Science, Key Laboratory of Microbial Physiology and Metabolic Engineering , Institute of Microbiology, Chinese Academy of Sciences , Beijing , 100101 , People's Republic of China
| | - Wenbing Yin
- State Key Laboratory of Mycology , Institute of Microbiology, Chinese Academy of Sciences , Beijing , 100101 , People's Republic of China
- Savaid Medical School , University of Chinese Academy of Sciences , Beijing , 100049 , People's Republic of China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics , Institute of Genetics and Developmental Biology, Chinese Academy of Sciences , Beijing , 100101 , People's Republic of China
| | - Hongwei Liu
- State Key Laboratory of Mycology , Institute of Microbiology, Chinese Academy of Sciences , Beijing , 100101 , People's Republic of China
- Savaid Medical School , University of Chinese Academy of Sciences , Beijing , 100049 , People's Republic of China
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Minami A, Ozaki T, Liu C, Oikawa H. Cyclopentane-forming di/sesterterpene synthases: widely distributed enzymes in bacteria, fungi, and plants. Nat Prod Rep 2018; 35:1330-1346. [DOI: 10.1039/c8np00026c] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cyclization mechanisms and structural diversification strategies of novel cyclopentane-forming terpene synthases from various organisms are reviewed.
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Affiliation(s)
- Atsushi Minami
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo
- Japan
| | - Taro Ozaki
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo
- Japan
| | - Chengwei Liu
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo
- Japan
| | - Hideaki Oikawa
- Division of Chemistry
- Graduate School of Science
- Hokkaido University
- Sapporo
- Japan
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55
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Rudolf JD, Chang CY, Ma M, Shen B. Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function. Nat Prod Rep 2017; 34:1141-1172. [PMID: 28758170 PMCID: PMC5585785 DOI: 10.1039/c7np00034k] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to January 2017Cytochrome P450 enzymes (P450s) are some of the most exquisite and versatile biocatalysts found in nature. In addition to their well-known roles in steroid biosynthesis and drug metabolism in humans, P450s are key players in natural product biosynthetic pathways. Natural products, the most chemically and structurally diverse small molecules known, require an extensive collection of P450s to accept and functionalize their unique scaffolds. In this review, we survey the current catalytic landscape of P450s within the Streptomyces genus, one of the most prolific producers of natural products, and comprehensively summarize the functionally characterized P450s from Streptomyces. A sequence similarity network of >8500 P450s revealed insights into the sequence-function relationships of these oxygen-dependent metalloenzymes. Although only ∼2.4% and <0.4% of streptomycete P450s have been functionally and structurally characterized, respectively, the study of streptomycete P450s involved in the biosynthesis of natural products has revealed their diverse roles in nature, expanded their catalytic repertoire, created structural and mechanistic paradigms, and exposed their potential for biomedical and biotechnological applications. Continued study of these remarkable enzymes will undoubtedly expose their true complement of chemical and biological capabilities.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
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Abstract
![]()
The
year 2017 marks the twentieth anniversary of terpenoid cyclase
structural biology: a trio of terpenoid cyclase structures reported
together in 1997 were the first to set the foundation for understanding
the enzymes largely responsible for the exquisite chemodiversity of
more than 80000 terpenoid natural products. Terpenoid cyclases catalyze
the most complex chemical reactions in biology, in that more than
half of the substrate carbon atoms undergo changes in bonding and
hybridization during a single enzyme-catalyzed cyclization reaction.
The past two decades have witnessed structural, functional, and computational
studies illuminating the modes of substrate activation that initiate
the cyclization cascade, the management and manipulation of high-energy
carbocation intermediates that propagate the cyclization cascade,
and the chemical strategies that terminate the cyclization cascade.
The role of the terpenoid cyclase as a template for catalysis is paramount
to its function, and protein engineering can be used to reprogram
the cyclization cascade to generate alternative and commercially important
products. Here, I review key advances in terpenoid cyclase structural
and chemical biology, focusing mainly on terpenoid cyclases and related
prenyltransferases for which X-ray crystal structures have informed
and advanced our understanding of enzyme structure and function.
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Affiliation(s)
- David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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57
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Tomita T, Kim SY, Teramoto K, Meguro A, Ozaki T, Yoshida A, Motoyoshi Y, Mori N, Ishigami K, Watanabe H, Nishiyama M, Kuzuyama T. Structural Insights into the CotB2-Catalyzed Cyclization of Geranylgeranyl Diphosphate to the Diterpene Cyclooctat-9-en-7-ol. ACS Chem Biol 2017; 12:1621-1628. [PMID: 28463490 DOI: 10.1021/acschembio.7b00154] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The diterpene cyclase CotB2 catalyzes the cyclization of geranylgeranyl diphosphate (GGPP) to the tricyclic cyclooctat-9-en-7-ol, which is characterized by a 5-8-5-fused ring skeleton. We have previously proposed a cyclization cascade involving a unique carbon-carbon bond rearrangement combined with multiple hydride shifts, all occurring at a single active site. Here, we report the first high-resolution X-ray crystal structure of CotB2 with bound substrate analog geranylgeranyl thiodiphosphate (GGSPP). In the GGSPP-bound form, GGSPP folds into a unique S-shaped conformation that probably reflects the substrate-bound state prior to ionization of the substrate GGPP. The folded framework of GGSPP is surrounded by hydrophobic residues and several aromatic and asparagine residues that are well-positioned to stabilize a series of reactive carbocation intermediates through a combination of cation-π and dipole charge interactions. The combined crystal structures and mutagenesis-based biochemical assays provide a structural basis for exquisite control of ring formation and stereochemistry during CotB2 catalysis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Makoto Nishiyama
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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58
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Affiliation(s)
- Jeroen S. Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry; Rheinische Friedrich Wilhelms University of Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
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59
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Biosynthetic studies on terpenoids produced by Streptomyces. J Antibiot (Tokyo) 2017; 70:811-818. [PMID: 28196976 PMCID: PMC5509993 DOI: 10.1038/ja.2017.12] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 11/25/2016] [Indexed: 12/12/2022]
Abstract
Terpenoids are a large and highly diverse group of natural products. All terpenoids are biosynthesized from isoprenyl diphosphate formed by the consecutive condensation of the five-carbon monomer isopentenyl diphosphate (IPP) to its isomer dimethylallyl diphosphate (DMAPP). Two distinct biosynthetic pathways produce the essential primary metabolites IPP and DMAPP: the 2-C-methylerythritol 4-phosphate pathway and the mevalonate pathway. The isoprenyl substrates can be cyclized by terpene cyclase into single-ring or multi-ring products, which can be further diversified by subsequent modification reactions, such as hydroxylation and glycosylation. This review article describes the biosynthetic pathways of terpenoids produced by Streptomyces and their related novel enzymes.
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60
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Rabe P, Samborskyy M, Leadlay PF, Dickschat JS. Isoafricanol synthase from Streptomyces malaysiensis. Org Biomol Chem 2017; 15:2353-2358. [DOI: 10.1039/c7ob00234c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A terpene cyclases from Streptomyces malaysiensis was characterised as (+)-isoafricanol synthase and its mechanism was investigated using isotopically labelled substrates.
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Affiliation(s)
- Patrick Rabe
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
| | | | | | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
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61
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17-[16,17-Dihydroxycyclooctatinyl]-hexaketide ester from Streptomyces sp. SR107. Chin J Nat Med 2016; 14:931-933. [DOI: 10.1016/s1875-5364(17)30018-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 11/21/2022]
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62
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Amino-group carrier-protein-mediated secondary metabolite biosynthesis in Streptomyces. Nat Chem Biol 2016; 12:967-972. [DOI: 10.1038/nchembio.2181] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 07/27/2016] [Indexed: 11/08/2022]
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63
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Rabe P, Schmitz T, Dickschat JS. Mechanistic investigations on six bacterial terpene cyclases. Beilstein J Org Chem 2016; 12:1839-1850. [PMID: 27829890 PMCID: PMC5082573 DOI: 10.3762/bjoc.12.173] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/01/2016] [Indexed: 11/26/2022] Open
Abstract
The products obtained by incubation of farnesyl diphosphate (FPP) with six purified bacterial terpene cyclases were characterised by one- and two-dimensional NMR spectroscopic methods, allowing for a full structure elucidation. The absolute configurations of four terpenes were determined based on their optical rotary powers. Incubation experiments with 13C-labelled isotopomers of FPP in buffers containing water or deuterium oxide allowed for detailed insights into the cyclisation mechanisms of the bacterial terpene cyclases.
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Affiliation(s)
- Patrick Rabe
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Thomas Schmitz
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
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64
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Identification, characterization and molecular adaptation of class I redox systems for the production of hydroxylated diterpenoids. Microb Cell Fact 2016; 15:86. [PMID: 27216162 PMCID: PMC4877809 DOI: 10.1186/s12934-016-0487-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/11/2016] [Indexed: 12/31/2022] Open
Abstract
Background De novo production of multi-hydroxylated diterpenoids is challenging due to the lack of efficient redox systems. Results In this study a new reductase/ferredoxin system from Streptomyces afghaniensis (AfR·Afx) was identified, which allowed the Escherichia coli-based production of the trihydroxylated diterpene cyclooctatin, a potent inhibitor of human lysophospholipase. This production system provides a 43-fold increase in cyclooctatin yield (15 mg/L) compared to the native producer. AfR·Afx is superior in activating the cylcooctatin-specific class I P450s CotB3/CotB4 compared to the conventional Pseudomonas putida derived PdR·Pdx model. To enhance the activity of the PdR·Pdx system, the molecular basis for these activity differences, was examined by molecular engineering. Conclusion We demonstrate that redox system engineering can boost and harmonize the catalytic efficiency of class I hydroxylase enzyme cascades. Enhancing CotB3/CotB4 activities also provided for identification of CotB3 substrate promiscuity and sinularcasbane D production, a functionalized diterpenoid originally isolated from the soft coral Sinularia sp. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0487-6) contains supplementary material, which is available to authorized users.
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65
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Genome mining of the sordarin biosynthetic gene cluster from Sordaria araneosa Cain ATCC 36386: characterization of cycloaraneosene synthase and GDP-6-deoxyaltrose transferase. J Antibiot (Tokyo) 2016; 69:541-8. [PMID: 27072286 DOI: 10.1038/ja.2016.40] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/04/2016] [Accepted: 03/13/2016] [Indexed: 01/24/2023]
Abstract
Sordarin is a glycoside antibiotic with a unique tetracyclic diterpene aglycone structure called sordaricin. To understand its intriguing biosynthetic pathway that may include a Diels-Alder-type [4+2]cycloaddition, genome mining of the gene cluster from the draft genome sequence of the producer strain, Sordaria araneosa Cain ATCC 36386, was carried out. A contiguous 67 kb gene cluster consisting of 20 open reading frames encoding a putative diterpene cyclase, a glycosyltransferase, a type I polyketide synthase, and six cytochrome P450 monooxygenases were identified. In vitro enzymatic analysis of the putative diterpene cyclase SdnA showed that it catalyzes the transformation of geranylgeranyl diphosphate to cycloaraneosene, a known biosynthetic intermediate of sordarin. Furthermore, a putative glycosyltransferase SdnJ was found to catalyze the glycosylation of sordaricin in the presence of GDP-6-deoxy-d-altrose to give 4'-O-demethylsordarin. These results suggest that the identified sdn gene cluster is responsible for the biosynthesis of sordarin. Based on the isolated potential biosynthetic intermediates and bioinformatics analysis, a plausible biosynthetic pathway for sordarin is proposed.
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66
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Abstract
This review summarises the characterised bacterial terpene cyclases and their products and discusses the enzyme mechanisms.
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Affiliation(s)
- Jeroen S. Dickschat
- University of Bonn
- Kekulé-Institute of Organic Chemistry and Biochemistry
- 53121 Bonn
- Germany
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67
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"Cation-Stitching Cascade": exquisite control of terpene cyclization in cyclooctatin biosynthesis. Sci Rep 2015; 5:18471. [PMID: 26681256 PMCID: PMC4683443 DOI: 10.1038/srep18471] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/16/2015] [Indexed: 12/23/2022] Open
Abstract
Terpene cyclization is orchestrated by terpene cyclases, which are involved in the biosynthesis of various cyclic natural products, but understanding the origin and mechanism of the selectivity of terpene cyclization is challenging. In this work, we describe an in-depth mechanistic study on cyclooctatin biosynthesis by means of theoretical calculations combined with experimental methods. We show that the main framework of cyclooctatin is formed through domino-type carbocation transportation along the terpene chain, which we call a “cation-stitching cascade”, including multiple hydrogen-shifts and a ring rearrangement that elegantly determine the stereoselectivity.
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68
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Rinkel J, Dickschat JS. Recent highlights in biosynthesis research using stable isotopes. Beilstein J Org Chem 2015; 11:2493-508. [PMID: 26734097 PMCID: PMC4685789 DOI: 10.3762/bjoc.11.271] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/23/2015] [Indexed: 02/03/2023] Open
Abstract
The long and successful history of isotopic labeling experiments within natural products research has both changed and deepened our understanding of biosynthesis. As demonstrated in this article, the usage of isotopes is not at all old-fashioned, but continues to give important insights into biosynthetic pathways of secondary metabolites. This review with 85 cited references is structured by separate discussions of compounds from different classes including polyketides, non-ribosomal peptides, their hybrids, terpenoids, and aromatic compounds formed via the shikimate pathway. The text does not aim at a comprehensive overview, but instead a selection of recent important examples of isotope usage within biosynthetic studies is presented, with a special emphasis on mechanistic surprises.
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Affiliation(s)
- Jan Rinkel
- Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
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69
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Wu YH, Chen GD, He RR, Wang CX, Hu D, Wang GQ, Guo LD, Yao XS, Gao H. Pericolactines A-C, a New Class of Diterpenoid Alkaloids with Unusual Tetracyclic Skeleton. Sci Rep 2015; 5:17082. [PMID: 26611465 PMCID: PMC4661464 DOI: 10.1038/srep17082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/26/2015] [Indexed: 01/30/2023] Open
Abstract
Fusicoccane diterpenoids usually possess a fused 5-8-5 tricyclic ring system, which are biogenetically generated from geranylgeranyl diphosphate (GGDP). In our report, three novel diterpenoid alkaloids with fusicoccane skeleton, pericolactines A-C (1-3), were isolated from Periconia sp.. Their structures with absolute configurations were determined by spectroscopic analyses and quantum chemical ECD calculation. Pericolactines A-C (1-3) are a new class of diterpenoid alkaloids with an unusual fused 5-5-8-5 tetracyclic ring system, which derive from a geranylgeranyl diphosphate (GGDP) and serine conjugated biosynthesis. They belong to the atypical diterpenoid alkaloids.
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Affiliation(s)
- Yue-Hua Wu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Guo-Dong Chen
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Rong-Rong He
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Chuan-Xi Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Dan Hu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Gao-Qian Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Xin-Sheng Yao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Hao Gao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, People’s Republic of China
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Görner C, Hirte M, Huber S, Schrepfer P, Brück T. Stereoselective chemo-enzymatic oxidation routes for (1R,3E,7E,11S,12S)-3,7,18-dolabellatriene. Front Microbiol 2015; 6:1115. [PMID: 26528263 PMCID: PMC4602142 DOI: 10.3389/fmicb.2015.01115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
The diterpene (1R,3E,7E,11S,12S)-3,7,18-dolabellatriene from the marine brown alga Dilophus spiralis belongs to the dolabellanes natural product family and has antimicrobial activity against multi-drug resistant Staphylococcus aureus. Recently, we generated a CotB2 diterpene synthase mutant (W288G), which instead of its native product cyclooctat-9-en-7-ol, generates (1R,3E,7E,11S,12S)-3,7,18-dolabellatriene. In vivo CotB2 W288G reconstitution in an Escherichia coli based terpene production system, allowed efficient production of this olefinic macrocycle. To diversify the 3,7,18-dolabellatriene bioactivity we evaluated chemical and enzymatic methods for selective oxidation. Epoxidation by acetic peracid, which was formed in situ by a lipase catalyzed reaction of acetic acid with H2O2, provided efficient access to two monooxidized dolabellanes and to a novel di-epoxidated dolabellane species. These compounds could act as synthons en-route to new dolabellanes with diversified bioactivities. Furthermore, we demonstrate the almost quantitative 3,7,18-dolabellatriene conversion into the new, non-natural compound (1R,3E,7E,11S,12S,18R)-dolabella-3,7-diene-20-ol by hydroboration-oxidation with an enantiomeric excess of 94%, for the first time.
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Affiliation(s)
- Christian Görner
- Fachgebiet für Industrielle Biokatalyse, Department für Chemie, Technische Universität München Garching, Germany
| | - Max Hirte
- Fachgebiet für Industrielle Biokatalyse, Department für Chemie, Technische Universität München Garching, Germany
| | - Stephanie Huber
- Fachgebiet für Industrielle Biokatalyse, Department für Chemie, Technische Universität München Garching, Germany
| | - Patrick Schrepfer
- Fachgebiet für Industrielle Biokatalyse, Department für Chemie, Technische Universität München Garching, Germany
| | - Thomas Brück
- Fachgebiet für Industrielle Biokatalyse, Department für Chemie, Technische Universität München Garching, Germany
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71
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Beites T, Mendes MV. Chassis optimization as a cornerstone for the application of synthetic biology based strategies in microbial secondary metabolism. Front Microbiol 2015; 6:906. [PMID: 26441855 PMCID: PMC4563238 DOI: 10.3389/fmicb.2015.00906] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/19/2015] [Indexed: 02/06/2023] Open
Abstract
The increased number of bacterial genome sequencing projects has generated over the last years a large reservoir of genomic information. In silico analysis of this genomic data has renewed the interest in bacterial bioprospecting for bioactive compounds by unveiling novel biosynthetic gene clusters of unknown or uncharacterized metabolites. However, only a small fraction of those metabolites is produced under laboratory-controlled conditions; the remaining clusters represent a pool of novel metabolites that are waiting to be “awaken”. Activation of the biosynthetic gene clusters that present reduced or no expression (known as cryptic or silent clusters) by heterologous expression has emerged as a strategy for the identification and production of novel bioactive molecules. Synthetic biology, with engineering principles at its core, provides an excellent framework for the development of efficient heterologous systems for the expression of biosynthetic gene clusters. However, a common problem in its application is the host-interference problem, i.e., the unpredictable interactions between the device and the host that can hamper the desired output. Although an effort has been made to develop orthogonal devices, the most proficient way to overcome the host-interference problem is through genome simplification. In this review we present an overview on the strategies and tools used in the development of hosts/chassis for the heterologous expression of specialized metabolites biosynthetic gene clusters. Finally, we introduce the concept of specialized host as the next step of development of expression hosts.
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Affiliation(s)
- Tiago Beites
- I3S Instituto de Investigação e Inovação em Saúde, Universidade do Porto Porto, Portugal ; Instituto de Biologia Molecular e Celular, Universidade do Porto Porto, Portugal
| | - Marta V Mendes
- I3S Instituto de Investigação e Inovação em Saúde, Universidade do Porto Porto, Portugal ; Instituto de Biologia Molecular e Celular, Universidade do Porto Porto, Portugal
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72
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Nakano C, Oshima M, Kurashima N, Hoshino T. Identification of a New Diterpene Biosynthetic Gene Cluster that ProducesO-Methylkolavelool inHerpetosiphon aurantiacus. Chembiochem 2015; 16:772-81. [DOI: 10.1002/cbic.201402652] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Indexed: 11/12/2022]
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73
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Meguro A, Motoyoshi Y, Teramoto K, Ueda S, Totsuka Y, Ando Y, Tomita T, Kim SY, Kimura T, Igarashi M, Sawa R, Shinada T, Nishiyama M, Kuzuyama T. An Unusual Terpene Cyclization Mechanism Involving a Carbon-Carbon Bond Rearrangement. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411923] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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74
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Meguro A, Motoyoshi Y, Teramoto K, Ueda S, Totsuka Y, Ando Y, Tomita T, Kim SY, Kimura T, Igarashi M, Sawa R, Shinada T, Nishiyama M, Kuzuyama T. An Unusual Terpene Cyclization Mechanism Involving a Carbon-Carbon Bond Rearrangement. Angew Chem Int Ed Engl 2015; 54:4353-6. [DOI: 10.1002/anie.201411923] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Indexed: 11/07/2022]
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75
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Seipke RF. Strain-level diversity of secondary metabolism in Streptomyces albus. PLoS One 2015; 10:e0116457. [PMID: 25635820 PMCID: PMC4312078 DOI: 10.1371/journal.pone.0116457] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/10/2014] [Indexed: 12/26/2022] Open
Abstract
Streptomyces spp. are robust producers of medicinally-, industrially- and agriculturally-important small molecules. Increased resistance to antibacterial agents and the lack of new antibiotics in the pipeline have led to a renaissance in natural product discovery. This endeavor has benefited from inexpensive high quality DNA sequencing technology, which has generated more than 140 genome sequences for taxonomic type strains and environmental Streptomyces spp. isolates. Many of the sequenced streptomycetes belong to the same species. For instance, Streptomyces albus has been isolated from diverse environmental niches and seven strains have been sequenced, consequently this species has been sequenced more than any other streptomycete, allowing valuable analyses of strain-level diversity in secondary metabolism. Bioinformatics analyses identified a total of 48 unique biosynthetic gene clusters harboured by Streptomyces albus strains. Eighteen of these gene clusters specify the core secondary metabolome of the species. Fourteen of the gene clusters are contained by one or more strain and are considered auxiliary, while 16 of the gene clusters encode the production of putative strain-specific secondary metabolites. Analysis of Streptomyces albus strains suggests that each strain of a Streptomyces species likely harbours at least one strain-specific biosynthetic gene cluster. Importantly, this implies that deep sequencing of a species will not exhaust gene cluster diversity and will continue to yield novelty.
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Affiliation(s)
- Ryan F. Seipke
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
- * E-mail:
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76
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Yamada Y, Kuzuyama T, Komatsu M, Shin-Ya K, Omura S, Cane DE, Ikeda H. Terpene synthases are widely distributed in bacteria. Proc Natl Acad Sci U S A 2015; 112:857-62. [PMID: 25535391 PMCID: PMC4311827 DOI: 10.1073/pnas.1422108112] [Citation(s) in RCA: 330] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Odoriferous terpene metabolites of bacterial origin have been known for many years. In genome-sequenced Streptomycetaceae microorganisms, the vast majority produces the degraded sesquiterpene alcohol geosmin. Two minor groups of bacteria do not produce geosmin, with one of these groups instead producing other sesquiterpene alcohols, whereas members of the remaining group do not produce any detectable terpenoid metabolites. Because bacterial terpene synthases typically show no significant overall sequence similarity to any other known fungal or plant terpene synthases and usually exhibit relatively low levels of mutual sequence similarity with other bacterial synthases, simple correlation of protein sequence data with the structure of the cyclized terpene product has been precluded. We have previously described a powerful search method based on the use of hidden Markov models (HMMs) and protein families database (Pfam) search that has allowed the discovery of monoterpene synthases of bacterial origin. Using an enhanced set of HMM parameters generated using a training set of 140 previously identified bacterial terpene synthase sequences, a Pfam search of 8,759,463 predicted bacterial proteins from public databases and in-house draft genome data has now revealed 262 presumptive terpene synthases. The biochemical function of a considerable number of these presumptive terpene synthase genes could be determined by expression in a specially engineered heterologous Streptomyces host and spectroscopic identification of the resulting terpene products. In addition to a wide variety of terpenes that had been previously reported from fungal or plant sources, we have isolated and determined the complete structures of 13 previously unidentified cyclic sesquiterpenes and diterpenes.
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Affiliation(s)
- Yuuki Yamada
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Kanagawa 252-0373, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, University of Tokyo, Tokyo 113-8657, Japan
| | - Mamoru Komatsu
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Kanagawa 252-0373, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Satoshi Omura
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Tokyo 108-8461, Japan; and
| | - David E Cane
- Department of Chemistry, Brown University, Providence, RI 02912-9108
| | - Haruo Ikeda
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, Kanagawa 252-0373, Japan;
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Janocha S, Schmitz D, Bernhardt R. Terpene hydroxylation with microbial cytochrome P450 monooxygenases. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 148:215-50. [PMID: 25682070 DOI: 10.1007/10_2014_296] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Terpenoids comprise a highly diverse group of natural products. In addition to their basic carbon skeleton, they differ from one another in their functional groups. Functional groups attached to the carbon skeleton are the basis of the terpenoids' diverse properties. Further modifications of terpene olefins include the introduction of acyl-, aryl-, or sugar moieties and usually start with oxidations catalyzed by cytochrome P450 monooxygenases (P450s, CYPs). P450s are ubiquitously distributed throughout nature, involved in essential biological pathways such as terpenoid biosynthesis as well as the tailoring of terpenoids and other natural products. Their ability to introduce oxygen into nonactivated C-H bonds is unique and makes P450s very attractive for applications in biotechnology. Especially in the field of terpene oxidation, biotransformation methods emerge as an attractive alternative to classical chemical synthesis. For this reason, microbial P450s depict a highly interesting target for protein engineering approaches in order to increase selectivity and activity, respectively. Microbial P450s have been described to convert industrial and pharmaceutically interesting terpenoids such as ionones, limone, valencene, resin acids, and triterpenes (including steroids) as well as vitamin D3. Highly selective and active mutants have been evolved by applying classical site-directed mutagenesis as well as directed evolution of proteins. As P450s usually depend on electron transfer proteins, mutagenesis has also been applied to improve the interactions between P450s and their respective redox partners. This chapter provides an overview of terpenoid hydroxylation reactions catalyzed by bacterial P450s and highlights the achievements made by protein engineering to establish productive hydroxylation processes.
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Affiliation(s)
- Simon Janocha
- Department of Biochemistry, Saarland University, Campus B2 2, 66123, Saarbruecken, Germany
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78
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Hong YJ, Tantillo DJ. The energetic viability of an unexpected skeletal rearrangement in cyclooctatin biosynthesis. Org Biomol Chem 2015; 13:10273-8. [DOI: 10.1039/c5ob01785h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Results of density functional theory calculations on possible mechanisms for formation of the diterpenoid cyclooctatin are described.
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Affiliation(s)
- Young J. Hong
- Department of Chemistry
- Univeristy of California-Davis
- Davis
- USA
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79
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Xu M, Hillwig ML, Lane AL, Tiernan MS, Moore BS, Peters RJ. Characterization of an orphan diterpenoid biosynthetic operon from Salinispora arenicola. JOURNAL OF NATURAL PRODUCTS 2014; 77:2144-7. [PMID: 25203741 PMCID: PMC4176389 DOI: 10.1021/np500422d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Indexed: 05/29/2023]
Abstract
While more commonly associated with plants than microbes, diterpenoid natural products have been reported to have profound effects in marine microbe-microbe interactions. Intriguingly, the genome of the marine bacterium Salinispora arenicola CNS-205 contains a putative diterpenoid biosynthetic operon, terp1. Here recombinant expression studies are reported, indicating that this three-gene operon leads to the production of isopimara-8,15-dien-19-ol (4). Although 4 is not observed in pure cultures of S. arenicola, it is plausible that the terp1 operon is only expressed under certain physiologically relevant conditions such as in the presence of other marine organisms.
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Affiliation(s)
- Meimei Xu
- Department of Biochemistry, Biophysics
& Molecular Biology, Iowa State University, Ames, Iowa 50011 United States
| | - Matthew L. Hillwig
- Department of Biochemistry, Biophysics
& Molecular Biology, Iowa State University, Ames, Iowa 50011 United States
| | - Amy L. Lane
- Scripps
Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical
Sciences, University of California at San
Diego, La Jolla, California 92093 United States
| | - Mollie S. Tiernan
- Department of Biochemistry, Biophysics
& Molecular Biology, Iowa State University, Ames, Iowa 50011 United States
| | - Bradley S. Moore
- Scripps
Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical
Sciences, University of California at San
Diego, La Jolla, California 92093 United States
| | - Reuben J. Peters
- Department of Biochemistry, Biophysics
& Molecular Biology, Iowa State University, Ames, Iowa 50011 United States
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80
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Janke R, Görner C, Hirte M, Brück T, Loll B. The first structure of a bacterial diterpene cyclase: CotB2. ACTA ACUST UNITED AC 2014; 70:1528-37. [PMID: 24914964 DOI: 10.1107/s1399004714005513] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/11/2014] [Indexed: 02/05/2023]
Abstract
Sesquiterpenes and diterpenes are a diverse class of secondary metabolites that are predominantly derived from plants and some prokaryotes. The properties of these natural products encompass antitumor, antibiotic and even insecticidal activities. Therefore, they are interesting commercial targets for the chemical and pharmaceutical industries. Owing to their structural complexity, these compounds are more efficiently accessed by metabolic engineering of microbial systems than by chemical synthesis. This work presents the first crystal structure of a bacterial diterpene cyclase, CotB2 from the soil bacterium Streptomyces melanosporofaciens, at 1.64 Å resolution. CotB2 is a diterpene cyclase that catalyzes the cyclization of the linear geranylgeranyl diphosphate to the tricyclic cyclooctat-9-en-7-ol. The subsequent oxidation of cyclooctat-9-en-7-ol by two cytochrome P450 monooxygenases leads to bioactive cyclooctatin. Plasticity residues that decorate the active site of CotB2 have been mutated, resulting in alternative monocyclic, dicyclic and tricyclic compounds that show bioactivity. These new compounds shed new light on diterpene cyclase reaction mechanisms. Furthermore, the product of mutant CotB2(W288G) produced the new antibiotic compound (1R,3E,7E,11S,12S)-3,7,18-dolabellatriene, which acts specifically against multidrug-resistant Staphylococcus aureus. This opens a sustainable route for the industrial-scale production of this bioactive compound.
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Affiliation(s)
- Ronja Janke
- Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Christian Görner
- Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Max Hirte
- Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Thomas Brück
- Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Bernhard Loll
- Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
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81
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Grishko VV, Nogovitsina YM, Ivshina IB. Bacterial transformation of terpenoids. RUSSIAN CHEMICAL REVIEWS 2014. [DOI: 10.1070/rc2014v083n04abeh004396] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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82
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Gong HY, Zeng Y, Chen XY. Diterpene synthases and their responsible cyclic natural products. NATURAL PRODUCTS AND BIOPROSPECTING 2014; 4:59-72. [PMID: 24858310 PMCID: PMC4004862 DOI: 10.1007/s13659-014-0012-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/23/2014] [Indexed: 05/11/2023]
Abstract
This review provides an overview of diterpene synthases which were initially identified via genetic and/or biochemical means, traversing all organisms researched to date.
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Affiliation(s)
- Hai-Yan Gong
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ying Zeng
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 China
| | - Xiao-Ya Chen
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, 200032 China
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83
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Zhang X, Shang G, Gu L, Shen Y. Crystallization and preliminary X-ray diffraction analysis of the diterpene cyclooctatin synthase (CYC) from Streptomyces sp. LZ35. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:366-9. [PMID: 24598929 DOI: 10.1107/s2053230x14003100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 02/11/2014] [Indexed: 11/10/2022]
Abstract
Terpenoids are a large and highly diverse group of natural products, with the most chemically diverse pool of structures. Terpene synthase is the key enzyme in the process of terpenoid synthesis. In this paper, the first diterpene synthase (CYC) of bacterial origin was successfully crystallized. Native and SeMet-derivative crystals diffracted to 1.75 and 2.6 Å resolution, respectively. The native crystal belonged to space group P212121, with unit-cell parameters a = 59.10, b = 101.73, c = 108.93 Å, and contained two molecules per asymmetric unit. The SeMet-derivative crystal belonged to space group P21, with unit-cell parameters a = 58.64, b = 109.47, c = 58.73 Å, β = 119.35°, and had two molecules per asymmetric unit.
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Affiliation(s)
- Xiulei Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, People's Republic of China
| | - Guijun Shang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, People's Republic of China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, People's Republic of China
| | - Yuemao Shen
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, People's Republic of China
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84
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Unusual site-specific DNA integration into the highly active pseudo-attB of the Streptomyces albus J1074 genome. Appl Microbiol Biotechnol 2014; 98:5095-104. [PMID: 24566921 DOI: 10.1007/s00253-014-5605-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/07/2014] [Accepted: 02/08/2014] [Indexed: 10/25/2022]
Abstract
The φC31-encoded recombination system has become a widely used tool for genetic analysis of streptomycetes, gene therapy and generation of transgenic animals. However, the application of this system, even in the context of its natural host genus, Streptomyces, may require a specific approach for each species. In this study, we have identified a novel pseudo-attB site, called pseB4, for integration of vectors using the φC31 system. More than 90 % of clones contained two copies of pSET152- or pOJ436-based cosmids, after their introduction into S. albus. The efficiency of the integration of φC31-based vectors into pseB4 is therefore comparable to that of the integration into attB. Moreover, in contrast with integration into the native attB, integration into pseB4 is not polar and does not require a complementary sequence in the TT-core region. Furthermore, an analysis of conjugation frequency revealed mutual inhibition of plasmid integration into either site when both the attB and pseB4 sites were present in the genome.
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85
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Zaburannyi N, Rabyk M, Ostash B, Fedorenko V, Luzhetskyy A. Insights into naturally minimised Streptomyces albus J1074 genome. BMC Genomics 2014; 15:97. [PMID: 24495463 PMCID: PMC3937824 DOI: 10.1186/1471-2164-15-97] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 02/01/2014] [Indexed: 11/10/2022] Open
Abstract
Background The Streptomyces albus J1074 strain is one of the most widely used chassis for the heterologous production of bioactive natural products. The fast growth and an efficient genetic system make this strain an attractive model for expressing cryptic biosynthetic pathways to aid drug discovery. Results To improve its capabilities for the heterologous expression of biosynthetic gene clusters, the complete genomic sequence of S. albus J1074 was obtained. With a size of 6,841,649 bp, coding for 5,832 genes, its genome is the smallest within the genus streptomycetes. Genome analysis revealed a strong tendency to reduce the number of genetic duplicates. The whole transcriptomes were sequenced at different time points to identify the early metabolic switch from the exponential to the stationary phase in S. albus J1074. Conclusions S. albus J1074 carries the smallest genome among the completely sequenced species of the genus Streptomyces. The detailed genome and transcriptome analysis discloses its capability to serve as a premium host for the heterologous production of natural products. Moreover, the genome revealed 22 additional putative secondary metabolite gene clusters that reinforce the strain’s potential for natural product synthesis.
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Affiliation(s)
| | | | | | | | - Andriy Luzhetskyy
- Helmholtz-Institute for Pharmaceutical Research Saarland, Saarland University Campus, Building C2,3, 66123 Saarbrücken, Germany.
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86
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Iterative marker excision system. Appl Microbiol Biotechnol 2014; 98:4557-70. [DOI: 10.1007/s00253-014-5523-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/03/2014] [Accepted: 01/05/2014] [Indexed: 10/25/2022]
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87
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Genome rearrangements of Streptomyces albus J1074 lead to the carotenoid gene cluster activation. Appl Microbiol Biotechnol 2013; 98:795-806. [PMID: 24337397 DOI: 10.1007/s00253-013-5440-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/24/2013] [Accepted: 11/25/2013] [Indexed: 10/25/2022]
Abstract
Streptomyces albus J1074 is a derivative of the S. albus G1 strain defective in SalG1 restriction-modification system. Genome sequencing of S. albus J1074 revealed that the size of its chromosome is 6.8 Mb with unusually short terminal arms of only 0.3 and 0.4 Mb. Here we present our attempts to evaluate the dispensability of subtelomeric regions of the S. albus J1074 chromosome. A number of large site-directed genomic deletions led to circularization of the S. albus J1074 chromosome and to the overall genome reduction by 307 kb. Two spontaneous mutants with an activated carotenoid cluster were obtained. Genome sequencing and transcriptome analysis indicated that phenotypes of these mutants resulted from the right terminal 0.42 Mb chromosomal region deletion, followed by the carotenoid cluster amplification. Our results indicate that the right terminal 0.42 Mb fragment is dispensable under laboratory conditions. In contrast, the left terminal arm of the S. albus J1074 chromosome contains essential genes and only 42 kb terminal region is proved to be dispensable. We identified overexpressed carotenoid compounds and determined fitness costs of the large genomic rearrangements.
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88
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Functional conservation of the capacity for ent-kaurene biosynthesis and an associated operon in certain rhizobia. J Bacteriol 2013; 196:100-6. [PMID: 24142247 DOI: 10.1128/jb.01031-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial interactions with plants are accompanied by complex signal exchange processes. Previously, the nitrogen-fixing symbiotic (rhizo)bacterium Bradyrhizobium japonicum was found to carry adjacent genes encoding two sequentially acting diterpene cyclases that together transform geranylgeranyl diphosphate to ent-kaurene, the olefin precursor to the gibberellin plant hormones. Species from the three other major genera of rhizobia were found to have homologous terpene synthase genes. Cloning and functional characterization of a representative set of these enzymes confirmed the capacity of each genus to produce ent-kaurene. Moreover, comparison of their genomic context revealed that these diterpene synthases are found in a conserved operon which includes an adjacent isoprenyl diphosphate synthase, shown here to produce the geranylgeranyl diphosphate precursor, providing a critical link to central metabolism. In addition, the rest of the operon consists of enzymatic genes that presumably lead to a more elaborated diterpenoid, although the production of gibberellins was not observed. Nevertheless, it has previously been shown that the operon is selectively expressed during nodulation, and the scattered distribution of the operon via independent horizontal gene transfer within the symbiotic plasmid or genomic island shown here suggests that such diterpenoid production may modulate the interaction of these particular symbionts with their host plants.
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89
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Meguro A, Tomita T, Nishiyama M, Kuzuyama T. Identification and characterization of bacterial diterpene cyclases that synthesize the cembrane skeleton. Chembiochem 2013; 14:316-21. [PMID: 23386483 PMCID: PMC3790952 DOI: 10.1002/cbic.201200651] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Indexed: 11/20/2022]
Affiliation(s)
- Ayuko Meguro
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Tokyo 113-8657, Japan
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90
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Görner C, Häuslein I, Schrepfer P, Eisenreich W, Brück T. Targeted Engineering of Cyclooctat-9-en-7-ol Synthase: A Stereospecific Access to Two New Non-natural Fusicoccane-Type Diterpenes. ChemCatChem 2013. [DOI: 10.1002/cctc.201300285] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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91
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The International Conference of Natural Product Biosynthesis (ICNPB, 8th US-Japan seminar on the Biosynthesis of Natural Products). J Antibiot (Tokyo) 2012; 65:587-90. [PMID: 22990380 DOI: 10.1038/ja.2012.74] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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92
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de Boer AH, de Vries-van Leeuwen IJ. Fusicoccanes: diterpenes with surprising biological functions. TRENDS IN PLANT SCIENCE 2012; 17:360-8. [PMID: 22465041 DOI: 10.1016/j.tplants.2012.02.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 02/14/2012] [Accepted: 02/20/2012] [Indexed: 05/25/2023]
Abstract
Fusicoccin is the best-studied member of a class of diterpenes sharing a 5-8-5 ring structure, called fusicoccanes. Fusicoccin was and still is a 'tool in plant physiology', targeting the main engine of plasma membrane transport, the P-type H(+)-ATPase, assisted by members of the 14-3-3 family. The key position of 14-3-3 proteins in cell biology, combined with a broader specificity of other fusicoccanes as shown by crystallography studies, make fusicoccanes a versatile tool in plant and animal biology. In this review, we examine recent evidence that fusicoccanes act on animal cells, describe the discovery of the fungal biosynthetic pathway and emphasize that lower (liverworts) and higher plants produce fusicoccanes with intriguing biological activities.
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Affiliation(s)
- Albertus H de Boer
- Department of Structural Biology, Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
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93
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Smanski MJ, Peterson RM, Huang SX, Shen B. Bacterial diterpene synthases: new opportunities for mechanistic enzymology and engineered biosynthesis. Curr Opin Chem Biol 2012; 16:132-41. [PMID: 22445175 DOI: 10.1016/j.cbpa.2012.03.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2012] [Revised: 02/22/2012] [Accepted: 03/02/2012] [Indexed: 11/15/2022]
Abstract
Diterpenoid biosynthesis has been extensively studied in plants and fungi, yet cloning and engineering diterpenoid pathways in these organisms remain challenging. Bacteria are emerging as prolific producers of diterpenoid natural products, and bacterial diterpene synthases are poised to make significant contributions to our understanding of terpenoid biosynthesis. Here we will first survey diterpenoid natural products of bacterial origin and briefly review their biosynthesis with emphasis on diterpene synthases (DTSs) that channel geranylgeranyl diphosphate to various diterpenoid scaffolds. We will then highlight differences of DTSs of bacterial and higher organism origins and discuss the challenges in discovering novel bacterial DTSs. We will conclude by discussing new opportunities for DTS mechanistic enzymology and applications of bacterial DTS in biocatalysis and metabolic pathway engineering.
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Affiliation(s)
- Michael J Smanski
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
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94
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Abstract
Terpenoid compounds are generally considered to be plant or fungal metabolites, although a small number of odorous terpenoid metabolites of bacterial origin have been known for many years. Recently, extensive bacterial genome sequencing and bioinformatic analysis of deduced bacterial proteins using a profile hidden Markov model have revealed more than a hundred distinct predicted terpene synthase genes. Although some of these synthase genes might be silent in the parent microorganisms under normal laboratory culture conditions, the controlled overexpression of these genes in a versatile heterologous host has made it possible to identify the biochemical function of cryptic genes and isolate new terpenoid metabolites.
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95
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Sato T, Yoshida S, Hoshino H, Tanno M, Nakajima M, Hoshino T. Sesquarterpenes (C35 Terpenes) Biosynthesized via the Cyclization of a Linear C35 Isoprenoid by a Tetraprenyl-β-curcumene Synthase and a Tetraprenyl-β-curcumene Cyclase: Identification of a New Terpene Cyclase. J Am Chem Soc 2011; 133:9734-7. [DOI: 10.1021/ja203779h] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tsutomu Sato
- Department of Applied Biological Chemistry, Faculty of Agriculture, and Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Satoru Yoshida
- Department of Applied Biological Chemistry, Faculty of Agriculture, and Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Hiroko Hoshino
- Department of Applied Biological Chemistry, Faculty of Agriculture, and Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Mizuki Tanno
- Department of Applied Biological Chemistry, Faculty of Agriculture, and Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Mami Nakajima
- Center for Instrumental Analysis, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Tsutomu Hoshino
- Department of Applied Biological Chemistry, Faculty of Agriculture, and Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
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96
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Kawamura A, Iacovidou M, Hirokawa E, Soll CE, Trujillo M. 17-Hydroxycyclooctatin, a fused 5-8-5 ring diterpene, from Streptomyces sp. MTE4a. JOURNAL OF NATURAL PRODUCTS 2011; 74:492-495. [PMID: 21314175 PMCID: PMC3064735 DOI: 10.1021/np100921m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A new diterpene with a fused 5-8-5 ring system was isolated from the fermentation broth of a soil actinomycete. The stereochemistry at C-15 was determined in an unusual manner using a decomposition product.
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Affiliation(s)
- Akira Kawamura
- To whom correspondence should be addressed. Tel 212-650-3095, Fax 212-772-5332, (A.K.). Tel 718-631-6049, Fax 718-631-6678. (M.T.)
| | | | | | | | - Monica Trujillo
- To whom correspondence should be addressed. Tel 212-650-3095, Fax 212-772-5332, (A.K.). Tel 718-631-6049, Fax 718-631-6678. (M.T.)
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97
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Zhang H, Boghigian BA, Armando J, Pfeifer BA. Methods and options for the heterologous production of complex natural products. Nat Prod Rep 2011; 28:125-51. [PMID: 21060956 PMCID: PMC9896020 DOI: 10.1039/c0np00037j] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This review will detail the motivations, experimental approaches, and growing list of successful cases associated with the heterologous production of complex natural products.
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Affiliation(s)
- Haoran Zhang
- Department of Chemical & Biological Engineering, Science & Technology Center, Tufts University, Medford, MA 02155, USA.
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98
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Unprecedented acetoacetyl-coenzyme A synthesizing enzyme of the thiolase superfamily involved in the mevalonate pathway. Proc Natl Acad Sci U S A 2010; 107:11265-70. [PMID: 20534558 DOI: 10.1073/pnas.1000532107] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acetoacetyl-CoA is the precursor of 3-hydroxy-3-methylglutaryl (HMG)-CoA in the mevalonate pathway, which is essential for terpenoid backbone biosynthesis. Acetoacetyl-CoA is also the precursor of poly-beta-hydroxybutyrate, a polymer belonging to the polyester class produced by microorganisms. The de novo synthesis of acetoacetyl-CoA is usually catalyzed by acetoacetyl-CoA thiolase via a thioester-dependent Claisen condensation reaction between two molecules of acetyl-CoA. Here, we report that nphT7, found in the mevalonate pathway gene cluster from a soil-isolated Streptomyces sp. strain, encodes an unusual acetoacetyl-CoA synthesizing enzyme. The recombinant enzyme overexpressed in Escherichia coli catalyzes a single condensation of acetyl-CoA and malonyl-CoA to give acetoacetyl-CoA and CoA. Replacement of malonyl-CoA with malonyl-(acyl carrier protein) resulted in loss of the condensation activity. No acetoacetyl-CoA synthesizing activity was detected through the condensation of two molecules of acetyl-CoA. Based on these properties of NphT7, we propose to name this unusual enzyme of the thiolase superfamily acetoacetyl-CoA synthase. Coexpression of nphT7 with the HMG-CoA synthase gene and the HMG-CoA reductase gene in a heterologous host allowed 3.5-fold higher production of mevalonate than when only the HMG-CoA synthase and HMG-CoA reductase genes were expressed. This result suggests that nphT7 can be used to significantly increase the concentration of acetoacetyl-CoA in cells, eventually leading to the production of useful terpenoids and poly-beta-hydroxybutyrate.
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