1
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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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2
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Brazeau-Henrie JT, Paquette AR, Boddy CN. In Vitro Biochemical Characterization of Excised Macrocyclizing Thioesterase Domains from Non-ribosomal Peptide Synthetases. Methods Mol Biol 2023; 2670:101-125. [PMID: 37184701 DOI: 10.1007/978-1-0716-3214-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Characterization of thioesterases (TEs) is an important step in understanding natural product biosynthesis. Studying non-ribosomal peptide synthetase (NRPS) TEs presents a unique set of challenges with specific cloning and expression issues as well as the challenging synthesis of the thioester peptides substrate required for characterization of the TE. In this method, we describe the cloning and expression of NRPS TEs, the synthesis of thioester peptides, and the in vitro biochemical characterization of the enzyme.
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Affiliation(s)
| | - André R Paquette
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada.
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3
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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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4
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Curran SC, Pereira JH, Baluyot MJ, Lake J, Puetz H, Rosenburg DJ, Adams P, Keasling JD. Structure and Function of BorB, the Type II Thioesterase from the Borrelidin Biosynthetic Gene Cluster. Biochemistry 2020; 59:1630-1639. [PMID: 32250597 DOI: 10.1021/acs.biochem.0c00126] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
α/β hydrolases make up a large and diverse protein superfamily. In natural product biosynthesis, cis-acting thioesterase α/β hydrolases can terminate biosynthetic assembly lines and release products by hydrolyzing or cyclizing the biosynthetic intermediate. Thioesterases can also act in trans, removing aberrant intermediates and restarting stalled biosynthesis. Knockout of this "editing" function leads to reduced product titers. The borrelidin biosynthetic gene cluster from Streptomyces parvulus Tü4055 contains a hitherto uncharacterized stand-alone thioesterase, borB. In this work, we demonstrate that purified BorB cleaves acyl substrates with a preference for propionate, which supports the hypothesis that it is also an editing thioesterase. The crystal structure of BorB shows a wedgelike hydrophobic substrate binding crevice that limits substrate length. To investigate the structure-function relationship, we made chimeric BorB variants using loop regions from characterized homologues with different specificities. BorB chimeras slightly reduced activity, arguing that the modified region is a not major determinant of substrate preference. The structure-function relationships described here contribute to the process of elimination for understanding thioesterase specificity and, ultimately, engineering and applying trans-acting thioesterases in biosynthetic assembly lines.
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Affiliation(s)
- Samuel C Curran
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Jose H Pereira
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Marian-Joy Baluyot
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Julie Lake
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Hendrik Puetz
- Department of Biochemistry, University of Cologne, 50923 Albertus-Magnus-Platz, Cologne 51149, Germany.,Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | | | - Paul Adams
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Jay D Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
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5
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Yuet KP, Liu CW, Lynch SR, Kuo J, Michaels W, Lee RB, McShane AE, Zhong BL, Fischer CR, Khosla C. Complete Reconstitution and Deorphanization of the 3 MDa Nocardiosis-Associated Polyketide Synthase. J Am Chem Soc 2020; 142:5952-5957. [PMID: 32182063 DOI: 10.1021/jacs.0c00904] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several Nocardia strains associated with nocardiosis, a potentially life-threatening disease, house a nonamodular assembly line polyketide synthase (PKS) that presumably synthesizes an unknown polyketide. Here, we report the discovery and structure elucidation of the NOCAP (nocardiosis-associated polyketide) aglycone by first fully reconstituting the NOCAP synthase in vitro from purified protein components followed by heterologous expression in E. coli and spectroscopic analysis of the purified products. The NOCAP aglycone has an unprecedented structure comprised of a substituted resorcylaldehyde headgroup linked to a 15-carbon tail that harbors two conjugated all-trans trienes separated by a stereogenic hydroxyl group. This report is the first example of reconstituting a trans-acyltransferase assembly line PKS in vitro and of using these approaches to "deorphanize" a complete assembly line PKS identified via genomic sequencing. With the NOCAP aglycone in hand, the stage is set for understanding how this PKS and associated tailoring enzymes confer an advantage to their native hosts during human Nocardia infections.
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6
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Pogorevc D, Panter F, Schillinger C, Jansen R, Wenzel SC, Müller R. Production optimization and biosynthesis revision of corallopyronin A, a potent anti-filarial antibiotic. Metab Eng 2019; 55:201-211. [PMID: 31340171 DOI: 10.1016/j.ymben.2019.07.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 07/16/2019] [Accepted: 07/20/2019] [Indexed: 10/26/2022]
Abstract
Corallopyronins (COR) are α-pyrone antibiotics from myxobacteria representing highly promising lead structures for the development of antibacterial therapeutic agents. Their ability to inhibit RNA polymerase through interaction with the "switch region", a novel target, distant from binding sites of previously characterized RNA polymerase inhibitors (e.g. rifampicin), makes them particularly promising as antibiotic candidates. Corallopyronin A is currently also investigated as a lead compound for the treatment of lymphatic filariasis because of its superb activity against the nematode symbiont Wolbachia. As total synthesis is not a valid production option biotechnological optimization of compound supply is of utmost importance to further develop this highly potent compound class. Here we describe decisive improvements of the previously reported heterologous COR production and engineering platform yielding production of ~100 mg/L COR A. Furthermore, we provide a revised model of COR biosynthesis shedding light on the function of several biosynthetic proteins, including an unusual ECH-like enzyme providing dehydration functionality in trans and an uncharacterized protein conferring COR self-resistance in the myxobacterial heterologous host Myxococcus xanthus DK1622. We also report two new COR derivatives, COR D and oxyCOR A discovered in genetically engineered strains.
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Affiliation(s)
- Domen Pogorevc
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) / Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Fabian Panter
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) / Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Carolina Schillinger
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) / Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Rolf Jansen
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Silke C Wenzel
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) / Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) / Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany.
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7
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Kalkreuter E, CroweTipton JM, Lowell AN, Sherman DH, Williams GJ. Engineering the Substrate Specificity of a Modular Polyketide Synthase for Installation of Consecutive Non-Natural Extender Units. J Am Chem Soc 2019; 141:1961-1969. [PMID: 30676722 DOI: 10.1021/jacs.8b10521] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There is significant interest in diversifying the structures of polyketides to create new analogues of these bioactive molecules. This has traditionally been done by focusing on engineering the acyltransferase (AT) domains of polyketide synthases (PKSs) responsible for the incorporation of malonyl-CoA extender units. Non-natural extender units have been utilized by engineered PKSs previously; however, most of the work to date has been accomplished with ATs that are either naturally promiscuous and/or located in terminal modules lacking downstream bottlenecks. These limitations have prevented the engineering of ATs with low native promiscuity and the study of any potential gatekeeping effects by domains downstream of an engineered AT. In an effort to address this gap in PKS engineering knowledge, the substrate preferences of the final two modules of the pikromycin PKS were compared for several non-natural extender units and through active site mutagenesis. This led to engineering of the methylmalonyl-CoA specificity of both modules and inversion of their selectivity to prefer consecutive non-natural derivatives. Analysis of the product distributions of these bimodular reactions revealed unexpected metabolites resulting from gatekeeping by the downstream ketoreductase and ketosynthase domains. Despite these new bottlenecks, AT engineering provided the first full-length polyketide products incorporating two non-natural extender units. Together, this combination of tandem AT engineering and the identification of previously poorly characterized bottlenecks provides a platform for future advancements in the field.
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Affiliation(s)
- Edward Kalkreuter
- Department of Chemistry , NC State University , Raleigh , North Carolina 27695 , United States.,Comparative Medicine Institute , NC State University , Raleigh , North Carolina 27695 , United States
| | - Jared M CroweTipton
- Department of Chemistry , NC State University , Raleigh , North Carolina 27695 , United States
| | - Andrew N Lowell
- Life Sciences Institute, Department of Medicinal Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - David H Sherman
- Life Sciences Institute, Department of Medicinal Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Chemistry and Department of Microbiology & Immunology , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Gavin J Williams
- Department of Chemistry , NC State University , Raleigh , North Carolina 27695 , United States.,Comparative Medicine Institute , NC State University , Raleigh , North Carolina 27695 , United States
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8
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Grote M, Kushnir S, Pryk N, Möller D, Erver J, Ismail-Ali A, Schulz F. Identification of crucial bottlenecks in engineered polyketide biosynthesis. Org Biomol Chem 2019; 17:6374-6385. [DOI: 10.1039/c9ob00831d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Quo vadis combinatorial biosynthesis: STOP signs through substrate scope limitations lower the yields in engineered polyketide biosynthesis using cis-AT polyketide synthases.
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Affiliation(s)
- Marius Grote
- Organische Chemie 1
- AG Naturstoffchemie und –biochemie
- Fakultät für Chemie und Biochemie
- Ruhr-Universität Bochum
- 44780 Bochum
| | - Susanna Kushnir
- Organische Chemie 1
- AG Naturstoffchemie und –biochemie
- Fakultät für Chemie und Biochemie
- Ruhr-Universität Bochum
- 44780 Bochum
| | - Niclas Pryk
- Organische Chemie 1
- AG Naturstoffchemie und –biochemie
- Fakultät für Chemie und Biochemie
- Ruhr-Universität Bochum
- 44780 Bochum
| | - David Möller
- Organische Chemie 1
- AG Naturstoffchemie und –biochemie
- Fakultät für Chemie und Biochemie
- Ruhr-Universität Bochum
- 44780 Bochum
| | - Julian Erver
- Organische Chemie 1
- AG Naturstoffchemie und –biochemie
- Fakultät für Chemie und Biochemie
- Ruhr-Universität Bochum
- 44780 Bochum
| | - Ahmed Ismail-Ali
- Organische Chemie 1
- AG Naturstoffchemie und –biochemie
- Fakultät für Chemie und Biochemie
- Ruhr-Universität Bochum
- 44780 Bochum
| | - Frank Schulz
- Organische Chemie 1
- AG Naturstoffchemie und –biochemie
- Fakultät für Chemie und Biochemie
- Ruhr-Universität Bochum
- 44780 Bochum
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9
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Recycling of Overactivated Acyls by a Type II Thioesterase during Calcimycin Biosynthesis in Streptomyces chartreusis NRRL 3882. Appl Environ Microbiol 2018; 84:AEM.00587-18. [PMID: 29654175 DOI: 10.1128/aem.00587-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 03/30/2018] [Indexed: 02/01/2023] Open
Abstract
Type II thioesterases typically function as editing enzymes, removing acyl groups that have been misconjugated to acyl carrier proteins during polyketide secondary metabolite biosynthesis as a consequence of biosynthetic errors. Streptomyces chartreusis NRRL 3882 produces the pyrrole polyether ionophoric antibiotic, and we have identified the presence of a putative type II thioesterase-like sequence, calG, within the biosynthetic gene cluster involved in the antibiotic's synthesis. However, targeted gene mutagenesis experiments in which calG was inactivated in the organism did not lead to a decrease in calcimycin production but rather reduced the strain's production of its biosynthetic precursor, cezomycin. Results from in vitro activity assays of purified, recombinant CalG protein indicated that it was involved in the hydrolysis of cezomycin coenzyme A (cezomycin-CoA), as well as other acyl CoAs, but was not active toward 3-S-N-acetylcysteamine (SNAC; the mimic of the polyketide chain-releasing precursor). Further investigation of the enzyme's activity showed that it possessed a cezomycin-CoA hydrolysis Km of 0.67 mM and a kcat of 17.77 min-1 and was significantly inhibited by the presence of Mn2+ and Fe2+ divalent cations. Interestingly, when S. chartreusis NRRL 3882 was cultured in the presence of inorganic nitrite, NaNO2, it was observed that the production of calcimycin rather than cezomycin was promoted. Also, supplementation of S. chartreusis NRRL 3882 growth medium with the divalent cations Ca2+, Mg2+, Mn2+, and Fe2+ had a similar effect. Taken together, these observations suggest that CalG is not responsible for megasynthase polyketide precursor chain release during the synthesis of calcimycin or for retaining the catalytic efficiency of the megasynthase enzyme complex as is supposed to be the function for type II thioesterases. Rather, our results suggest that CalG is a dedicated thioesterase that prevents the accumulation of cezomycin-CoA when intracellular nitrogen is limited, an apparently new and previously unreported function of type II thioesterases.IMPORTANCE Type II thioesterases (TEIIs) are generally regarded as being responsible for removing aberrant acyl groups that block polyketide production, thereby maintaining the efficiency of the megasynthase involved in this class of secondary metabolites' biosynthesis. Specifically, this class of enzyme is believed to be involved in editing misprimed precursors, controlling initial units, providing key intermediates, and releasing final synthetic products in the biosynthesis of this class of secondary metabolites. Our results indicate that the putative TEII CalG present in the calcimycin (A23187)-producing organism Streptomyces chartreusis NRRL 3882 is not important either for the retention of catalytic efficiency of, or for the release of the product compound from, the megasynthase involved in calcimycin biosynthesis. Rather, the enzyme is involved in regulating/controlling the pool size of the calcimycin biosynthetic precursor, cezomycin, by hydrolysis of its CoA derivative. This novel function of CalG suggests a possible additional activity for enzymes belonging to the TEII protein family and promotes better understanding of the overall biosynthetic mechanisms involved in the production of this class of secondary metabolites.
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10
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Weissman KJ. Polyketide stereocontrol: a study in chemical biology. Beilstein J Org Chem 2017; 13:348-371. [PMID: 28326145 PMCID: PMC5331325 DOI: 10.3762/bjoc.13.39] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/01/2017] [Indexed: 11/23/2022] Open
Abstract
The biosynthesis of reduced polyketides in bacteria by modular polyketide synthases (PKSs) proceeds with exquisite stereocontrol. As the stereochemistry is intimately linked to the strong bioactivity of these molecules, the origins of stereochemical control are of significant interest in attempts to create derivatives of these compounds by genetic engineering. In this review, we discuss the current state of knowledge regarding this key aspect of the biosynthetic pathways. Given that much of this information has been obtained using chemical biology tools, work in this area serves as a showcase for the power of this approach to provide answers to fundamental biological questions.
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Affiliation(s)
- Kira J Weissman
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, Avenue de la Forêt de Haye, BP 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
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11
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Taguchi T, Awakawa T, Nishihara Y, Kawamura M, Ohnishi Y, Ichinose K. Bifunctionality of ActIV as a Cyclase-Thioesterase Revealed by in Vitro Reconstitution of Actinorhodin Biosynthesis in Streptomyces coelicolor A3(2). Chembiochem 2017; 18:316-323. [PMID: 27897367 DOI: 10.1002/cbic.201600589] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Indexed: 11/11/2022]
Abstract
Type II polyketide synthases iteratively generate a nascent polyketide thioester of the acyl carrier protein (ACP); this is structurally modified to produce an ACP-free intermediate towards the final metabolite. However, the timing of ACP off-loading is not well defined because of the lack of an apparent thioesterase (TE) among relevant biosynthetic enzymes. Here, ActIV, which had been assigned as a second ring cyclase (CYC) in actinorhodin (ACT) biosynthesis, was shown to possess TE activity in vitro with a model substrate, anthraquinone-2-carboxylic acid-N-acetylcysteamine. In order to investigate its function further, the ACT biosynthetic pathway in Streptomyces coelicolor A3(2) was reconstituted in vitro in a stepwise fashion up to (S)-DNPA, and the product of ActIV reaction was characterized as an ACP-free bicyclic intermediate. These findings indicate that ActIV is a bifunctional CYC-TE and provide clear evidence for the release timing of the intermediate from the ACP anchor.
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Affiliation(s)
- Takaaki Taguchi
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Takayoshi Awakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.,Present address: Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yukitaka Nishihara
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Michiho Kawamura
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | - Yasuo Ohnishi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Koji Ichinose
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
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12
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Huang H, Ren SX, Yang S, Hu HF. Comparative analysis of rapamycin biosynthesis clusters between Actinoplanes sp. N902-109 and Streptomyces hygroscopicus ATCC29253. Chin J Nat Med 2015; 13:90-8. [PMID: 25769891 DOI: 10.1016/s1875-5364(15)60012-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Indexed: 12/27/2022]
Abstract
The present study was designed to identify the difference between two rapamycin biosynthetic gene clusters from Streptomyces hygroscopicus ATCC29253 and Actinoplanes sp. N902-109 by comparing the sequence and organization of the gene clusters. The biosynthetic gene cluster for rapamycin in Streptomyces hygroscopicus ATCC29253 was reported in 1995. The second rapamycin producer, Actinoplanes sp. N902-109, which was isolated in 1995, could produce more rapamycin than Streptomyces hygroscopicus ATCC29253. The genomic map of Actinoplanes sp. N902-109 has been elucidated in our laboratory. Two gene clusters were compared using the online software anti-SMASH, Glimmer 3.02 and Subsystem Technology (RAST). Comparative analysis revealed that the organization of the multifunctional polyketide synthases (PKS) genes: RapA, RapB, RapC, and NRPS-like RapP were identical in the two clusters. The genes responsible for precursor synthesis and macrolactone modification flanked the PKS core region in N902-109, while the homologs of those genes located downstream of the PKS core region in ATCC29253. Besides, no homolog of the gene encoding a putative type II thioesterase that may serve as a PKS "editing" enzyme accounted for over-production of rapamycin in N902-109, was found in ATCC29253. Furthermore, no homologs of genes rapQ (encoding a methyltransferase) and rapG in N902-109 were found in ATCC29253, however, an extra rapM gene encoding methyltransferase was discovered in ATCC29253. Two rapamycin biosynthetic gene clusters displayed overall high homology as well as some differences in gene organization and functions.
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Affiliation(s)
- He Huang
- Shanghai Institute of Pharmaceutical Industry, Shanghai 200040, China; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Shuang-Xi Ren
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Sheng Yang
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hai-Feng Hu
- Shanghai Institute of Pharmaceutical Industry, Shanghai 200040, China.
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13
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Payero TD, Vicente CM, Rumbero Á, Barreales EG, Santos-Aberturas J, de Pedro A, Aparicio JF. Functional analysis of filipin tailoring genes from Streptomyces filipinensis reveals alternative routes in filipin III biosynthesis and yields bioactive derivatives. Microb Cell Fact 2015; 14:114. [PMID: 26246267 PMCID: PMC4527110 DOI: 10.1186/s12934-015-0307-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/28/2015] [Indexed: 12/11/2022] Open
Abstract
Background Streptomyces filipinensis is the industrial producer of filipin, a pentaene macrolide, archetype of non-glycosylated polyenes, and widely used for the detection and the quantitation of cholesterol in biological membranes and as a tool for the diagnosis of Niemann–Pick type C disease. Genetic manipulations of polyene biosynthetic pathways have proven useful for the discovery of products with improved properties. Here, we describe the late biosynthetic steps for filipin III biosynthesis and strategies for the generation of bioactive filipin III derivatives at high yield. Results A region of 13,778 base pairs of DNA from the S. filipinensis genome was isolated, sequenced, and characterized. Nine complete genes and two truncated ORFs were located. Disruption of genes proved that this genomic region is part of the biosynthetic cluster for the 28-membered ring of the polyene macrolide filipin. This set of genes includes two cytochrome P450 monooxygenase encoding genes, filC and filD, which are proposed to catalyse specific hydroxylations of the macrolide ring at C26 and C1′ respectively. Gene deletion and complementation experiments provided evidence for their role during filipin III biosynthesis. Filipin III derivatives were accumulated by the recombinant mutants at high yield. These have been characterized by mass spectrometry and nuclear magnetic resonance following high-performance liquid chromatography purification thus revealing the post-polyketide steps during polyene biosynthesis. Two alternative routes lead to the formation of filipin III from the initial product of polyketide synthase chain assembly and cyclization filipin I, one trough filipin II, and the other one trough 1′-hydroxyfilipin I, all filipin III intermediates being biologically active. Moreover, minimal inhibitory concentration values against Candida utilis and Saccharomyces cerevisiae were obtained for all filipin derivatives, finding that 1′-hydroxyfilipin and especially filipin II show remarkably enhanced antifungal bioactivity. Complete nuclear magnetic resonance assignments have been obtained for the first time for 1′-hydroxyfilipin I. Conclusions This report reveals the existence of two alternative routes for filipin III formation and opens new possibilities for the generation of biologically active filipin derivatives at high yield and with improved properties. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0307-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tamara D Payero
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain. .,Institute of Biotechnology INBIOTEC, Parque Científico de León, Avda. Real, no 1, 24006, León, Spain.
| | - Cláudia M Vicente
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain. .,Institute of Biotechnology INBIOTEC, Parque Científico de León, Avda. Real, no 1, 24006, León, Spain.
| | - Ángel Rumbero
- Department of Organic Chemistry, Faculty of Sciences, Campus de Cantoblanco, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Eva G Barreales
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain.
| | - Javier Santos-Aberturas
- Institute of Biotechnology INBIOTEC, Parque Científico de León, Avda. Real, no 1, 24006, León, Spain. .,Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Antonio de Pedro
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain.
| | - Jesús F Aparicio
- Area of Microbiology, Faculty of Biology, Universidad de León, 24071, León, Spain.
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14
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Nakamura H, Wang JX, Balskus EP. Assembly line termination in cylindrocyclophane biosynthesis: discovery of an editing type II thioesterase domain in a type I polyketide synthase. Chem Sci 2015; 6:3816-3822. [PMID: 29218151 PMCID: PMC5707447 DOI: 10.1039/c4sc03132f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 04/11/2015] [Indexed: 01/18/2023] Open
Abstract
Investigation of cylindrocyclophane biosynthesis reveals a C-terminal thioesterase domain involved in PKS assembly line editing, not termination.
The termination step is an important source of structural diversity in polyketide biosynthesis. Most type I polyketide synthase (PKS) assembly lines are terminated by a thioesterase (TE) domain located at the C-terminus of the final module, while other PKS assembly lines lack a terminal TE domain and are instead terminated by a separate enzyme in trans. In cylindrocyclophane biosynthesis, the type I modular PKS assembly line is terminated by a freestanding type III PKS (CylI). Unexpectedly, the final module of the type I PKS (CylH) also possesses a C-terminal TE domain. Unlike typical type I PKSs, the CylH TE domain does not influence assembly line termination by CylI in vitro. Instead, this domain phylogenetically resembles a type II TE and possesses activity consistent with an editing function. This finding may shed light on the evolution of unusual PKS termination logic. In addition, the presence of related type II TE domains in many cryptic type I PKS and nonribosomal peptide synthetase (NRPS) assembly lines has implications for pathway annotation, product prediction, and engineering.
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Affiliation(s)
- H Nakamura
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , USA .
| | - J X Wang
- Small Molecule Mass Spectrometry Facility , FAS Division of Science , Cambridge , Massachusetts 02138 , USA
| | - E P Balskus
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , USA .
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15
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Chen X, Ji R, Jiang X, Yang R, Liu F, Xin Y. Iterative type I polyketide synthases involved in enediyne natural product biosynthesis. IUBMB Life 2014; 66:587-95. [PMID: 25278375 DOI: 10.1002/iub.1316] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/14/2014] [Indexed: 12/12/2022]
Abstract
Enediyne natural products are potent antibiotics structurally characterized by an enediyne core containing two acetylenic groups conjugated to a double bond in a 9- or 10-membered carbocycle. The biosynthetic gene clusters for enediynes encode a novel iterative type I polyketide synthase (PKSE), which is generally believed to initiate the biosynthetic process of enediyne cores. This review article will cover research efforts made since its discovery to elucidate the role of the PKSE in enediyne core biosynthesis. Topics covered include the unique domain architecture, identification, and characterization of turnover products, and interaction with partner thioesterase protein.
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Affiliation(s)
- Xiaolei Chen
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
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16
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Kotowska M, Pawlik K. Roles of type II thioesterases and their application for secondary metabolite yield improvement. Appl Microbiol Biotechnol 2014; 98:7735-46. [PMID: 25081554 PMCID: PMC4147253 DOI: 10.1007/s00253-014-5952-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 12/31/2022]
Abstract
A large number of antibiotics and other industrially important microbial secondary metabolites are synthesized by polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). These multienzymatic complexes provide an enormous flexibility in formation of diverse chemical structures from simple substrates, such as carboxylic acids and amino acids. Modular PKSs and NRPSs, often referred to as megasynthases, have brought about a special interest due to the colinearity between enzymatic domains in the proteins working as an “assembly line” and the chain elongation and modification steps. Extensive efforts toward modified compound biosynthesis by changing organization of PKS and NRPS domains in a combinatorial manner laid good grounds for rational design of new structures and their controllable biosynthesis as proposed by the synthetic biology approach. Despite undeniable progress made in this field, the yield of such “unnatural” natural products is often not satisfactory. Here, we focus on type II thioesterases (TEIIs)—discrete hydrolytic enzymes often encoded within PKS and NRPS gene clusters which can be used to enhance product yield. We review diverse roles of TEIIs (removal of aberrant residues blocking the megasynthase, participation in substrate selection, intermediate, and product release) and discuss their application in new biosynthetic systems utilizing PKS and NRPS parts.
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Affiliation(s)
- Magdalena Kotowska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, ul. Rudolfa Weigla 12, 53-114, Wroclaw, Poland,
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17
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Wang YY, Ran XX, Chen WB, Liu SP, Zhang XS, Guo YY, Jiang XH, Jiang H, Li YQ. Characterization of type II thioesterases involved in natamycin biosynthesis in Streptomyces chattanoogensis L10. FEBS Lett 2014; 588:3259-64. [PMID: 25064840 DOI: 10.1016/j.febslet.2014.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 07/11/2014] [Accepted: 07/11/2014] [Indexed: 01/11/2023]
Abstract
The known functions of type II thioesterases (TEIIs) in type I polyketide synthases (PKSs) include selecting of starter acyl units, removal of aberrant extender acyl units, releasing of final products, and dehydration of polyketide intermediates. In this study, we characterized two TEIIs (ScnI and PKSIaTEII) from Streptomyces chattanoogensis L10. Deletion of scnI in S. chattanoogensis L10 decreased the natamycin production by about 43%. Both ScnI and PKSIaTEII could remove acyl units from the acyl carrier proteins (ACPs) involved in the natamycin biosynthesis. Our results show that the TEII could play important roles in both the initiation step and the elongation steps of a polyketide biosynthesis; the intracellular TEIIs involved in different biosynthetic pathways could complement each other.
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Affiliation(s)
- Yue-Yue Wang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xin-Xin Ran
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Wei-Bin Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shui-Ping Liu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiao-Sheng Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuan-Yang Guo
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xin-Hang Jiang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Jiang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China,; Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, Zhejiang 310058, China.
| | - Yong-Quan Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China,; Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, Zhejiang 310058, China.
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18
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Li J, Neubauer P. Escherichia coli as a cell factory for heterologous production of nonribosomal peptides and polyketides. N Biotechnol 2014; 31:579-85. [PMID: 24704144 DOI: 10.1016/j.nbt.2014.03.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/21/2014] [Accepted: 03/24/2014] [Indexed: 12/18/2022]
Abstract
Nonribosomal peptides (NRPs) and polyketides (PKs) are two classes of natural products with numerous bioactivities such as antiviral, antimicrobial and anticancer activity. However, pharmaceutical applications of these products are often impeded because many native producers are difficult to cultivate or show a low productivity. Over the last decade, with the development of synthetic biology and metabolic engineering, more and more bioactive natural products including NRPs and PKs have been heterologously produced using easy-to-handle surrogate microbes. In this process, the full biosynthetic pathway for the production of a target compound is first identified and isolated from the native producer, and then reconstituted in a well-characterized and easily culturable heterologous producer like Escherichia coli. Thereafter, the productivity could be rationally improved through multiple strategies from strain to bioprocess optimization. This review summarizes the endeavors and progresses made in the heterologous production of NRPs, PKs and NRP/PK hybrids using E. coli as a robust whole-cell factory in recent years.
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Affiliation(s)
- Jian Li
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße76, ACK24, D-13355 Berlin, Germany.
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstraße76, ACK24, D-13355 Berlin, Germany
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19
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Aigle B, Lautru S, Spiteller D, Dickschat JS, Challis GL, Leblond P, Pernodet JL. Genome mining of Streptomyces ambofaciens. J Ind Microbiol Biotechnol 2013; 41:251-63. [PMID: 24258629 DOI: 10.1007/s10295-013-1379-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 10/30/2013] [Indexed: 02/04/2023]
Abstract
Since the discovery of the streptomycin produced by Streptomyces griseus in the middle of the last century, members of this bacterial genus have been largely exploited for the production of secondary metabolites with wide uses in medicine and in agriculture. They have even been recognized as one of the most prolific producers of natural products among microorganisms. With the onset of the genomic era, it became evident that these microorganisms still represent a major source for the discovery of novel secondary metabolites. This was highlighted with the complete genome sequencing of Streptomyces coelicolor A3(2) which revealed an unexpected potential of this organism to synthesize natural products undetected until then by classical screening methods. Since then, analysis of sequenced genomes from numerous Streptomyces species has shown that a single species can carry more than 30 secondary metabolite gene clusters, reinforcing the idea that the biosynthetic potential of this bacterial genus is far from being fully exploited. This review highlights our knowledge on the potential of Streptomyces ambofaciens ATCC 23877 to synthesize natural products. This industrial strain was known for decades to only produce the drug spiramycin and another antibacterial compound, congocidine. Mining of its genome allowed the identification of 23 clusters potentially involved in the production of other secondary metabolites. Studies of some of these clusters resulted in the characterization of novel compounds and of previously known compounds but never characterized in this Streptomyces species. In addition, genome mining revealed that secondary metabolite gene clusters of phylogenetically closely related Streptomyces are mainly species-specific.
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Affiliation(s)
- Bertrand Aigle
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, 54506, Vandœuvre-lès-Nancy, France,
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20
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SlnM gene overexpression with different promoters on natamycin production in Streptomyces lydicus A02. J Ind Microbiol Biotechnol 2013; 41:163-72. [PMID: 24174215 DOI: 10.1007/s10295-013-1370-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 10/16/2013] [Indexed: 10/26/2022]
Abstract
Natamycin is an important polyene macrolide antifungal agent produced by several Streptomyces strains and is widely used as a food preservative and fungicide in food, medicinal and veterinary products. In order to increase the yield of natamycin, this study aimed at cloning and overexpressing a natamycin-positive regulator, slnM2, with different promoters in the newly isolated strain Streptomyces lydicus A02, which is capable of producing natamycin. The slnM gene in S. lydicus is highly similar to gene pimM (scnRII), the pathway-specific positive regulator of natamycin biosynthesis in S. natalensis and S. chattanoogensis, which are PAS-LuxR regulators. Three engineered strains of S. lydicus, AM01, AM02 and AM03, were generated by inserting an additional copy of slnM2 with an ermEp* promoter, inserting an additional copy of slnM2 with dual promoters, ermEp* and its own promoter, and inserting an additional copy of slnM2 with its own promoter, respectively. No obvious changes in growth were observed between the engineered and wild-type strains. However, natamycin production in the engineered strains was significantly enhanced, by 2.4-fold in strain AM01, 3.0-fold in strain AM02 and 1.9-fold in strain AM03 when compared to the strain A02 in YEME medium without sucrose. These results indicated that the ermEp* promoter was more active than the native promoter of slnM2. Overall, dual promoters displayed the highest transcription of biosynthetic genes and yield of natamycin.
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21
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Zhang W, Fortman JL, Carlson JC, Yan J, Liu Y, Bai F, Guan W, Jia J, Matainaho T, Sherman DH, Li S. Characterization of the bafilomycin biosynthetic gene cluster from Streptomyces lohii. Chembiochem 2013; 14:301-6. [PMID: 23362147 PMCID: PMC3771327 DOI: 10.1002/cbic.201200743] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Indexed: 11/08/2022]
Abstract
New hope for old bones: The plecomacrolide bafilomycin has been explored for decades as an anti-osteoporotic. However, its structural complexity has limited the synthesis of analogues. The cloning of the bafilomycin biosynthetic gene cluster from the environmental isolate Streptomyces lohii opens the door to the production of new analogues through bioengineering.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, Shandong 266101 (P. R. China), Fax: (+86)-532-8066-2778
| | - J. L. Fortman
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA), Fax: (+1)-734-615-3641
| | - Jacob C. Carlson
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA), Fax: (+1)-734-615-3641
| | - Jiyong Yan
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, Shandong 266101 (P. R. China), Fax: (+86)-532-8066-2778
| | - Yi Liu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, Shandong 266101 (P. R. China), Fax: (+86)-532-8066-2778
| | - Fali Bai
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, Shandong 266101 (P. R. China), Fax: (+86)-532-8066-2778
| | - Wenna Guan
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, Shandong 266101 (P. R. China), Fax: (+86)-532-8066-2778
| | - Junyong Jia
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA), Fax: (+1)-734-615-3641
| | - Teatulohi Matainaho
- Professor Teatulohi Matainaho, Department of Pharmacology, University of Papua New Guinea, Port Morseby (Papua New Guinea)
| | - David H. Sherman
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA), Fax: (+1)-734-615-3641
| | - Shengying Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, Shandong 266101 (P. R. China), Fax: (+86)-532-8066-2778
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22
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Yan J, Hazzard C, Bonnett SA, Reynolds KA. Functional modular dissection of DEBS1-TE changes triketide lactone ratios and provides insight into Acyl group loading, hydrolysis, and ACP transfer. Biochemistry 2012; 51:9333-41. [PMID: 23116287 DOI: 10.1021/bi300830q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DEBS1-TE fusion protein is comprised of the loading module, the first two extension modules, and the terminal TE domain of the Saccharopolyspora erythraea 6-deoxyerythronolide B synthase. DEBS1-TE produces triketide lactones that differ on the basis of the starter unit selected by the loading module. Typical fermentations with plasmid-based expression of DEBS1-TE produce a 6:1 ratio of propionate to isobutyrate-derived triketide lactones. Functional dissection of the loading module from the remainder of DEBS1-TE results in 50% lower titers of triketide lactone and a dramatic shift in the production to a 1:4 ratio of propionate to isobutyrate-derived products. A series of radiolabeling studies of the loading module has shown that transfer from the AT to the ACP occurs much faster for propionate than for isobutyrate. However, the equilibrium occupancy of the AT favors isobutyrate such that propionate is outcompeted for ACP occupancy. Thus, propionyl-ACP is the kinetic product, while isobutyryl-ACP is the thermodynamic product. A slowed transfer from the loading domain ACP to first-extension module KS due to functional dissection of DEBS1-TE allows this isobutyryl-ACP-favored equilibrium to be realized and likely accounts for the observed shift in triketide lactone products.
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Affiliation(s)
- John Yan
- Department of Chemistry, Portland State University, Portland, Oregon 97201, United States
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Kushnir S, Sundermann U, Yahiaoui S, Brockmeyer A, Janning P, Schulz F. Minimally Invasive Mutagenesis Gives Rise to a Biosynthetic Polyketide Library. Angew Chem Int Ed Engl 2012; 51:10664-9. [DOI: 10.1002/anie.201202438] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 06/29/2012] [Indexed: 11/08/2022]
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Kushnir S, Sundermann U, Yahiaoui S, Brockmeyer A, Janning P, Schulz F. Aufbau einer biosynthetischen Polyketid-Bibliothek durch minimalinvasive Mutagenese. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202438] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Shen Y, Huang H, Zhu L, Luo M, Chen D. Type II thioesterase gene (ECO-orf27) from Amycolatopsis orientalis influences production of the polyketide antibiotic, ECO-0501 (LW01). Biotechnol Lett 2012; 34:2087-91. [PMID: 22850790 DOI: 10.1007/s10529-012-1010-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 07/05/2012] [Indexed: 11/26/2022]
Abstract
ECO-orf27 associated with the cluster of ECO-0501 (LW01) from Amycolatopsis orientalis is deduced to encode a type II thioesterase. Disruption of ECO-orf27 reduced LW01 production by 95 %. Complementation of the disrupted mutant with intact ECO-orf27 restored the production of LW01 suggesting that ECO-orf27 is crucial for LW01 biosynthesis. ECO-TE I, the gene encoding type I thioesterase from LW01 polyketide synthases, cannot complement ECO-orf27 deficient mutant distinguishing ECO-orf27 from type I thioesterase gene. Type II thioesterase gene pikAV from Streptomyces venezuelae could complement ECO-orf27 in A. orientalis indicating that the two genes are equivalent in their function. Overexpression of ECO-orf27 resulted in a 20 % increase in LW01 production providing an alternative approach for yield improvement.
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Affiliation(s)
- Yang Shen
- School of Biotechnology, East China University of Science and Technology, Meilong Rd. 130#, Shanghai, People's Republic of China
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26
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Abstract
Complex biosynthetic enzymes such as polyketide synthases make mistakes. In this issue of Chemistry & Biology, Jensen et al. report that a discrete family of acyltransferases is responsible for error correction, hydrolyzing key biosynthetic intermediates from a multi-enzyme complex. This activity might find use in understanding polyketide biosynthesis, particularly in uncultivated organisms and in tailoring the synthesis of small molecules.
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Affiliation(s)
- Jason C Kwan
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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27
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Vagstad AL, Bumpus SB, Belecki K, Kelleher NL, Townsend CA. Interrogation of global active site occupancy of a fungal iterative polyketide synthase reveals strategies for maintaining biosynthetic fidelity. J Am Chem Soc 2012; 134:6865-77. [PMID: 22452347 DOI: 10.1021/ja3016389] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nonreducing iterative polyketide synthases (NR-PKSs) are responsible for assembling the core of fungal aromatic natural products with diverse biological properties. Despite recent advances in the field, many mechanistic details of polyketide assembly by these megasynthases remain unknown. To expand our understanding of substrate loading, polyketide elongation, cyclization, and product release, active site occupancy and product output were explored by Fourier transform mass spectrometry using the norsolorinic acid anthrone-producing polyketide synthase, PksA, from the aflatoxin biosynthetic pathway in Aspergillus parasiticus. Here we report the simultaneous observation of covalent intermediates from all catalytic domains of PksA from in vitro reconstitution reactions. The data provide snapshots of iterative catalysis and reveal an underappreciated editing function for the C-terminal thioesterase domain beyond its recently established synthetic role in Claisen/Dieckmann cyclization and product release. The specificity of thioesterase catalyzed hydrolysis was explored using biosynthetically relevant protein-bound and small molecule acyl substrates and demonstrated activity against hexanoyl and acetyl, but not malonyl. Processivity of polyketide extension was supported by the inability of a nonhydrolyzable malonyl analog to trap products of intermediate chain lengths and by the detection of only fully extended species observed covalently bound to, and as the predominant products released by, PksA. High occupancy of the malonyl transacylase domain and fast relative rate of malonyl transfer compared to starter unit transfer indicate that rapid loading of extension units onto the carrier domain facilitates efficient chain extension in a manner kinetically favorable to ultimate product formation.
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Affiliation(s)
- Anna L Vagstad
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland, USA
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Bonnett SA, Rath CM, Shareef AR, Joels JR, Chemler JA, Håkansson K, Reynolds K, Sherman DH. Acyl-CoA subunit selectivity in the pikromycin polyketide synthase PikAIV: steady-state kinetics and active-site occupancy analysis by FTICR-MS. ACTA ACUST UNITED AC 2012; 18:1075-81. [PMID: 21944746 DOI: 10.1016/j.chembiol.2011.07.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 06/23/2011] [Accepted: 07/04/2011] [Indexed: 10/17/2022]
Abstract
Polyketide natural products generated by type I modular polyketide synthases (PKSs) are vital components in our drug repertoire. To reprogram these biosynthetic assembly lines, we must first understand the steps that occur within the modular "black boxes." Herein, key steps of acyl-CoA extender unit selection are explored by in vitro biochemical analysis of the PikAIV PKS model system. Two complementary approaches are employed: a fluorescent-probe assay for steady-state kinetic analysis, and Fourier Transform Ion Cyclotron Resonance-mass spectrometry (FTICR-MS) to monitor active-site occupancy. Findings from five enzyme variants and four model substrates have enabled a model to be proposed involving catalysis based upon acyl-CoA substrate loading followed by differential rates of hydrolysis. These efforts suggest a strategy for future pathway engineering efforts using unnatural extender units with slow rates of hydrolytic off-loading from the acyltransferase domain.
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Affiliation(s)
- Shilah A Bonnett
- Department of Chemistry, Portland State University, Portland, OR 97201, USA
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29
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Abstract
The mycobactin siderophore system is present in many Mycobacterium species, including M. tuberculosis and other clinically relevant mycobacteria. This siderophore system is believed to be utilized by both pathogenic and nonpathogenic mycobacteria for iron acquisition in both in vivo and ex vivo iron-limiting environments, respectively. Several M. tuberculosis genes located in a so-called mbt gene cluster have been predicted to be required for the biosynthesis of the core scaffold of mycobactin based on sequence analysis. A systematic and controlled mutational analysis probing the hypothesized essential nature of each of these genes for mycobactin production has been lacking. The degree of conservation of mbt gene cluster orthologs remains to be investigated as well. In this study, we sought to conclusively establish whether each of nine mbt genes was required for mycobactin production and to examine the conservation of gene clusters orthologous to the M. tuberculosis mbt gene cluster in other bacteria. We report a systematic mutational analysis of the mbt gene cluster ortholog found in Mycobacterium smegmatis. This mutational analysis demonstrates that eight of the nine mbt genes investigated are essential for mycobactin production. Our genome mining and phylogenetic analyses reveal the presence of orthologous mbt gene clusters in several bacterial species. These gene clusters display significant organizational differences originating from an intricate evolutionary path that might have included horizontal gene transfers. Altogether, the findings reported herein advance our understanding of the genetic requirements for the biosynthesis of an important mycobacterial secondary metabolite with relevance to virulence.
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Isolation, structural elucidation, and biosynthesis of 15-norlankamycin derivatives produced by a type-II thioesterase disruptant of Streptomyces rochei. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.05.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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31
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Whicher JR, Florova G, Sydor PK, Singh R, Alhamadsheh M, Challis GL, Reynolds KA, Smith JL. Structure and function of the RedJ protein, a thioesterase from the prodiginine biosynthetic pathway in Streptomyces coelicolor. J Biol Chem 2011; 286:22558-69. [PMID: 21543318 PMCID: PMC3121400 DOI: 10.1074/jbc.m110.213512] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prodiginines are a class of red-pigmented natural products with immunosuppressant, anticancer, and antimalarial activities. Recent studies on prodiginine biosynthesis in Streptomyces coelicolor have elucidated the function of many enzymes within the pathway. However, the function of RedJ, which was predicted to be an editing thioesterase based on sequence similarity, is unknown. We report here the genetic, biochemical, and structural characterization of the redJ gene product. Deletion of redJ in S. coelicolor leads to a 75% decrease in prodiginine production, demonstrating its importance for prodiginine biosynthesis. RedJ exhibits thioesterase activity with selectivity for substrates having long acyl chains and lacking a β-carboxyl substituent. The thioesterase has 1000-fold greater catalytic efficiency with substrates linked to an acyl carrier protein (ACP) than with the corresponding CoA thioester substrates. Also, RedJ strongly discriminates against the streptomycete ACP of fatty acid biosynthesis in preference to RedQ, an ACP of the prodiginine pathway. The 2.12 Å resolution crystal structure of RedJ provides insights into the molecular basis for the observed substrate selectivity. A hydrophobic pocket in the active site chamber is positioned to bind long acyl chains, as suggested by a long-chain ligand from the crystallization solution bound in this pocket. The accessibility of the active site is controlled by the position of a highly flexible entrance flap. These data combined with previous studies of prodiginine biosynthesis in S. coelicolor support a novel role for RedJ in facilitating transfer of a dodecanoyl chain from one acyl carrier protein to another en route to the key biosynthetic intermediate 2-undecylpyrrole.
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Affiliation(s)
- Jonathan R Whicher
- Chemical Biology Graduate Program, University of Michigan, Ann Arbor, Michigan 48109, USA
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Gottardi EM, Krawczyk JM, von Suchodoletz H, Schadt S, Mühlenweg A, Uguru GC, Pelzer S, Fiedler HP, Bibb MJ, Stach JEM, Süssmuth RD. Abyssomicin biosynthesis: formation of an unusual polyketide, antibiotic-feeding studies and genetic analysis. Chembiochem 2011; 12:1401-10. [PMID: 21656887 PMCID: PMC3625739 DOI: 10.1002/cbic.201100172] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Indexed: 11/24/2022]
Affiliation(s)
- Elvira M Gottardi
- Technische Universität Berlin, Institut für ChemieStrasse des 17. Juni 124, 10623 Berlin (Germany), Fax: (+49) 30-314-79651
| | - Joanna M Krawczyk
- Technische Universität Berlin, Institut für ChemieStrasse des 17. Juni 124, 10623 Berlin (Germany), Fax: (+49) 30-314-79651
| | - Hanna von Suchodoletz
- Technische Universität Berlin, Institut für ChemieStrasse des 17. Juni 124, 10623 Berlin (Germany), Fax: (+49) 30-314-79651
| | - Simone Schadt
- Technische Universität Berlin, Institut für ChemieStrasse des 17. Juni 124, 10623 Berlin (Germany), Fax: (+49) 30-314-79651
| | - Agnes Mühlenweg
- Technische Universität Berlin, Institut für ChemieStrasse des 17. Juni 124, 10623 Berlin (Germany), Fax: (+49) 30-314-79651
| | - Gabriel C Uguru
- School of Biology, Newcastle UniversityNewcastle-upon-Tyne, NE1 7RU (UK)
| | - Stefan Pelzer
- B.R.A.I.N. AktiengesellschaftDarmstädter Strasse 34, 64673 Zwingenberg (Germany)
| | - Hans-Peter Fiedler
- Dept. of Microbiology/Biotechnology, Universität TübingenAuf der Morgenstelle 28, 72076 Tübingen (Germany)
| | - Mervyn J Bibb
- Department of Molecular Microbiology, John Innes CentreNorwich, NR4 7UH (UK)
| | - James E M Stach
- School of Biology, Newcastle UniversityNewcastle-upon-Tyne, NE1 7RU (UK)
| | - Roderich D Süssmuth
- Technische Universität Berlin, Institut für ChemieStrasse des 17. Juni 124, 10623 Berlin (Germany), Fax: (+49) 30-314-79651
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Chavadi SS, Edupuganti UR, Vergnolle O, Fatima I, Singh SM, Soll CE, Quadri LEN. Inactivation of tesA reduces cell wall lipid production and increases drug susceptibility in mycobacteria. J Biol Chem 2011; 286:24616-25. [PMID: 21592957 DOI: 10.1074/jbc.m111.247601] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phthiocerol dimycocerosates (PDIMs) and phenolic glycolipids (PGLs) are structurally related lipids noncovalently bound to the outer cell wall layer of Mycobacterium tuberculosis, Mycobacterium leprae, and several opportunistic mycobacterial human pathogens. PDIMs and PGLs are important effectors of virulence. Elucidation of the biosynthesis of these complex lipids will not only expand our understanding of mycobacterial cell wall biosynthesis, but it may also illuminate potential routes to novel therapeutics against mycobacterial infections. We report the construction of an in-frame deletion mutant of tesA (encoding a type II thioesterase) in the opportunistic human pathogen Mycobacterium marinum and the characterization of this mutant and its corresponding complemented strain control in terms of PDIM and PGL production. The growth and antibiotic susceptibility of these strains were also probed and compared with the parental wild-type strain. We show that deletion of tesA leads to a mutant that produces only traces of PDIMs and PGLs, has a slight growth yield increase and displays a substantial hypersusceptibility to several antibiotics. We also provide a robust model for the three-dimensional structure of M. marinum TesA (TesAmm) and demonstrate that a Ser-to-Ala substitution in the predicted catalytic Ser of TesAmm renders a mutant that recapitulates the phenotype of the tesA deletion mutant. Overall, our studies demonstrate a critical role for tesA in mycobacterial biology, advance our understanding of the biosynthesis of an important group of polyketide synthase-derived mycobacterial lipids, and suggest that drugs aimed at blocking PDIM and/or PGL production might synergize with antibiotic therapy in the control of mycobacterial infections.
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Evans BS, Ntai I, Chen Y, Robinson SJ, Kelleher NL. Proteomics-based discovery of koranimine, a cyclic imine natural product. J Am Chem Soc 2011; 133:7316-9. [PMID: 21520944 DOI: 10.1021/ja2015795] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are large enzymes responsible for the biosynthesis of medically and ecologically important secondary metabolites. In a previous report, we described a proteomics approach to screen for expressed NRPSs or PKSs from bacteria with or without sequenced genomes. Here we used this proteome mining approach to discover a novel natural product arising from rare adenylation (A) and reductase (Red) domains in its biosynthetic machinery. We also cloned the entire gene cluster and elucidated the biosynthesis of the new compound, which is produced by an unsequenced Bacillus sp. isolated from soil collected in Koran, Louisiana.
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Affiliation(s)
- Bradley S Evans
- Institute of Genomic Biology, University of Illinois Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
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Kalaitzis JA, Cheng Q, Meluzzi D, Xiang L, Izumikawa M, Dorrestein PC, Moore BS. Policing starter unit selection of the enterocin type II polyketide synthase by the type II thioesterase EncL. Bioorg Med Chem 2011; 19:6633-8. [PMID: 21531566 DOI: 10.1016/j.bmc.2011.04.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 04/05/2011] [Accepted: 04/11/2011] [Indexed: 11/18/2022]
Abstract
Enterocin is an atypical type II polyketide synthase (PKS) product from the marine actinomycete 'Streptomyces maritimus'. The enterocin biosynthesis gene cluster (enc) codes for proteins involved in the assembly and attachment of the rare benzoate primer that initiates polyketide assembly with the addition of seven malonate molecules and culminates in a Favorskii-like rearrangement of the linear poly-β-ketone to give its distinctive non-aromatic, caged core structure. Fundamental to enterocin biosynthesis, which utilizes a single acyl carrier protein (ACP), EncC, for both priming with benzoate and elongating with malonate, involves maintaining the correct balance of acyl-EncC substrates for efficient polyketide assembly. Here, we report the characterization of EncL as a type II thioesterase that functions to edit starter unit (mis)priming of EncC. We performed a series of in vivo mutational studies, heterologous expression experiments, in vitro reconstitution studies, and Fourier-transform mass spectrometry-monitored competitive enzyme assays that together support the proposed selective hydrolase activity of EncL toward misprimed acetyl-ACP over benzoyl-ACP to facilitate benzoyl priming of the enterocin PKS complex. While this system resembles the R1128 PKS that also utilizes an editing thioesterase (ZhuC) to purge acetate molecules from its initiation module ACP in favor of alkylacyl groups, the enterocin system is distinct in its usage of a single ACP for both priming and elongating reactions with different substrates.
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Affiliation(s)
- John A Kalaitzis
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
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36
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Identification of a bioactive 51-membered macrolide complex by activation of a silent polyketide synthase in Streptomyces ambofaciens. Proc Natl Acad Sci U S A 2011; 108:6258-63. [PMID: 21444795 DOI: 10.1073/pnas.1019077108] [Citation(s) in RCA: 240] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
There is a constant need for new and improved drugs to combat infectious diseases, cancer, and other major life-threatening conditions. The recent development of genomics-guided approaches for novel natural product discovery has stimulated renewed interest in the search for natural product-based drugs. Genome sequence analysis of Streptomyces ambofaciens ATCC23877 has revealed numerous secondary metabolite biosynthetic gene clusters, including a giant type I modular polyketide synthase (PKS) gene cluster, which is composed of 25 genes (nine of which encode PKSs) and spans almost 150 kb, making it one of the largest polyketide biosynthetic gene clusters described to date. The metabolic product(s) of this gene cluster are unknown, and transcriptional analyses showed that it is not expressed under laboratory growth conditions. The constitutive expression of a regulatory gene within the cluster, encoding a protein that is similar to Large ATP binding of the LuxR (LAL) family proteins, triggered the expression of the biosynthetic genes. This led to the identification of four 51-membered glycosylated macrolides, named stambomycins A-D as metabolic products of the gene cluster. The structures of these compounds imply several interesting biosynthetic features, including incorporation of unusual extender units into the polyketide chain and in trans hydroxylation of the growing polyketide chain to provide the hydroxyl group for macrolide formation. Interestingly, the stambomycins possess promising antiproliferative activity against human cancer cell lines. Database searches identify genes encoding LAL regulators within numerous cryptic biosynthetic gene clusters in actinomycete genomes, suggesting that constitutive expression of such pathway-specific activators represents a powerful approach for novel bioactive natural product discovery.
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37
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Mo X, Wang Z, Wang B, Ma J, Huang H, Tian X, Zhang S, Zhang C, Ju J. Cloning and characterization of the biosynthetic gene cluster of the bacterial RNA polymerase inhibitor tirandamycin from marine-derived Streptomyces sp. SCSIO1666. Biochem Biophys Res Commun 2011; 406:341-7. [DOI: 10.1016/j.bbrc.2011.02.040] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 02/11/2011] [Indexed: 10/18/2022]
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38
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Kwan DH, Tosin M, Schläger N, Schulz F, Leadlay PF. Insights into the stereospecificity of ketoreduction in a modular polyketide synthase. Org Biomol Chem 2011; 9:2053-6. [DOI: 10.1039/c1ob00022e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Characterization of the biosynthesis gene cluster for the pyrrole polyether antibiotic calcimycin (A23187) in Streptomyces chartreusis NRRL 3882. Antimicrob Agents Chemother 2010; 55:974-82. [PMID: 21173184 DOI: 10.1128/aac.01130-10] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pyrrole polyether antibiotic calcimycin (A23187) is a rare ionophore that is specific for divalent cations. It is widely used as a biochemical and pharmacological tool because of its multiple, unique biological effects. Here we report on the cloning, sequencing, and mutational analysis of the 64-kb biosynthetic gene cluster from Streptomyces chartreusis NRRL 3882. Gene replacements confirmed the identity of the gene cluster, and in silico analysis of the DNA sequence revealed 27 potential genes, including 3 genes for the biosynthesis of the α-ketopyrrole moiety, 5 genes that encode modular type I polyketide synthases for the biosynthesis of the spiroketal ring, 4 genes for the biosynthesis of 3-hydroxyanthranilic acid, an N-methyltransferase tailoring gene, a resistance gene, a type II thioesterase gene, 3 regulatory genes, 4 genes with other functions, and 5 genes of unknown function. We propose a pathway for the biosynthesis of calcimycin and assign the genes to the biosynthesis steps. Our findings set the stage for producing much desired calcimycin derivatives using genetic modification instead of chemical synthesis.
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40
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Liew CW, Sharff A, Kotaka M, Kong R, Sun H, Qureshi I, Bricogne G, Liang ZX, Lescar J. Induced-fit upon ligand binding revealed by crystal structures of the hot-dog fold thioesterase in dynemicin biosynthesis. J Mol Biol 2010; 404:291-306. [PMID: 20888341 DOI: 10.1016/j.jmb.2010.09.041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 09/16/2010] [Accepted: 09/20/2010] [Indexed: 11/27/2022]
Abstract
Dynemicins are structurally related 10-membered enediyne natural products isolated from Micromonospora chernisa with potent antitumor and antibiotic activity. The early biosynthetic steps of the enediyne moiety of dynemicins are catalyzed by an iterative polyketide synthase (DynE8) and a thioesterase (DynE7). Recent studies indicate that the function of DynE7 is to off-load the linear biosynthetic intermediate assembled on DynE8. Here, we report crystal structures of DynE7 in its free form at 2.7 Å resolution and of DynE7 in complex with the DynE8-produced all-trans pentadecen-2-one at 2.1 Å resolution. These crystal structures reveal that upon ligand binding, significant conformational changes throughout the substrate-binding tunnel result in an expanded tunnel that traverses an entire monomer of the tetrameric DynE7 protein. The enlarged inner segment of the channel binds the carbonyl-conjugated polyene mainly through hydrophobic interactions, whereas the putative catalytic residues are located in the outer segment of the channel. The crystallographic information reinforces an unusual catalytic mechanism that involves a strictly conserved arginine residue for this subfamily of hot-dog fold thioesterases, distinct from the typical mechanism for hot-dog fold thioesterases that utilizes an acidic residue for catalysis.
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Affiliation(s)
- Chong Wai Liew
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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41
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Alber BE. Biotechnological potential of the ethylmalonyl-CoA pathway. Appl Microbiol Biotechnol 2010; 89:17-25. [PMID: 20882276 DOI: 10.1007/s00253-010-2873-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 08/22/2010] [Accepted: 08/24/2010] [Indexed: 11/26/2022]
Abstract
The ethylmalonyl-CoA pathway is central to the carbon metabolism of many α-proteobacteria, like Rhodobacter sphaeroides and Methylobacterium extorquens as well as actinomycetes, like Streptomyces spp. Its function is to convert acetyl-CoA, a central carbon intermediate, to other precursor metabolites for cell carbon biosynthesis. In contrast to the glyoxylate cycle--another widely distributed acetyl-CoA assimilation strategy--the ethylmalonyl-CoA pathway contains many unique CoA-ester intermediates, such as (2R)- and (2S)-ethylmalonyl-CoA, (2S)-methylsuccinyl-CoA, mesaconyl-(C1)-CoA, and (2R, 3S)-methylmalyl-CoA. With this come novel catalysts that interconvert these compounds. Among these unique enzymes is a novel carboxylase that reductively carboxylates crotonyl-CoA, crotonyl-CoA carboxylase/reductase, and (3S)-malyl-CoA thioesterase. The latter represents the first example of a non-Claisen condensation enzyme of the malate synthase superfamily and defines a new class of thioesterases apart from the hotdog-fold and α/β-fold thioesterases. The biotechnological implications of the ethylmalonyl-CoA pathway are tremendous as one looks to tap into the potential of using these new intermediates and catalysts to produce value-added products.
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Affiliation(s)
- Birgit E Alber
- The Department of Microbiology, Ohio State University, 484 West 12th Ave, Room 417, Columbus, OH, USA.
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42
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Chen X, Guo ZF, Lai PM, Sze KH, Guo Z. Identification of a Nonaketide Product for the Iterative Polyketide Synthase in Biosynthesis of the Nine-Membered Enediyne C-1027. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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43
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Chen X, Guo ZF, Lai PM, Sze KH, Guo Z. Identification of a Nonaketide Product for the Iterative Polyketide Synthase in Biosynthesis of the Nine-Membered Enediyne C-1027. Angew Chem Int Ed Engl 2010; 49:7926-8. [DOI: 10.1002/anie.201003369] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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44
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Guo ZF, Sun Y, Zheng S, Guo Z. Preferential hydrolysis of aberrant intermediates by the type II thioesterase in Escherichia coli nonribosomal enterobactin synthesis: substrate specificities and mutagenic studies on the active-site residues. Biochemistry 2010; 48:1712-22. [PMID: 19193103 DOI: 10.1021/bi802165x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The type II thioesterase EntH is a hotdog fold protein required for optimal nonribosomal biosynthesis of enterobactin in Escherichia coli. Its proposed proofreading activity in the biosynthesis is confirmed by its efficient restoration of enterobactin synthesis blocked in vitro by analogs of the cognate precursor 2,3-dihydroxybenzoate. Steady-state kinetic studies show that EntH recognizes the phosphopantetheine group and the pattern of hydroxylation in the aryl moiety of its thioester substrates. Remarkably, it is able to distinguish aberrant intermediates from the normal one in the enterobactin assembly line by demonstrating at least 10-fold higher catalytic efficiency toward thioesters derived from aberrant aryl precursors without a para-hydroxyl group, such as salicylate. By structural comparison and site-directed mutagenesis, the thioesterase is found to possess an active site closely resembling that of the 4-hydroxybenzoyl-CoA thioesterase from Arthrobacter sp. strain SU and to involve an acidic residue (glutamate-63) as the catalytic base or nucleophile like all other hotdog thioesterases. In addition, the EntH specificities toward the substrate hydroxylation pattern are found to depend on the active-site histidine-54, threonine-64, serine-67, and methionine-68 with the selectivity significantly reduced or even reversed when they are individually replaced by alanine. These residues are likely responsible for differential interaction of the enzyme with the substrates which leads to distinction between the normal and aberrant precursors in the enterobactin assembly line. These results show that the type II thioesterase evolves its distinctive ability to recognize the aberrant intermediates from the versatile catalytic platform of hotdog proteins and suggests an active search mechanism for type II thioesterases in nonribosomal peptide synthesis.
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Affiliation(s)
- Zu-Feng Guo
- Department of Chemistry, Center for Cancer Research, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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Rui Z, Petrícková K, Skanta F, Pospísil S, Yang Y, Chen CY, Tsai SF, Floss HG, Petrícek M, Yu TW. Biochemical and genetic insights into asukamycin biosynthesis. J Biol Chem 2010; 285:24915-24. [PMID: 20522559 DOI: 10.1074/jbc.m110.128850] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Asukamycin, a member of the manumycin family metabolites, is an antimicrobial and potential antitumor agent isolated from Streptomyces nodosus subsp. asukaensis. The entire asukamycin biosynthetic gene cluster was cloned, assembled, and expressed heterologously in Streptomyces lividans. Bioinformatic analysis and mutagenesis studies elucidated the biosynthetic pathway at the genetic and biochemical level. Four gene sets, asuA-D, govern the formation and assembly of the asukamycin building blocks: a 3-amino-4-hydroxybenzoic acid core component, a cyclohexane ring, two triene polyketide chains, and a 2-amino-3-hydroxycyclopent-2-enone moiety to form the intermediate protoasukamycin. AsuE1 and AsuE2 catalyze the conversion of protoasukamycin to 4-hydroxyprotoasukamycin, which is epoxidized at C5-C6 by AsuE3 to the final product, asukamycin. Branched acyl CoA starter units, derived from Val, Leu, and Ile, can be incorporated by the actions of the polyketide synthase III (KSIII) AsuC3/C4 as well as the cellular fatty acid synthase FabH to produce the asukamycin congeners A2-A7. In addition, the type II thioesterase AsuC15 limits the cellular level of omega-cyclohexyl fatty acids and likely maintains homeostasis of the cellular membrane.
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Affiliation(s)
- Zhe Rui
- Department of Biological Science, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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46
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Buntin K, Weissman KJ, Müller R. An Unusual Thioesterase Promotes Isochromanone Ring Formation in Ajudazol Biosynthesis. Chembiochem 2010; 11:1137-46. [DOI: 10.1002/cbic.200900712] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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47
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Liang ZX. Complexity and simplicity in the biosynthesis of enediyne natural products. Nat Prod Rep 2010; 27:499-528. [DOI: 10.1039/b908165h] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Schinko E, Schad K, Eys S, Keller U, Wohlleben W. Phosphinothricin-tripeptide biosynthesis: an original version of bacterial secondary metabolism? PHYTOCHEMISTRY 2009; 70:1787-1800. [PMID: 19878959 DOI: 10.1016/j.phytochem.2009.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 09/03/2009] [Accepted: 09/04/2009] [Indexed: 05/28/2023]
Abstract
Streptomyces viridochromogenes Tü494 produces the herbicide phosphinothricyl-alanyl-alanine (phosphinothricin-tripeptide=PTT; bialaphos). Its bioactive moiety phosphinothricin competitively inhibits bacterial and plant glutamine synthetases. The biosynthesis of PTT includes the synthesis of the unusual amino acid N-acetyl-demethyl-phosphinothricin and a three step condensation via non-ribosomal peptide synthetases. Two characteristics within the PTT biosynthesis make it suitable to study the evolution of secondary metabolism biosynthesis. First, PTT biosynthesis represents the only known system where all peptide synthetase modules are located on separate proteins. This 'single enzyme system' might be an archetype of the multimodular and multienzymatic non-ribosomal peptide synthetases in evolutionary terms. The second interesting feature of PTT biosynthesis is the pathway-specific aconitase Pmi that is involved in the supply of N-acetyl-demethyl-phosphinothricin. Pmi is highly similar to the tricarboxylic acid aconitase AcnA. They share 64% identity at the DNA level and both belong to the Iron-Regulatory-Protein/AcnA family. Despite their high sequence similarity, AcnA and Pmi catalyze different reactions and are not able to substitute for each other. Thus, the enzyme pair AcnA/Pmi presents an example of the evolution of a secondary metabolite-specific enzyme from a primary metabolism enzyme.
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Affiliation(s)
- Eva Schinko
- Mikrobiologie/Biotechnologie, Eberhard-Karls-Universität Tübingen, Tübingen, Germany
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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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50
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Kotaka M, Kong R, Qureshi I, Ho QS, Sun H, Liew CW, Goh LP, Cheung P, Mu Y, Lescar J, Liang ZX. Structure and catalytic mechanism of the thioesterase CalE7 in enediyne biosynthesis. J Biol Chem 2009; 284:15739-49. [PMID: 19357082 PMCID: PMC2708871 DOI: 10.1074/jbc.m809669200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 03/19/2009] [Indexed: 11/06/2022] Open
Abstract
The biosynthesis of the enediyne moiety of the antitumor natural product calicheamicin involves an iterative polyketide synthase (CalE8) and other ancillary enzymes. In the proposed mechanism for the early stage of 10-membered enediyne biosynthesis, CalE8 produces a carbonyl-conjugated polyene with the assistance of a putative thioesterase (CalE7). We have determined the x-ray crystal structure of CalE7 and found that the subunit adopts a hotdog fold with an elongated and kinked substrate-binding channel embedded between two subunits. The 1.75-A crystal structure revealed that CalE7 does not contain a critical catalytic residue (Glu or Asp) conserved in other hotdog fold thioesterases. Based on biochemical and site-directed mutagenesis studies, we proposed a catalytic mechanism in which the conserved Arg(37) plays a crucial role in the hydrolysis of the thioester bond, and that Tyr(29) and a hydrogen-bonded water network assist the decarboxylation of the beta-ketocarboxylic acid intermediate. Moreover, computational docking suggested that the substrate-binding channel binds a polyene substrate that contains a single cis double bond at the C4/C5 position, raising the possibility that the C4=C5 double bond in the enediyne moiety could be generated by the iterative polyketide synthase. Together, the results revealed a hotdog fold thioesterase distinct from the common type I and type II thioesterases associated with polyketide biosynthesis and provided interesting insight into the enediyne biosynthetic mechanism.
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Affiliation(s)
- Masayo Kotaka
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Rong Kong
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Insaf Qureshi
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Qin Shi Ho
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Huihua Sun
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Chong Wai Liew
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Lan Pei Goh
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Peter Cheung
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Yuguang Mu
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Julien Lescar
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Zhao-Xun Liang
- From the School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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