1
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Yan D, Zhou M, Adduri A, Zhuang Y, Guler M, Liu S, Shin H, Kovach T, Oh G, Liu X, Deng Y, Wang X, Cao L, Sherman DH, Schultz PJ, Kersten RD, Clement JA, Tripathi A, Behsaz B, Mohimani H. Discovering type I cis-AT polyketides through computational mass spectrometry and genome mining with Seq2PKS. Nat Commun 2024; 15:5356. [PMID: 38918378 PMCID: PMC11199612 DOI: 10.1038/s41467-024-49587-1] [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: 07/14/2023] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
Type 1 polyketides are a major class of natural products used as antiviral, antibiotic, antifungal, antiparasitic, immunosuppressive, and antitumor drugs. Analysis of public microbial genomes leads to the discovery of over sixty thousand type 1 polyketide gene clusters. However, the molecular products of only about a hundred of these clusters are characterized, leaving most metabolites unknown. Characterizing polyketides relies on bioactivity-guided purification, which is expensive and time-consuming. To address this, we present Seq2PKS, a machine learning algorithm that predicts chemical structures derived from Type 1 polyketide synthases. Seq2PKS predicts numerous putative structures for each gene cluster to enhance accuracy. The correct structure is identified using a variable mass spectral database search. Benchmarks show that Seq2PKS outperforms existing methods. Applying Seq2PKS to Actinobacteria datasets, we discover biosynthetic gene clusters for monazomycin, oasomycin A, and 2-aminobenzamide-actiphenol.
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Affiliation(s)
- Donghui Yan
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Muqing Zhou
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Abhinav Adduri
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yihao Zhuang
- Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
| | - Mustafa Guler
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Sitong Liu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Hyonyoung Shin
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Torin Kovach
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Gloria Oh
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiao Liu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yuting Deng
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaofeng Wang
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Liu Cao
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - David H Sherman
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Pamela J Schultz
- Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | | | - Ashootosh Tripathi
- Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA.
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
| | - Bahar Behsaz
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
- Chemia Biosciences Inc, Pittsburgh, PA, USA.
| | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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2
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Sood U, Müller M, Lan T, Garg G, Singhvi N, Hira P, Singh P, Nigam A, Verma M, Lata P, Kaur H, Kumar A, Rawat CD, Lal S, Aldrich C, Bechthold A, Lal R. Amycolatopsis mediterranei: A Sixty-Year Journey from Strain Isolation to Unlocking Its Potential of Rifamycin Analogue Production by Combinatorial Biosynthesis. JOURNAL OF NATURAL PRODUCTS 2024; 87:424-438. [PMID: 38289177 DOI: 10.1021/acs.jnatprod.3c00686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Ever since the isolation of Amycolatopsis mediterranei in 1957, this strain has been the focus of research worldwide. In the last 60 years or more, our understanding of the taxonomy, development of cloning vectors and conjugation system, physiology, genetics, genomics, and biosynthetic pathway of rifamycin B production in A. mediterranei has substantially increased. In particular, the development of cloning vectors, transformation system, characterization of the rifamycin biosynthetic gene cluster, and the regulation of rifamycin B production by the pioneering work of Heinz Floss have made the rifamycin polyketide biosynthetic gene cluster (PKS) an attractive target for extensive genetic manipulations to produce rifamycin B analogues which could be effective against multi-drug-resistant tuberculosis. Additionally, a better understanding of the regulation of rifamycin B production and the application of newer genomics tools, including CRISPR-assisted genome editing systems, might prove useful to overcome the limitations associated with low production of rifamycin analogues.
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Affiliation(s)
- Utkarsh Sood
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi-110007, India
| | - Moritz Müller
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany
| | - Tian Lan
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Gauri Garg
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi-110007, India
| | - Nirjara Singhvi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, Uttarakhand 248007, India
| | - Princy Hira
- Department of Zoology, Maitreyi College, University of Delhi, Delhi-110003, India
| | - Priya Singh
- Department of Zoology, Maitreyi College, University of Delhi, Delhi-110003, India
| | - Aeshna Nigam
- Department of Zoology, Shivaji College, University of Delhi, Delhi-110027, India
| | - Mansi Verma
- Department of Zoology, Hansraj College, University of Delhi, Delhi-110007, India
| | - Pushp Lata
- Department of Zoology, University of Delhi, Delhi-110007, India
| | - Hardeep Kaur
- Department of Zoology, Ramjas College, University of Delhi, Delhi-110007, India
| | - Abhilash Kumar
- Department of Zoology, Ramjas College, University of Delhi, Delhi-110007, India
| | - Charu Dogra Rawat
- Department of Zoology, Ramjas College, University of Delhi, Delhi-110007, India
| | - Sukanya Lal
- PhiXGen Private Limited, Gurugram, Haryana-122001, India
| | - Courtney Aldrich
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Andreas Bechthold
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany
| | - Rup Lal
- PhiXGen Private Limited, Gurugram, Haryana-122001, India
- Acharya Narendra Dev College, University of Delhi, Delhi-110019, India
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3
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Kudo F, Kishikawa K, Tsuboi K, Kido T, Usui T, Hashimoto J, Shin-Ya K, Miyanaga A, Eguchi T. Acyltransferase Domain Exchange between Two Independent Type I Polyketide Synthases in the Same Producer Strain of Macrolide Antibiotics. Chembiochem 2023; 24:e202200670. [PMID: 36602093 DOI: 10.1002/cbic.202200670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/06/2023]
Abstract
Streptomyces graminofaciens A-8890 produces two macrolide antibiotics, FD-891 and virustomycin A, both of which show significant biological activity. In this study, we identified the virustomycin A biosynthetic gene cluster, which encodes type I polyketide synthases (PKSs), ethylmalonyl-CoA biosynthetic enzymes, methoxymalony-acyl carrier protein biosynthetic enzymes, and post-PKS modification enzymes. Next, we demonstrated that the acyltransferase domain can be exchanged between the Vsm PKSs and the PKSs involved in FD-891 biosynthesis (Gfs PKSs), without any supply problems of the unique extender units. We exchanged the malonyltransferase domain in the loading module of Gfs PKS with the ethylmalonyltransferase domain and the methoxymalonyltransferase domain of Vsm PKSs. Consequently, the expected two-carbon-elongated analog 26-ethyl-FD-891 was successfully produced with a titer comparable to FD-891 production by the wild type; however, exchange with the methoxymalonyltransferase domain did not produce any FD-891 analogs. Furthermore, 26-ethyl-FD-891 showed potent cytotoxic activity against HeLa cells, like natural FD-891.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Kosuke Kishikawa
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Kazuma Tsuboi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Takafusa Kido
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Takeo Usui
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572, Ibaraki, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
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4
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Magar RT, Pham VTT, Poudel PB, Nguyen HT, Bridget AF, Sohng JK. Biosynthetic pathway of peucemycin and identification of its derivative from Streptomyces peucetius. Appl Microbiol Biotechnol 2023; 107:1217-1231. [PMID: 36680588 DOI: 10.1007/s00253-023-12385-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/22/2023]
Abstract
Streptomyces peucetius ATCC 27952 is a well-known producer of important anticancer compounds, daunorubicin and doxorubicin. In this study, we successfully identified a new macrolide, 25-hydroxy peucemycin, that exhibited an antibacterial effect on some pathogens. Based on the structure of a newly identified compound and through the inactivation of a polyketide synthase gene, we successfully identified its biosynthetic gene cluster which was considered to be the cryptic biosynthetic gene cluster. The biosynthetic gene cluster spans 51 kb with 16 open reading frames. Five type I polyketide synthase (PKS) genes encode eight modules that synthesize the polyketide chain of peucemycin before undergoing post-PKS tailoring steps. In addition to the regular starter and extender units, some modules have specificity towards ethylmalonyl-CoA and unusual butylmalonyl-CoA. A credible explanation for the specificity of the unusual extender unit has been searched for. Moreover, the enzyme responsible for the final tailoring pathway was also identified. Based on all findings, a plausible biosynthetic pathway is here proposed. KEY POINTS: • Identification of a new macrolide, 25-hydroxy peucemycin. • An FMN-dependent monooxygenase is responsible for the hydroxylation of peucemycin. • The module encoded by peuC is unique to accept the butylmalonyl-CoA as an unusual extender unit.
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Affiliation(s)
- Rubin Thapa Magar
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Van Thuy Thi Pham
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Purna Bahadur Poudel
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Hue Thi Nguyen
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Adzemye Fovennso Bridget
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea.
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea.
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5
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Geyer K, Hartmann S, Singh RR, Erb TJ. Multiple Functions of the Type II Thioesterase Associated with the Phoslactomycin Polyketide Synthase. Biochemistry 2022; 61:2662-2671. [DOI: 10.1021/acs.biochem.2c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Kyra Geyer
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, D-35043 Marburg, Germany
| | - Steffen Hartmann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, D-35043 Marburg, Germany
| | - Randolph R. Singh
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, L-4367 Belvaux, Luxembourg
| | - Tobias J. Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Street 10, D-35043 Marburg, Germany
- SYNMIKRO Center for Synthetic Microbiology, Karl-von-Frisch-Street 16, D-35043 Marburg, Germany
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6
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Kresna IDM, Wuisan ZG, Pohl JM, Mettal U, Otoya VL, Gand M, Marner M, Otoya LL, Böhringer N, Vilcinskas A, Schäberle TF. Genome-Mining-Guided Discovery and Characterization of the PKS-NRPS-Hybrid Polyoxyperuin Produced by a Marine-Derived Streptomycete. JOURNAL OF NATURAL PRODUCTS 2022; 85:888-898. [PMID: 35239335 DOI: 10.1021/acs.jnatprod.1c01018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The azinothricin family comprises several cyclic hexadepsipeptides with diverse pharmacological bioactivities, including antimicrobial, antitumoral, and apoptosis induction. In this work, using a genome mining approach, a biosynthetic gene cluster encoding an azinothricin-like compound was identified from the Streptomyces sp. s120 genome sequence (pop BGC). Comparative MS analysis of extracts from the native producer and a knockout mutant led to the identification of metabolites corresponding to the pop BGC. Furthermore, regulatory elements of the BGC were identified. By overexpression of an LmbU-like transcriptional activator, the production yield of 1 and 2 was increased, enabling isolation and structure elucidation of polyoxyperuin A seco acid (1) and polyoxyperuin A (2) using high-resolution mass spectrometry and NMR spectroscopy. Compound 1 exhibited a low antibiotic effect against Micrococcus luteus, while 2 showed a strong Gram-positive antibiotic effect in a micro-broth-dilution assay.
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Affiliation(s)
- I Dewa M Kresna
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
| | - Zerlina G Wuisan
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
- German Center of Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392 Giessen, Germany
| | - Jean-Marie Pohl
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
| | - Ute Mettal
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
| | - Virginia Linares Otoya
- Unidad de Posgrado en Farmacia y Bioquímica, Facultad de Farmacia y Bioquímica, Universidad Nacional de Trujillo, 13011. Trujillo, Peru
| | - Martin Gand
- Institute of Food Chemistry and Food Biotechnology, Faculty of Biology and Chemistry, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Michael Marner
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
| | - Luis Linares Otoya
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Nils Böhringer
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
- German Center of Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392 Giessen, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany
- German Center of Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392 Giessen, Germany
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7
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Galanie S, Entwistle D, Lalonde J. Engineering biosynthetic enzymes for industrial natural product synthesis. Nat Prod Rep 2021; 37:1122-1143. [PMID: 32364202 DOI: 10.1039/c9np00071b] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: 2000 to 2020 Natural products and their derivatives are commercially important medicines, agrochemicals, flavors, fragrances, and food ingredients. Industrial strategies to produce these structurally complex molecules encompass varied combinations of chemical synthesis, biocatalysis, and extraction from natural sources. Interest in engineering natural product biosynthesis began with the advent of genetic tools for pathway discovery. Genes and strains can now readily be synthesized, mutated, recombined, and sequenced. Enzyme engineering has succeeded commercially due to the development of genetic methods, analytical technologies, and machine learning algorithms. Today, engineered biosynthetic enzymes from organisms spanning the tree of life are used industrially to produce diverse molecules. These biocatalytic processes include single enzymatic steps, multienzyme cascades, and engineered native and heterologous microbial strains. This review will describe how biosynthetic enzymes have been engineered to enable commercial and near-commercial syntheses of natural products and their analogs.
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Affiliation(s)
- Stephanie Galanie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
| | - David Entwistle
- Process Chemistry, Codexis, Inc., Redwood City, California, USA
| | - James Lalonde
- Microbial Digital Genome Engineering, Inscripta, Inc., Pleasanton, California, USA
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8
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Li P, Chen M, Tang W, Guo Z, Zhang Y, Wang M, Horsman GP, Zhong J, Lu Z, Chen Y. Initiating polyketide biosynthesis by on-line methyl esterification. Nat Commun 2021; 12:4499. [PMID: 34301953 PMCID: PMC8302727 DOI: 10.1038/s41467-021-24846-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 07/09/2021] [Indexed: 12/04/2022] Open
Abstract
Aurantinins (ARTs) are antibacterial polyketides featuring a unique 6/7/8/5-fused tetracyclic ring system and a triene side chain with a carboxyl terminus. Here we identify the art gene cluster and dissect ART’s C-methyl incorporation patterns to study its biosynthesis. During this process, an apparently redundant methyltransferase Art28 was characterized as a malonyl-acyl carrier protein O-methyltransferase, which represents an unusual on-line methyl esterification initiation strategy for polyketide biosynthesis. The methyl ester bond introduced by Art28 is kept until the last step of ART biosynthesis, in which it is hydrolyzed by Art9 to convert inactive ART 9B to active ART B. The cryptic reactions catalyzed by Art28 and Art9 represent a protecting group biosynthetic logic to render the ART carboxyl terminus inert to unwanted side reactions and to protect producing organisms from toxic ART intermediates. Further analyses revealed a wide distribution of this initiation strategy for polyketide biosynthesis in various bacteria. Aurantinins are polyketides with unusual connectivities and broad antibacterial activity. Here the authors show the biosynthesis of aurantinins, which proceeds via an on-line methyl esterification at the terminus that enables the iterative chain elongations prior to condensation and cyclization.
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Affiliation(s)
- Pengwei Li
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Meng Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wei Tang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhengyan Guo
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuwei Zhang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Min Wang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong, China
| | - Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Jin Zhong
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agriculture University, Nanjing, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
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9
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The biosynthetic pathway to tetromadurin (SF2487/A80577), a polyether tetronate antibiotic. PLoS One 2020; 15:e0239054. [PMID: 32925967 PMCID: PMC7489565 DOI: 10.1371/journal.pone.0239054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/30/2020] [Indexed: 12/03/2022] Open
Abstract
The type I polyketide SF2487/A80577 (herein referred to as tetromadurin) is a polyether tetronate ionophore antibiotic produced by the terrestrial Gram-positive bacterium Actinomadura verrucosospora. Tetromadurin is closely related to the polyether tetronates tetronasin (M139603) and tetronomycin, all of which are characterised by containing a tetronate, cyclohexane, tetrahydropyran, and at least one tetrahydrofuran ring. We have sequenced the genome of Actinomadura verrucosospora to identify the biosynthetic gene cluster responsible for tetromadurin biosynthesis (the mad gene cluster). Based on bioinformatic analysis of the 32 genes present within the cluster a plausible biosynthetic pathway for tetromadurin biosynthesis is proposed. Functional confirmation of the mad gene cluster is obtained by performing in-frame deletions in each of the genes mad10 and mad31, which encode putative cyclase enzymes responsible for cyclohexane and tetrahydropyran formation, respectively. Furthermore, the A. verrucosospora Δmad10 mutant produces a novel tetromadurin metabolite that according to mass spectrometry analysis is analogous to the recently characterised partially cyclised tetronasin intermediate lacking its cyclohexane and tetrahydropyran rings. Our results therefore elucidate the biosynthetic machinery of tetromadurin biosynthesis and lend support for a conserved mechanism of cyclohexane and tetrahydropyran biosynthesis across polyether tetronates.
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10
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Drufva EE, Hix EG, Bailey CB. Site directed mutagenesis as a precision tool to enable synthetic biology with engineered modular polyketide synthases. Synth Syst Biotechnol 2020; 5:62-80. [PMID: 32637664 PMCID: PMC7327777 DOI: 10.1016/j.synbio.2020.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/04/2022] Open
Abstract
Modular polyketide synthases (PKSs) are a multidomain megasynthase class of biosynthetic enzymes that have great promise for the development of new compounds, from new pharmaceuticals to high value commodity and specialty chemicals. Their colinear biosynthetic logic has been viewed as a promising platform for synthetic biology for decades. Due to this colinearity, domain swapping has long been used as a strategy to introduce molecular diversity. However, domain swapping often fails because it perturbs critical protein-protein interactions within the PKS. With our increased level of structural elucidation of PKSs, using judicious targeted mutations of individual residues is a more precise way to introduce molecular diversity with less potential for global disruption of the protein architecture. Here we review examples of targeted point mutagenesis to one or a few residues harbored within the PKS that alter domain specificity or selectivity, affect protein stability and interdomain communication, and promote more complex catalytic reactivity.
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Key Words
- ACP, acyl carrier protein
- AT, acyltransferase
- DEBS, 6-deoxyerthronolide B synthase
- DH, dehydratase
- EI, enoylisomerase
- ER, enoylreductase
- KR, ketoreductase
- KS, ketosynthase
- LM, loading module
- MT, methyltransferase
- Mod, module
- PKS, polyketide synthase
- PS, pyran synthase
- Polyketide synthase
- Protein engineering
- Rational design
- SNAC, N-acetyl cysteamine
- Saturation mutagenesis
- Site directed mutagenesis
- Synthetic biology
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Affiliation(s)
- Erin E. Drufva
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| | - Elijah G. Hix
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| | - Constance B. Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
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11
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Alanjary M, Cano-Prieto C, Gross H, Medema MH. Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines. Nat Prod Rep 2019; 36:1249-1261. [PMID: 31259995 DOI: 10.1039/c9np00021f] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2014 to 2019Nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) have been the subject of engineering efforts for multiple decades. Their modular assembly line architecture potentially allows unlocking vast chemical space for biosynthesis. However, attempts thus far are often met with mixed success, due to limited molecular compatibility of the parts used for engineering. Now, new engineering strategies, increases in genomic data, and improved computational tools provide more opportunities for major progress. In this review we highlight some of the challenges and progressive strategies for the re-design of NRPSs & type I PKSs and survey useful computational tools and approaches to attain the ultimate goal of semi-automated and design-based engineering of novel peptide and polyketide products.
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Affiliation(s)
- Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
| | - Carolina Cano-Prieto
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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12
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Rittner A, Paithankar KS, Drexler DJ, Himmler A, Grininger M. Probing the modularity of megasynthases by rational engineering of a fatty acid synthase Type I. Protein Sci 2018; 28:414-428. [PMID: 30394635 DOI: 10.1002/pro.3550] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022]
Abstract
Modularity is a fundamental property of megasynthases such as polyketide synthases (PKSs). In this study, we exploit the close resemblance between PKSs and animal fatty acid synthase (FAS) to re-engineer animal FAS to probe the modularity of the FAS/PKS family. Guided by sequence and structural information, we truncate and dissect animal FAS into its components, and reassemble them to generate new PKS-like modules as well as bimodular constructs. The novel re-engineered modules resemble all four common types of PKSs and demonstrate that this approach can be a powerful tool to deliver products with higher catalytic efficiency. Our data exemplify the inherent plasticity and robustness of the overall FAS/PKS fold, and open new avenues to explore FAS-based biosynthetic pathways for custom compound design.
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Affiliation(s)
- Alexander Rittner
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
| | - Karthik S Paithankar
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
| | - David Jan Drexler
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
| | - Aaron Himmler
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
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13
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Yao T, Liu Z, Li T, Zhang H, Liu J, Li H, Che Q, Zhu T, Li D, Li W. Characterization of the biosynthetic gene cluster of the polyene macrolide antibiotic reedsmycins from a marine-derived Streptomyces strain. Microb Cell Fact 2018; 17:98. [PMID: 29914489 PMCID: PMC6006980 DOI: 10.1186/s12934-018-0943-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/08/2018] [Indexed: 11/13/2022] Open
Abstract
Background Polyene antibiotics are important as antifungal medicines albeit with serious side effects such as nephrotoxicity. Reedsmycin (RDM) A (1), produced by marine-derived Streptomyces youssoufiensis OUC6819, is a non-glycosylated polyene macrolide antibiotic with antifungal activity comparable to that of clinically used nystatin. To elucidate its biosynthetic machinery, herein, the rdm biosynthetic gene cluster was cloned and characterized. Results The rdm cluster is located within a 104 kb DNA region harboring 21 open reading frames (ORFs), among which 15 ORFs were designated as rdm genes. The assembly line for RDM A is proposed on the basis of module and domain analysis of the polyketide synthetases (PKSs) RdmGHIJ, which catalyze 16 rounds of decarboxylative condensation using malonyl-CoA as the starter unit (loading module), two methylmalonyl-CoA (module 1 and 2), and fourteen malonyl-CoA (module 3–16) as extender units successively. However, the predicted substrate specificity of AT0 in the loading module is methylmalonyl-CoA instead of malonyl-CoA. Interestingly, the rdm cluster contains a five-gene regulation system RdmACDEF, which is different from other reported polyene gene clusters. In vivo experiments demonstrated the XRE family regulator RdmA and the PAS/LuxR family regulator RdmF function in negative and positive manner, respectively. Notably, inactivation of rdmA and overexpression of rdmF led to increased production of RDM A by ~ 2.0-fold and ~ 2.5-fold, reaching yields of 155.3 ± 1.89 and 184.8 ± 9.93 mg/L, respectively. Conclusions Biosynthesis of RDM A is accomplished on a linear assembly line catalyzed by Rdm PKSs harboring a unique AT0 under the control of a complex regulatory system. These findings enable generation of new biologically active RDM derivatives at high yield and with improved properties by engineered biosynthesis. Electronic supplementary material The online version of this article (10.1186/s12934-018-0943-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tingting Yao
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Zengzhi Liu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Tong Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Hui Zhang
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Jing Liu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Qian Che
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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14
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Klaus M, Grininger M. Engineering strategies for rational polyketide synthase design. Nat Prod Rep 2018; 35:1070-1081. [DOI: 10.1039/c8np00030a] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In this review, we highlight strategies in engineering polyketide synthases (PKSs). We focus on important protein–protein interactions that constitute an intact PKS assembly line.
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Affiliation(s)
- Maja Klaus
- Institute of Organic Chemistry and Chemical Biology
- Buchmann Institute for Molecular Life Sciences
- Cluster of Excellence for Macromolecular Complexes
- Goethe University Frankfurt
- 60438 Frankfurt am Main
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology
- Buchmann Institute for Molecular Life Sciences
- Cluster of Excellence for Macromolecular Complexes
- Goethe University Frankfurt
- 60438 Frankfurt am Main
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15
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Barajas JF, Blake-Hedges JM, Bailey CB, Curran S, Keasling JD. Engineered polyketides: Synergy between protein and host level engineering. Synth Syst Biotechnol 2017; 2:147-166. [PMID: 29318196 PMCID: PMC5655351 DOI: 10.1016/j.synbio.2017.08.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/26/2017] [Accepted: 08/26/2017] [Indexed: 01/01/2023] Open
Abstract
Metabolic engineering efforts toward rewiring metabolism of cells to produce new compounds often require the utilization of non-native enzymatic machinery that is capable of producing a broad range of chemical functionalities. Polyketides encompass one of the largest classes of chemically diverse natural products. With thousands of known polyketides, modular polyketide synthases (PKSs) share a particularly attractive biosynthetic logic for generating chemical diversity. The engineering of modular PKSs could open access to the deliberate production of both existing and novel compounds. In this review, we discuss PKS engineering efforts applied at both the protein and cellular level for the generation of a diverse range of chemical structures, and we examine future applications of PKSs in the production of medicines, fuels and other industrially relevant chemicals.
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Key Words
- ACP, Acyl carrier protein
- AT, Acyltransferase
- CoL, CoA-Ligase
- Commodity chemical
- DE, Dimerization element
- DEBS, 6-deoxyerythronolide B synthase
- DH, Dehydratase
- ER, Enoylreductase
- FAS, Fatty acid synthases
- KR, Ketoreductase
- KS, Ketosynthase
- LM, Loading module
- LTTR, LysR-type transcriptional regulator
- Metabolic engineering
- Natural products
- PCC, Propionyl-CoA carboxylase
- PDB, Precursor directed biosynthesis
- PK, Polyketide
- PKS, Polyketide synthase
- Polyketide
- Polyketide synthase
- R, Reductase domain
- SARP, Streptomyces antibiotic regulatory protein
- SNAC, N-acetylcysteamine
- Synthetic biology
- TE, Thioesterase
- TKL, Triketide lactone
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Affiliation(s)
| | | | - Constance B. Bailey
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Samuel Curran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jay. D. Keasling
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- QB3 Institute, University of California, Berkeley, Emeryville, CA 94608, USA
- Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, DK2970 Horsholm, Denmark
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16
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Komaki H, Ichikawa N, Oguchi A, Hamada M, Harunari E, Kodani S, Fujita N, Igarashi Y. Draft genome sequence of Streptomyces sp. TP-A0867, an alchivemycin producer. Stand Genomic Sci 2016; 11:85. [PMID: 27800124 PMCID: PMC5078962 DOI: 10.1186/s40793-016-0207-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 10/12/2016] [Indexed: 11/10/2022] Open
Abstract
Streptomyces sp. TP-A0867 (=NBRC 109436) produces structurally complex polyketides designated alchivemycins A and B. Here, we report the draft genome sequence of this strain together with features of the organism and assembly, annotation, and analysis of the genome sequence. The 9.9 Mb genome of Streptomyces sp. TP-A0867 encodes 8,385 putative ORFs, of which 7,232 were assigned with COG categories. We successfully identified a hybrid polyketide synthase (PKS)/ nonribosomal peptide synthetase (NRPS) gene cluster that could be responsible for alchivemycin biosynthesis, and propose the biosynthetic pathway. The alchivemycin biosynthetic gene cluster is also present in Streptomyces rapamycinicus NRRL 5491T, Streptomyces hygroscopicus subsp. hygroscopicus NBRC 16556, and Streptomyces ascomycinicus NBRC 13981T, which are taxonomically highly close to strain TP-A0867. This study shows a representative example that distribution of secondary metabolite genes is correlated with evolution within the genus Streptomyces.
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Affiliation(s)
- Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba, Japan
| | | | | | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba, Japan
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, Japan
| | - Shinya Kodani
- College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, Japan
| | | | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, Japan
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17
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Tautz T, Hoffmann J, Hoffmann T, Steinmetz H, Washausen P, Kunze B, Huch V, Kitsche A, Reichenbach H, Höfle G, Müller R, Kalesse M. Isolation, Structure Elucidation, Biosynthesis, and Synthesis of Antalid, a Secondary Metabolite from Polyangium species. Org Lett 2016; 18:2560-3. [DOI: 10.1021/acs.orglett.6b00810] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas Tautz
- Institute
for Organic Chemistry, Leibniz Universität Hannover, Schneiderberg
1B, D-30167 Hannover, Germany
| | - Judith Hoffmann
- Helmholtz
Institute for Pharmaceutical Research Saarland, Helmholtz Centre for
Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Building E8.1, D-66123 Saarbrücken, Germany
| | - Thomas Hoffmann
- Helmholtz
Institute for Pharmaceutical Research Saarland, Helmholtz Centre for
Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Building E8.1, D-66123 Saarbrücken, Germany
| | - Heinrich Steinmetz
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Peter Washausen
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Brigitte Kunze
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Volker Huch
- Institute
for Inorganic Chemistry, Saarland University, Building B2.2, D-66123 Saarbrücken, Germany
| | - Andreas Kitsche
- Institute
for Biostatistics, Leibniz Universität Hannover, Herrenhäuser
Straße 2, D-30419 Hannover, Germany
| | - Hans Reichenbach
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Gerhard Höfle
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz
Institute for Pharmaceutical Research Saarland, Helmholtz Centre for
Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Building E8.1, D-66123 Saarbrücken, Germany
| | - Markus Kalesse
- Institute
for Organic Chemistry, Leibniz Universität Hannover, Schneiderberg
1B, D-30167 Hannover, Germany
- Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, D-38124 Braunschweig, Germany
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18
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Abstract
Polyketides are a structurally and functionally diverse family of bioactive natural products that have found widespread application as pharmaceuticals, agrochemicals, and veterinary medicines. In bacteria complex polyketides are biosynthesized by giant multifunctional megaenzymes, termed modular polyketide synthases (PKSs), which construct their products in a highly coordinated assembly line-like fashion from a pool of simple precursor substrates. Not only is the multifaceted enzymology of PKSs a fascinating target for study, but it also presents considerable opportunities for the reengineering of these systems affording access to functionally optimized unnatural natural products. Here we provide an introductory primer to modular polyketide synthase structure and function, and highlight recent advances in the characterization and exploitation of these systems.
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Affiliation(s)
- Marisa Till
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
- BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Paul R Race
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
- BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
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19
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Wang F, Wang Y, Ji J, Zhou Z, Yu J, Zhu H, Su Z, Zhang L, Zheng J. Structural and functional analysis of the loading acyltransferase from avermectin modular polyketide synthase. ACS Chem Biol 2015; 10:1017-25. [PMID: 25581064 DOI: 10.1021/cb500873k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The loading acyltransferase (AT) domains of modular polyketide synthases (PKSs) control the choice of starter units incorporated into polyketides and are therefore attractive targets for the engineering of modular PKSs. Here, we report the structural and biochemical characterizations of the loading AT from avermectin modular PKS, which accepts more than 40 carboxylic acids as alternative starter units for the biosynthesis of a series of congeners. This first structural analysis of loading ATs from modular PKSs revealed the molecular basis for the relaxed substrate specificity. Residues important for substrate binding and discrimination were predicted by modeling a substrate into the active site. A mutant with altered specificity toward a panel of synthetic substrate mimics was generated by site-directed mutagenesis of the active site residues. The hydrolysis of the N-acetylcysteamine thioesters of racemic 2-methylbutyric acid confirmed the stereospecificity of the avermectin loading AT for an S configuration at the C-2 position of the substrate. Together, these results set the stage for region-specific modification of polyketides through active site engineering of loading AT domains of modular PKSs.
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Affiliation(s)
- Fen Wang
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Yanjie Wang
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Junjie Ji
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Zhan Zhou
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Jingkai Yu
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Hua Zhu
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute
of Microbiology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Zhiguo Su
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Lixin Zhang
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute
of Microbiology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Jianting Zheng
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
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20
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Hagen A, Poust S, de Rond T, Yuzawa S, Katz L, Adams PD, Petzold CJ, Keasling JD. In Vitro Analysis of Carboxyacyl Substrate Tolerance in the Loading and First Extension Modules of Borrelidin Polyketide Synthase. Biochemistry 2014; 53:5975-7. [DOI: 10.1021/bi500951c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew Hagen
- Synthetic Biology Engineering Research Center, 5885 Hollis Street, Emeryville, California 94608, United States
| | | | | | | | - Leonard Katz
- Synthetic Biology Engineering Research Center, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Paul D. Adams
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
| | - Christopher J. Petzold
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
| | - Jay D. Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Synthetic Biology Engineering Research Center, 5885 Hollis Street, Emeryville, California 94608, United States
- Physical
Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
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21
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Cummings M, Breitling R, Takano E. Steps towards the synthetic biology of polyketide biosynthesis. FEMS Microbiol Lett 2014; 351:116-25. [PMID: 24372666 PMCID: PMC4237116 DOI: 10.1111/1574-6968.12365] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 11/29/2022] Open
Abstract
Nature is providing a bountiful pool of valuable secondary metabolites, many of which possess therapeutic properties. However, the discovery of new bioactive secondary metabolites is slowing down, at a time when the rise of multidrug-resistant pathogens and the realization of acute and long-term side effects of widely used drugs lead to an urgent need for new therapeutic agents. Approaches such as synthetic biology are promising to deliver a much-needed boost to secondary metabolite drug development through plug-and-play optimized hosts and refactoring novel or cryptic bacterial gene clusters. Here, we discuss this prospect focusing on one comprehensively studied class of clinically relevant bioactive molecules, the polyketides. Extensive efforts towards optimization and derivatization of compounds via combinatorial biosynthesis and classical engineering have elucidated the modularity, flexibility and promiscuity of polyketide biosynthetic enzymes. Hence, a synthetic biology approach can build upon a solid basis of guidelines and principles, while providing a new perspective towards the discovery and generation of novel and new-to-nature compounds. We discuss the lessons learned from the classical engineering of polyketide synthases and indicate their importance when attempting to engineer biosynthetic pathways using synthetic biology approaches for the introduction of novelty and overexpression of products in a controllable manner.
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Affiliation(s)
- Matthew Cummings
- Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
| | - Rainer Breitling
- Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
| | - Eriko Takano
- Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
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22
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Abstract
Antibiotic discovery has a storied history. From the discovery of penicillin by Sir Alexander Fleming to the relentless quest for antibiotics by Selman Waksman, the stories have become like folklore used to inspire future generations of scientists. However, recent discovery pipelines have run dry at a time when multidrug-resistant pathogens are on the rise. Nature has proven to be a valuable reservoir of antimicrobial agents, which are primarily produced by modularized biochemical pathways. Such modularization is well suited to remodeling by an interdisciplinary approach that spans science and engineering. Herein, we discuss the biological engineering of small molecules, peptides, and non-traditional antimicrobials and provide an overview of the growing applicability of synthetic biology to antimicrobials discovery.
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Affiliation(s)
- Bijan Zakeri
- Synthetic Biology Group, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square, Cambridge MA 02139, USA
| | - Timothy K. Lu
- Synthetic Biology Group, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- MIT Synthetic Biology Center, 500 Technology Square, Cambridge MA 02139, USA
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23
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Jiang M, Pfeifer BA. Metabolic and pathway engineering to influence native and altered erythromycin production through E. coli. Metab Eng 2013; 19:42-9. [PMID: 23747605 DOI: 10.1016/j.ymben.2013.05.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 05/24/2013] [Accepted: 05/30/2013] [Indexed: 11/16/2022]
Abstract
The heterologous production of the complex antibiotic erythromycin through Escherichia coli provides a unique challenge in metabolic engineering. In addition to introducing the 19 foreign genes needed for heterologous biosynthesis, E. coli metabolism must be engineered to provide the propionyl-CoA and (2S)-methylmalonyl-CoA substrates required to allow erythromycin formation. In this work, three different pathways to propionyl-CoA were compared in the context of supporting E. coli erythromycin biosynthesis. The comparison revealed that alternative citramalate and threonine metabolic pathways (both starting from exogenous glycerol) were capable of supporting final compound formation equal to a proven pathway reliant upon exogenous propionate. Furthermore, two pathways to (2S)-methylmalonyl-CoA were compared in the production of a novel benzyl-erythromycin analog. A pathway dependent upon exogenous methylmalonate improved selectivity and facilitated antibiotic assessment of this new analog.
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Affiliation(s)
- Ming Jiang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Department of Chemical and Biological Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, USA
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24
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Kong D, Lee MJ, Lin S, Kim ES. Biosynthesis and pathway engineering of antifungal polyene macrolides in actinomycetes. ACTA ACUST UNITED AC 2013; 40:529-43. [DOI: 10.1007/s10295-013-1258-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 03/04/2013] [Indexed: 11/27/2022]
Abstract
Abstract
Polyene macrolides are a large family of natural products typically produced by soil actinomycetes. Polyene macrolides are usually biosynthesized by modular and large type I polyketide synthases (PKSs), followed by several steps of sequential post-PKS modifications such as region-specific oxidations and glycosylations. Although known as powerful antibiotics containing potent antifungal activities (along with additional activities against parasites, enveloped viruses and prion diseases), their high toxicity toward mammalian cells and poor distribution in tissues have led to the continuous identification and structural modification of polyene macrolides to expand their general uses. Advances in in-depth investigations of the biosynthetic mechanism of polyene macrolides and the genetic manipulations of the polyene biosynthetic pathways provide great opportunities to generate new analogues. Recently, a novel class of polyene antibiotics was discovered (a disaccharide-containing NPP) that displays better pharmacological properties such as improved water-solubility and reduced hemolysis. In this review, we summarize the recent advances in the biosynthesis, pathway engineering, and regulation of polyene antibiotics in actinomycetes.
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Affiliation(s)
- Dekun Kong
- grid.16821.3c 0000000403688293 State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology Shanghai Jiao Tong University 200240 Shanghai P. R. China
| | - Mi-Jin Lee
- grid.202119.9 0000000123648385 Department of Biological Engineering Inha University 402-751 Incheon Korea
| | - Shuangjun Lin
- grid.16821.3c 0000000403688293 State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology Shanghai Jiao Tong University 200240 Shanghai P. R. China
| | - Eung-Soo Kim
- grid.202119.9 0000000123648385 Department of Biological Engineering Inha University 402-751 Incheon Korea
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Cobb RE, Luo Y, Freestone T, Zhao H. Drug Discovery and Development via Synthetic Biology. Synth Biol (Oxf) 2013. [DOI: 10.1016/b978-0-12-394430-6.00010-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Initiation of polyene macrolide biosynthesis: interplay between polyketide synthase domains and modules as revealed via domain swapping, mutagenesis, and heterologous complementation. Appl Environ Microbiol 2011; 77:6982-90. [PMID: 21821762 DOI: 10.1128/aem.05781-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Polyene macrolides are important antibiotics used to treat fungal infections in humans. In this work, acyltransferase (AT) domain swaps, mutagenesis, and cross-complementation with heterologous polyketide synthase domain (PKS) loading modules were performed in order to facilitate production of new analogues of the polyene macrolide nystatin. Replacement of AT(0) in the nystatin PKS loading module NysA with the propionate-specific AT(1) from the nystatin PKS NysB, construction of hybrids between NysA and the loading module of rimocidin PKS RimA, and stepwise exchange of specific amino acids in the AT(0) domain by site-directed mutagenesis were accomplished. However, none of the NysA mutants constructed was able to initiate production of new nystatin analogues. Nevertheless, many NysA mutants and hybrids were functional, providing for different levels of nystatin biosynthesis. An interplay between certain residues in AT(0) and an active site residue in the ketosynthase (KS)-like domain of NysA in initiation of nystatin biosynthesis was revealed. Some hybrids between the NysA and RimA loading modules carrying the NysA AT(0) domain were able to prime rimocidin PKS with both acetate and butyrate units upon complementation of a rimA-deficient mutant of the rimocidin/CE-108 producer Streptomyces diastaticus. Expression of the PimS0 loading module from the pimaricin producer in the same host, however, resulted in production of CE-108 only. Taken together, these data indicate relaxed substrate specificity of NysA AT(0) domain, which is counteracted by a strict specificity of the first extender module KS domain in the nystatin PKS of Streptomyces noursei.
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Gulder TAM, Freeman MF, Piel J. The Catalytic Diversity of Multimodular Polyketide Synthases: Natural Product Biosynthesis Beyond Textbook Assembly Rules. Top Curr Chem (Cham) 2011. [PMID: 21360321 DOI: 10.1007/128_2010_113] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Bacterial multimodular polyketide synthases (PKSs) are responsible for the biosynthesis of a wide range of pharmacologically active natural products. These megaenzymes contain numerous catalytic and structural domains and act as biochemical templates to generate complex polyketides in an assembly line-like fashion. While the prototypical PKS is composed of only a few different domain types that are fused together in a combinatorial fashion, an increasing number of enzymes is being found that contain additional components. These domains can introduce remarkably diverse modifications into polyketides. This review discusses our current understanding of such noncanonical domains and their role in expanding the biosynthetic versatility of bacterial PKSs.
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Zhang H, Wang Y, Wu J, Skalina K, Pfeifer BA. Complete Biosynthesis of Erythromycin A and Designed Analogs Using E. coli as a Heterologous Host. ACTA ACUST UNITED AC 2010; 17:1232-40. [DOI: 10.1016/j.chembiol.2010.09.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/05/2010] [Accepted: 09/14/2010] [Indexed: 10/18/2022]
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Mast Y, Weber T, Gölz M, Ort-Winklbauer R, Gondran A, Wohlleben W, Schinko E. Characterization of the 'pristinamycin supercluster' of Streptomyces pristinaespiralis. Microb Biotechnol 2010; 4:192-206. [PMID: 21342465 PMCID: PMC3818860 DOI: 10.1111/j.1751-7915.2010.00213.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Pristinamycin, produced by Streptomyces pristinaespiralis Pr11, is a streptogramin antibiotic consisting of two chemically unrelated compounds, pristinamycin I and pristinamycin II. The semi‐synthetic derivatives of these compounds are used in human medicine as therapeutic agents against methicillin‐resistant Staphylococcus aureus strains. Only the partial sequence of the pristinamycin biosynthetic gene cluster has been previously reported. To complete the sequence, overlapping cosmids were isolated from a S. pristinaespiralis Pr11 gene library and sequenced. The boundaries of the cluster were deduced, limiting the cluster size to approximately 210 kb. In the central region of the cluster, previously unknown pristinamycin biosynthetic genes were identified. Combining the current and previously identified sequence information, we propose that all essential pristinamycin biosynthetic genes are included in the 210 kb region. A pristinamycin biosynthetic pathway was established. Furthermore, the pristinamycin gene cluster was found to be interspersed by a cryptic secondary metabolite cluster, which probably codes for a glycosylated aromatic polyketide. Gene inactivation experiments revealed that this cluster has no influence on pristinamycin production. Overall, this work provides new insights into pristinamycin biosynthesis and the unique genetic organization of the pristinamycin gene region, which is the largest antibiotic ‘supercluster’ known so far.
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Affiliation(s)
- Yvonne Mast
- Mikrobiologie/Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Fakultät für Biologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany.
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Buntin K, Irschik H, Weissman KJ, Luxenburger E, Blöcker H, Müller R. Biosynthesis of Thuggacins in Myxobacteria: Comparative Cluster Analysis Reveals Basis for Natural Product Structural Diversity. ACTA ACUST UNITED AC 2010; 17:342-56. [DOI: 10.1016/j.chembiol.2010.02.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 01/22/2010] [Accepted: 02/18/2010] [Indexed: 10/19/2022]
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Genetic engineering of macrolide biosynthesis: past advances, current state, and future prospects. Appl Microbiol Biotechnol 2009; 85:1227-39. [PMID: 19902203 DOI: 10.1007/s00253-009-2326-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 10/21/2009] [Accepted: 10/22/2009] [Indexed: 10/20/2022]
Abstract
Polyketides comprise one of the major families of natural products. They are found in a wide variety of bacteria, fungi, and plants and include a large number of medically important compounds. Polyketides are biosynthesized by polyketide synthases (PKSs). One of the major groups of polyketides are the macrolides, the activities of which are derived from the presence of a macrolactone ring to which one or more 6-deoxysugars are attached. The core macrocyclic ring is biosynthesized from acyl-CoA precursors by PKS. Genetic manipulation of PKS-encoding genes can result in predictable changes in the structure of the macrolactone component, many of which are not easily achieved through standard chemical derivatization or total synthesis. Furthermore, many of the changes, including post-PKS modifications such as glycosylation and oxidation, can be combined for further structural diversification. This review highlights the current state of novel macrolide production with a focus on the genetic engineering of PKS and post-PKS tailoring genes. Such engineering of the metabolic pathways for macrolide biosynthesis provides attractive alternatives for the production of diverse non-natural compounds. Other issues of importance, including the engineering of precursor pathways and heterologous expression of macrolide biosynthetic genes, are also considered.
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Insights into the evolution of macrolactam biosynthesis through cloning and comparative analysis of the biosynthetic gene cluster for a novel macrocyclic lactam, ML-449. Appl Environ Microbiol 2009; 76:283-93. [PMID: 19854930 DOI: 10.1128/aem.00744-09] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new compound, designated ML-449, structurally similar to the known 20-membered macrolactam BE-14106, was isolated from a marine sediment-derived Streptomyces sp. Cloning and sequencing of the 83-kb ML-449 biosynthetic gene cluster revealed its high level of similarity to the BE-14106 gene cluster. Comparison of the respective biosynthetic pathways indicated that the difference in the compounds' structures stems from the incorporation of one extra acetate unit during the synthesis of the acyl side chain. A phylogenetic analysis of the beta-ketosynthase (KS) domains from polyketide synthases involved in the biosynthesis of macrolactams pointed to a common ancestry for the two clusters. Furthermore, the analysis demonstrated the formation of a macrolactam-specific subclade for the majority of the KS domains from several macrolactam-biosynthetic gene clusters, indicating a closer relationship between macrolactam clusters than with the macrolactone clusters included in the analysis. Some KS domains from the ML-449, BE-14106, and salinilactam gene clusters did, however, show a closer relationship with KS domains from the polyene macrolide clusters, suggesting potential acquisition rather than duplication of certain PKS genes. Comparison of the ML-449, BE-14106, vicenistatin, and salinilactam biosynthetic gene clusters indicated an evolutionary relationship between them and provided new insights into the processes governing the evolution of small-ring macrolactam biosynthesis.
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Jørgensen H, Degnes KF, Sletta H, Fjærvik E, Dikiy A, Herfindal L, Bruheim P, Klinkenberg G, Bredholt H, Nygård G, Døskeland SO, Ellingsen TE, Zotchev SB. Biosynthesis of Macrolactam BE-14106 Involves Two Distinct PKS Systems and Amino Acid Processing Enzymes for Generation of the Aminoacyl Starter Unit. ACTA ACUST UNITED AC 2009; 16:1109-21. [DOI: 10.1016/j.chembiol.2009.09.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 09/15/2009] [Accepted: 09/18/2009] [Indexed: 10/20/2022]
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Developing Aspergillus as a host for heterologous expression. Biotechnol Adv 2009; 27:53-75. [DOI: 10.1016/j.biotechadv.2008.09.001] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 09/04/2008] [Accepted: 09/07/2008] [Indexed: 12/11/2022]
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Starcevic A, Zucko J, Simunkovic J, Long PF, Cullum J, Hranueli D. ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures. Nucleic Acids Res 2008; 36:6882-92. [PMID: 18978015 PMCID: PMC2588505 DOI: 10.1093/nar/gkn685] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The program package ‘ClustScan’ (Cluster Scanner) is designed for rapid, semi-automatic, annotation of DNA sequences encoding modular biosynthetic enzymes including polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS) and hybrid (PKS/NRPS) enzymes. The program displays the predicted chemical structures of products as well as allowing export of the structures in a standard format for analyses with other programs. Recent advances in understanding of enzyme function are incorporated to make knowledge-based predictions about the stereochemistry of products. The program structure allows easy incorporation of additional knowledge about domain specificities and function. The results of analyses are presented to the user in a graphical interface, which also allows easy editing of the predictions to incorporate user experience. The versatility of this program package has been demonstrated by annotating biochemical pathways in microbial, invertebrate animal and metagenomic datasets. The speed and convenience of the package allows the annotation of all PKS and NRPS clusters in a complete Actinobacteria genome in 2–3 man hours. The open architecture of ClustScan allows easy integration with other programs, facilitating further analyses of results, which is useful for a broad range of researchers in the chemical and biological sciences.
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Affiliation(s)
- Antonio Starcevic
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
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Karray F, Darbon E, Oestreicher N, Dominguez H, Tuphile K, Gagnat J, Blondelet-Rouault MH, Gerbaud C, Pernodet JL. Organization of the biosynthetic gene cluster for the macrolide antibiotic spiramycin in Streptomyces ambofaciens. MICROBIOLOGY-SGM 2008; 153:4111-4122. [PMID: 18048924 DOI: 10.1099/mic.0.2007/009746-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Spiramycin, a 16-membered macrolide antibiotic used in human medicine, is produced by Streptomyces ambofaciens; it comprises a polyketide lactone, platenolide, to which three deoxyhexose sugars are attached. In order to characterize the gene cluster governing the biosynthesis of spiramycin, several overlapping cosmids were isolated from an S. ambofaciens gene library, by hybridization with various probes (spiramycin resistance or biosynthetic genes, tylosin biosynthetic genes), and the sequences of their inserts were determined. Sequence analysis showed that the spiramycin biosynthetic gene cluster spanned a region of over 85 kb of contiguous DNA. In addition to the five previously described genes that encode the type I polyketide synthase involved in platenolide biosynthesis, 45 other genes have been identified. It was possible to propose a function for most of the inferred proteins in spiramycin biosynthesis, in its regulation, in resistance to the produced antibiotic or in the provision of extender units for the polyketide synthase. Two of these genes, predicted to be involved in deoxysugar biosynthesis, were inactivated by gene replacement, and the resulting mutants were unable to produce spiramycin, thus confirming their involvement in spiramycin biosynthesis. This work reveals the main features of spiramycin biosynthesis and constitutes a first step towards a detailed molecular analysis of the production of this medically important antibiotic.
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Affiliation(s)
- Fatma Karray
- CNRS UMR8621, Université Paris-Sud, Institut de Génétique et Microbiologie, Bâtiment 400, F-91405 Orsay Cedex, France
| | - Emmanuelle Darbon
- CNRS UMR8621, Université Paris-Sud, Institut de Génétique et Microbiologie, Bâtiment 400, F-91405 Orsay Cedex, France
| | - Nathalie Oestreicher
- CNRS UMR8621, Université Paris-Sud, Institut de Génétique et Microbiologie, Bâtiment 400, F-91405 Orsay Cedex, France
| | - Hélène Dominguez
- CNRS UMR8621, Université Paris-Sud, Institut de Génétique et Microbiologie, Bâtiment 400, F-91405 Orsay Cedex, France
| | - Karine Tuphile
- CNRS UMR8621, Université Paris-Sud, Institut de Génétique et Microbiologie, Bâtiment 400, F-91405 Orsay Cedex, France
| | - Josette Gagnat
- CNRS UMR8621, Université Paris-Sud, Institut de Génétique et Microbiologie, Bâtiment 400, F-91405 Orsay Cedex, France
| | | | - Claude Gerbaud
- CNRS UMR8621, Université Paris-Sud, Institut de Génétique et Microbiologie, Bâtiment 400, F-91405 Orsay Cedex, France
| | - Jean-Luc Pernodet
- CNRS UMR8621, Université Paris-Sud, Institut de Génétique et Microbiologie, Bâtiment 400, F-91405 Orsay Cedex, France
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Abstract
This review chronicles the synergistic growth of the fields of fatty acid and polyketide synthesis over the last century. In both animal fatty acid synthases and modular polyketide synthases, similar catalytic elements are covalently linked in the same order in megasynthases. Whereas in fatty acid synthases the basic elements of the design remain immutable, guaranteeing the faithful production of saturated fatty acids, in the modular polyketide synthases, the potential of the basic design has been exploited to the full for the elaboration of a wide range of secondary metabolites of extraordinary structural diversity.
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Affiliation(s)
- Stuart Smith
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, California 94609, USA.
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Tae H, Kong EB, Park K. ASMPKS: an analysis system for modular polyketide synthases. BMC Bioinformatics 2007; 8:327. [PMID: 17764579 PMCID: PMC2008767 DOI: 10.1186/1471-2105-8-327] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Accepted: 09/03/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polyketides are secondary metabolites of microorganisms with diverse biological activities, including pharmacological functions such as antibiotic, antitumor and agrochemical properties. Polyketides are synthesized by serialized reactions of a set of enzymes called polyketide synthase(PKS)s, which coordinate the elongation of carbon skeletons by the stepwise condensation of short carbon precursors. Due to their importance as drugs, the volume of data on polyketides is rapidly increasing and creating a need for computational analysis methods for efficient polyketide research. Moreover, the increasing use of genetic engineering to research new kinds of polyketides requires genome wide analysis. RESULTS We describe a system named ASMPKS (Analysis System for Modular Polyketide Synthesis) for computational analysis of PKSs against genome sequences. It also provides overall management of information on modular PKS, including polyketide database construction, new PKS assembly, and chain visualization. ASMPKS operates on a web interface to construct the database and to analyze PKSs, allowing polyketide researchers to add their data to this database and to use it easily. In addition, the ASMPKS can predict functional modules for a protein sequence submitted by users, estimate the chemical composition of a polyketide synthesized from the modules, and display the carbon chain structure on the web interface. CONCLUSION ASMPKS has powerful computation features to aid modular PKS research. As various factors, such as starter units and post-processing, are related to polyketide biosynthesis, ASMPKS will be improved through further development for study of the factors.
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Affiliation(s)
- Hongseok Tae
- Information Technology Institute, SmallSoft Co., Ltd., Jang-Dong 59-5, Yusung-Gu, Daejeon 305-343, South Korea
- Deptartment of Computer Engineering, Chungnam National University, 220 Gung-dong, Daejeon 305-764, South Korea
| | - Eun-Bae Kong
- Deptartment of Computer Engineering, Chungnam National University, 220 Gung-dong, Daejeon 305-764, South Korea
| | - Kiejung Park
- Information Technology Institute, SmallSoft Co., Ltd., Jang-Dong 59-5, Yusung-Gu, Daejeon 305-343, South Korea
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Abstract
6-Deoxyerythronolide B, the macrocyclic aglycone of the antibiotic erythromycin, is synthesized by a polyketide synthase (PKS) that has emerged as the prototypical modular megasynthase. A variety of molecular biological, protein chemical, and biosynthetic experiments over the past two decades have yielded insights into its mechanistic features. More recently, high-resolution structural images of portions of the 6-deoxyerythronolide B synthase have provided a platform for interpreting this wealth of biochemical data, while at the same time presenting a fundamentally new basis for the design of more detailed investigations into this remarkable enzyme. For example, the critical roles of domain-domain interactions and nonconserved linkers, as well as large interdomain movements in the structure and function of modular PKSs, have been highlighted. In turn, these insights point the way forward for more sophisticated and efficient biosynthetic engineering of complex polyketide natural products.
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Affiliation(s)
- Chaitan Khosla
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA.
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Rokem JS, Lantz AE, Nielsen J. Systems biology of antibiotic production by microorganisms. Nat Prod Rep 2007; 24:1262-87. [DOI: 10.1039/b617765b] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Perlova O, Gerth K, Kaiser O, Hans A, Müller R. Identification and analysis of the chivosazol biosynthetic gene cluster from the myxobacterial model strain Sorangium cellulosum So ce56. J Biotechnol 2006; 121:174-91. [PMID: 16313990 DOI: 10.1016/j.jbiotec.2005.10.011] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Revised: 09/22/2005] [Accepted: 10/10/2005] [Indexed: 11/17/2022]
Abstract
Myxobacteria belonging to the genus Sorangium are known to produce a variety of biologically active secondary metabolites. Chivosazol is a macrocyclic antibiotic active against yeast, filamentous fungi and especially against mammalian cells. The compound specifically destroys the actin skeleton of eucaryotic cells and does not show activity against bacteria. Chivosazol contains an oxazole ring and a glycosidically bound 6-deoxyglucose (except for chivosazol F). In this paper we describe the biosynthetic gene cluster that directs chivosazol biosynthesis in the model strain Sorangium cellulosum So ce56. This biosynthetic gene cluster spans 92 kbp on the chromosome and contains four polyketide synthase genes and one hybrid polyketide synthase/nonribosomal peptide synthetase gene. An additional gene encoding a protein with similarity to different methyltransferases and presumably involved in post-polyketide modification was identified downstream of the core biosynthetic gene cluster. The chivosazol biosynthetic gene locus belongs to the recently identified and rapidly growing class of trans-acyltransferase polyketide synthases, which do not contain acyltransferase domains integrated into the multimodular megasynthetases.
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Affiliation(s)
- Olena Perlova
- Pharmaceutical Biotechnology, Saarland University, P.O. Box 151150, D-66041 Saarbrücken, Germany
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Hill AM. The biosynthesis, molecular genetics and enzymology of the polyketide-derived metabolites. Nat Prod Rep 2005; 23:256-320. [PMID: 16572230 DOI: 10.1039/b301028g] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This review covers the biosynthesis of aliphatic and aromatic polyketides as well as mixed polyketide/NRPS metabolites, and discusses the molecular genetics and enzymology of the proteins responsible for their formation.
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Abstract
The bacterial multienzyme polyketide synthases (PKSs) produce a diverse array of products that have been developed into medicines, including antibiotics and anticancer agents. The modular genetic architecture of these PKSs suggests that it might be possible to engineer the enzymes to produce novel drug candidates, a strategy known as 'combinatorial biosynthesis'. So far, directed engineering of modular PKSs has resulted in the production of more than 200 new polyketides, but key challenges remain before the potential of combinatorial biosynthesis can be fully realized.
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Affiliation(s)
- Kira J Weissman
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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Bode HB, Müller R. Der Einfluss bakterieller Genomik auf die Naturstoff-Forschung. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501080] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
"There's life in the old dog yet!" This adage also holds true for natural product research. After the era of natural products was declared to be over, because of the introduction of combinatorial synthesis techniques, natural product research has taken a surprising turn back towards a major field of pharmaceutical research. Current challenges, such as emerging multidrug-resistant bacteria, might be overcome by developments which combine genomic knowledge with applied biology and chemistry to identify, produce, and alter the structure of new lead compounds. Significant biological activity is reported much less frequently for synthetic compounds, a fact reflected in the large proportion of natural products and their derivatives in clinical use. This Review describes the impact of microbial genomics on natural products research, in particularly the search for new lead structures and their optimization. The limitations of this research are also discussed, thus allowing a look into future developments.
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Affiliation(s)
- Helge B Bode
- Institut für Pharmazeutische Biotechnologie, Universität des Saarlandes, Postfach 151150, 66041 Saarbrücken, Germany
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Murli S, MacMillan KS, Hu Z, Ashley GW, Dong SD, Kealey JT, Reeves CD, Kennedy J. Chemobiosynthesis of novel 6-deoxyerythronolide B analogues by mutation of the loading module of 6-deoxyerythronolide B synthase 1. Appl Environ Microbiol 2005; 71:4503-9. [PMID: 16085842 PMCID: PMC1183267 DOI: 10.1128/aem.71.8.4503-4509.2005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chemobiosynthesis (J. R. Jacobsen, C. R. Hutchinson, D. E. Cane, and C. Khosla, Science 277:367-369, 1997) is an important route for the production of polyketide analogues and has been used extensively for the production of analogues of 6-deoxyerythronolide B (6-dEB). Here we describe a new route for chemobiosynthesis using a version of 6-deoxyerythronolide B synthase (DEBS) that lacks the loading module. When the engineered DEBS was expressed in both Escherichia coli and Streptomyces coelicolor and fed a variety of acyl-thioesters, several novel 15-R-6-dEB analogues were produced. The simpler "monoketide" acyl-thioester substrates required for this route of 15-R-6-dEB chemobiosynthesis allow greater flexibility and provide a cost-effective alternative to diketide-thioester feeding to DEBS KS1(o) for the production of 15-R-6-dEB analogues. Moreover, the facile synthesis of the monoketide acyl-thioesters allowed investigation of alternative thioester carriers. Several alternatives to N-acetyl cysteamine were found to work efficiently, and one of these, methyl thioglycolate, was verified as a productive thioester carrier for mono- and diketide feeding in both E. coli and S. coelicolor.
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Affiliation(s)
- Sumati Murli
- Kosan Biosciences Inc., 3832 Bay Center Place, Hayward, CA 94545, USA
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Chen H, Harrison PHM. Investigation of the origin of C2 units in biosynthesis of streptolydigin. Org Lett 2005; 6:4033-6. [PMID: 15496092 DOI: 10.1021/ol048317h] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] Isotope labeling studies show that malonate, not acetate, furnishes all four C(2) units in the acyltetramic acid streptolydigin. The results are compared with those for pramanicin, and implications for the biosynthetic pathway are discussed.
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Affiliation(s)
- Hao Chen
- Department of Chemistry, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4M1, Canada
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