1
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Buyachuihan L, Reiners S, Zhao Y, Grininger M. The malonyl/acetyl-transferase from murine fatty acid synthase is a promiscuous engineering tool for editing polyketide scaffolds. Commun Chem 2024; 7:187. [PMID: 39181936 PMCID: PMC11344766 DOI: 10.1038/s42004-024-01269-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 08/05/2024] [Indexed: 08/27/2024] Open
Abstract
Modular polyketide synthases (PKSs) play a vital role in the biosynthesis of complex natural products with pharmaceutically relevant properties. Their modular architecture makes them an attractive target for engineering to produce platform chemicals and drugs. In this study, we demonstrate that the promiscuous malonyl/acetyl-transferase domain (MAT) from murine fatty acid synthase serves as a highly versatile tool for the production of polyketide analogs. We evaluate the relevance of the MAT domain using three modular PKSs; the short trimodular venemycin synthase (VEMS), as well as modules of the PKSs deoxyerythronolide B synthase (DEBS) and pikromycin synthase (PIKS) responsible for the production of the antibiotic precursors erythromycin and pikromycin. To assess the performance of the MAT-swapped PKSs, we analyze the protein quality and run engineered polyketide syntheses in vitro. Our experiments include the chemoenzymatic synthesis of fluorinated macrolactones. Our study showcases MAT-based reprogramming of polyketide biosynthesis as a facile option for the regioselective editing of substituents decorating the polyketide scaffold.
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Affiliation(s)
- Lynn Buyachuihan
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Simon Reiners
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Yue Zhao
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
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2
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McCullough TM, Choudhary V, Akey DL, Skiba MA, Bernard SM, Kittendorf JD, Schmidt JJ, Sherman DH, Smith JL. Substrate Trapping in Polyketide Synthase Thioesterase Domains: Structural Basis for Macrolactone Formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599880. [PMID: 38948807 PMCID: PMC11213023 DOI: 10.1101/2024.06.20.599880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Emerging antibiotic resistance requires continual improvement in the arsenal of antimicrobial drugs, especially the critical macrolide antibiotics. Formation of the macrolactone scaffold of these polyketide natural products is catalyzed by a modular polyketide synthase (PKS) thioesterase (TE). The TE accepts a linear polyketide substrate from the termina PKS acyl carrier protein to generate an acyl-enzyme adduct that is resolved by attack of a substrate hydroxyl group to form the macrolactone. Our limited mechanistic understanding of TE selectivity for a substrate nucleophile and/or water has hampered development of TEs as biocatalysts that accommodate a variety of natural and non-natural substrates. To understand how TEs direct the substrate nucleophile for macrolactone formation, acyl-enzyme intermediates were trapped as stable amides by substituting the natural serine OH with an amino group. Incorporation of the unnatural amino acid, 1,3-diaminopropionic acid (DAP), was tested with five PKS TEs. DAP-modified TEs (TE DAP ) from the pikromycin and erythromycin pathways were purified and tested with six full-length polyketide intermediates from three pathways. The erythromycin TE had permissive substrate selectivity, whereas the pikromycin TE was selective for its native hexaketide and heptaketide substrates. In a crystal structure of a native substrate trapped in pikromycin TE DAP , the linear heptaketide was curled in the active site with the nucleophilic hydroxyl group positioned 4 Å from the amide-enzyme linkage. The curled heptaketide displayed remarkable shape complementarity with the TE acyl cavity. The strikingly different shapes of acyl cavities in TEs of known structure, including those reported here for juvenimicin, tylosin and fluvirucin biosynthesis, provide new insights to facilitate TE engineering and optimization.
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3
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Steele AD, Jiang H, Pan G, Lim SK, Kalkreuter E, Kwong T, Ju J, Rajski S, Shen B. Discrete Acyltransferases and Thioesterases in Iso-Migrastatin and Lactimidomycin Biosynthesis. Biochemistry 2024:10.1021/acs.biochem.3c00672. [PMID: 38345531 PMCID: PMC11623918 DOI: 10.1021/acs.biochem.3c00672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Iso-Migrastatin (iso-MGS) and lactimidomycin (LTM) are glutarimide-containing polyketide natural products (NPs) that are biosynthesized by homologous acyltransferase (AT)-less type I polyketide synthase (PKS) assembly lines. The biological activities of iso-MGS and LTM have inspired numerous efforts to generate analogues via genetic manipulation of their biosynthetic machinery in both native producers and model heterologous hosts. A detailed understanding of the MGS and LTM AT-less type I PKSs would serve to inspire future engineering efforts while advancing the fundamental knowledge of AT-less type I PKS enzymology. The mgs and ltm biosynthetic gene clusters (BGCs) encode for two discrete ATs of the architecture AT-enoylreductase (AT-ER) and AT-type II thioesterase (AT-TE). Herein, we report the functional characterization of the mgsB and ltmB and the mgsH and ltmH gene products, revealing that MgsB and LtmB function as type II thioesterases (TEs) and MgsH and LtmH are the dedicated trans-ATs for the MGS and LTM AT-less type I PKSs. In vivo and in vitro experiments demonstrated that MgsB was devoid of any AT activity, despite the presence of the conserved catalytic triad of canonical ATs. Cross-complementation experiments demonstrated that MgsH and LtmH are functionally interchangeable between the MGS and LTM AT-less type I PKSs. This work sets the stage for future mechanistic studies of AT-less type I PKSs and efforts to engineer the MGS and LTM AT-less type I PKS assembly lines for novel glutarimide-containing polyketides.
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Affiliation(s)
- Andrew D Steele
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida 33458, United States
| | - Hui Jiang
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Guohui Pan
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida 33458, United States
| | - Si-Kyu Lim
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Edward Kalkreuter
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida 33458, United States
| | - Thomas Kwong
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida 33458, United States
| | - Jianhua Ju
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Scott Rajski
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Ben Shen
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida 33458, United States
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida 33458, United States
- Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida 33458, United States
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, Florida 33458, United States
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4
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Liu L, Wang W, Chen M, Zhang Y, Mao H, Wang D, Chen Y, Li P. Characterization of three succinyl-CoA acyltransferases involved in polyketide chain assembly. Appl Microbiol Biotechnol 2023; 107:2403-2412. [PMID: 36929192 DOI: 10.1007/s00253-023-12481-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/18/2023]
Abstract
Polyketides are a class of natural products with astonishing structural diversities, fascinating biological activities, and a versatile of applications. In polyketides biosynthesis, acyltransferases (ATs) are the 'gatekeeping' enzymes selecting the specific CoA-activated acyl groups as building blocks and transferring them onto the phosphopantetheine arm of acyl carrier proteins (ACPs) to enable the following condensation reactions to assemble the polyketide chain. Herein, the Art2 protein from aurantinins, a group of the antibacterial polyketides, is characterized in vitro as an AT that can load a CoA-activated succinyl unit onto the first ACP domain of Art17 (ACPArt17-1). In addition, another two proteins, GbnB and EtnB, involved in the biosynthesis of gladiolin and etnangien respectively, were traced by literature mining, homologous searching, and product structure analysis and then identified as functional succinyl-CoA ATs by the ACPArt17-1 assays. Taken together, by the assay method employing ACPArt17-1 as an acyl acceptor, we identified three ATs that can introduce a succinyl unit into the polyketide assembly line, which enriches the toolbox of polyketide biosynthetic enzymes and sets a stage for incorporating a succinyl unit into polyketide backbones in synthetic biological manners. KEY POINTS: • Three acyltransferases that are able to load ACP with a succinyl unit were characterized in vitro. • ACPArt17-1 can be used as an acceptor to assay succinyl-CoA AT from different polyketides. • The succinyl unit can be incorporated into polyketides assembly process.
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Affiliation(s)
- Lilu Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenzhao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Meng Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuwei Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huijin Mao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dacheng Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengwei Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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5
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Ciavatta ML, Lefranc F, Vieira LM, Kiss R, Carbone M, van Otterlo WAL, Lopanik NB, Waeschenbach A. The Phylum Bryozoa: From Biology to Biomedical Potential. Mar Drugs 2020; 18:E200. [PMID: 32283669 PMCID: PMC7230173 DOI: 10.3390/md18040200] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/31/2020] [Accepted: 04/06/2020] [Indexed: 01/06/2023] Open
Abstract
Less than one percent of marine natural products characterized since 1963 have been obtained from the phylum Bryozoa which, therefore, still represents a huge reservoir for the discovery of bioactive metabolites with its ~6000 described species. The current review is designed to highlight how bryozoans use sophisticated chemical defenses against their numerous predators and competitors, and which can be harbored for medicinal uses. This review collates all currently available chemoecological data about bryozoans and lists potential applications/benefits for human health. The core of the current review relates to the potential of bryozoan metabolites in human diseases with particular attention to viral, brain, and parasitic diseases. It additionally weighs the pros and cons of total syntheses of some bryozoan metabolites versus the synthesis of non-natural analogues, and explores the hopes put into the development of biotechnological approaches to provide sustainable amounts of bryozoan metabolites without harming the natural environment.
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Affiliation(s)
- Maria Letizia Ciavatta
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Chimica Biomolecolare (ICB), Via Campi Flegrei 34, 80078 Pozzuoli, Italy; (M.L.C.); (M.C.)
| | - Florence Lefranc
- Service de Neurochirurgie, Hôpital Erasme, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Leandro M. Vieira
- Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE 50670-901, Brazil;
| | - Robert Kiss
- Retired – formerly at the Fonds National de la Recherche Scientifique (FRS-FNRS), 1000 Brussels, Belgium;
| | - Marianna Carbone
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Chimica Biomolecolare (ICB), Via Campi Flegrei 34, 80078 Pozzuoli, Italy; (M.L.C.); (M.C.)
| | - Willem A. L. van Otterlo
- Department of Chemistry and Polymer Science, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa;
| | - Nicole B. Lopanik
- School of Earth and Atmospheric Sciences, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA;
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6
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Yeo WL, Heng E, Tan LL, Lim YW, Ching KC, Tsai DJ, Jhang YW, Lauderdale TL, Shia KS, Zhao H, Ang EL, Zhang MM, Lim YH, Wong FT. Biosynthetic engineering of the antifungal, anti-MRSA auroramycin. Microb Cell Fact 2020; 19:3. [PMID: 31906943 PMCID: PMC6943886 DOI: 10.1186/s12934-019-1274-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/21/2019] [Indexed: 12/12/2022] Open
Abstract
Using an established CRISPR-Cas mediated genome editing technique for streptomycetes, we explored the combinatorial biosynthesis potential of the auroramycin biosynthetic gene cluster in Streptomyces roseosporous. Auroramycin is a potent anti-MRSA polyene macrolactam. In addition, auroramycin has antifungal activities, which is unique among structurally similar polyene macrolactams, such as incednine and silvalactam. In this work, we employed different engineering strategies to target glycosylation and acylation biosynthetic machineries within its recently elucidated biosynthetic pathway. Auroramycin analogs with variations in C-, N- methylation, hydroxylation and extender units incorporation were produced and characterized. By comparing the bioactivity profiles of five of these analogs, we determined that unique disaccharide motif of auroramycin is essential for its antimicrobial bioactivity. We further demonstrated that C-methylation of the 3, 5-epi-lemonose unit, which is unique among structurally similar polyene macrolactams, is key to its antifungal activity.
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Affiliation(s)
- Wan Lin Yeo
- Metabolic Engineering, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore
| | - Elena Heng
- Molecular Engineering Laboratory, Institute of Bioengineering and Nanotechnology, A*STAR, Biopolis, Singapore
| | - Lee Ling Tan
- Molecular Engineering Laboratory, Institute of Bioengineering and Nanotechnology, A*STAR, Biopolis, Singapore
| | - Yi Wee Lim
- Integrated Bio & Organic Chemistry, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore
| | - Kuan Chieh Ching
- Integrated Bio & Organic Chemistry, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore
| | - De-Juin Tsai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes (NHRI), Zhunan, Miaoli, Taiwan
| | - Yi Wun Jhang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes (NHRI), Zhunan, Miaoli, Taiwan
| | - Tsai-Ling Lauderdale
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes (NHRI), Zhunan, Miaoli, Taiwan
| | - Kak-Shan Shia
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes (NHRI), Zhunan, Miaoli, Taiwan
| | - Huimin Zhao
- Departments of Chemical and Biomolecular Engineering, Chemistry, Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ee Lui Ang
- Metabolic Engineering, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore
| | - Mingzi M Zhang
- Metabolic Engineering, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore.,Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Yee Hwee Lim
- Integrated Bio & Organic Chemistry, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore.
| | - Fong T Wong
- Molecular Engineering Laboratory, Institute of Bioengineering and Nanotechnology, A*STAR, Biopolis, Singapore.
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7
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Musiol-Kroll EM, Wohlleben W. Acyltransferases as Tools for Polyketide Synthase Engineering. Antibiotics (Basel) 2018; 7:antibiotics7030062. [PMID: 30022008 PMCID: PMC6164871 DOI: 10.3390/antibiotics7030062] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/14/2018] [Accepted: 07/16/2018] [Indexed: 12/16/2022] Open
Abstract
Polyketides belong to the most valuable natural products, including diverse bioactive compounds, such as antibiotics, anticancer drugs, antifungal agents, immunosuppressants and others. Their structures are assembled by polyketide synthases (PKSs). Modular PKSs are composed of modules, which involve sets of domains catalysing the stepwise polyketide biosynthesis. The acyltransferase (AT) domains and their “partners”, the acyl carrier proteins (ACPs), thereby play an essential role. The AT loads the building blocks onto the “substrate acceptor”, the ACP. Thus, the AT dictates which building blocks are incorporated into the polyketide structure. The precursor- and occasionally the ACP-specificity of the ATs differ across the polyketide pathways and therefore, the ATs contribute to the structural diversity within this group of complex natural products. Those features make the AT enzymes one of the most promising tools for manipulation of polyketide assembly lines and generation of new polyketide compounds. However, the AT-based PKS engineering is still not straightforward and thus, rational design of functional PKSs requires detailed understanding of the complex machineries. This review summarizes the attempts of PKS engineering by exploiting the AT attributes for the modification of polyketide structures. The article includes 253 references and covers the most relevant literature published until May 2018.
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Affiliation(s)
- Ewa Maria Musiol-Kroll
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
| | - Wolfgang Wohlleben
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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8
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Morita M, Schmidt EW. Parallel lives of symbionts and hosts: chemical mutualism in marine animals. Nat Prod Rep 2018; 35:357-378. [PMID: 29441375 PMCID: PMC6025756 DOI: 10.1039/c7np00053g] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: up to 2018 Symbiotic microbes interact with animals, often by producing natural products (specialized metabolites; secondary metabolites) that exert a biological role. A major goal is to determine which microbes produce biologically important compounds, a deceptively challenging task that often rests on correlative results, rather than hypothesis testing. Here, we examine the challenges and successes from the perspective of marine animal-bacterial mutualisms. These animals have historically provided a useful model because of their technical accessibility. By comparing biological systems, we suggest a common framework for establishing chemical interactions between animals and microbes.
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Affiliation(s)
- Maho Morita
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA 84112.
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9
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Slocum ST, Lowell AN, Tripathi A, Shende VV, Smith JL, Sherman DH. Chemoenzymatic Dissection of Polyketide β-Branching in the Bryostatin Pathway. Methods Enzymol 2018; 604:207-236. [PMID: 29779653 PMCID: PMC6327954 DOI: 10.1016/bs.mie.2018.01.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
β-Branching is an expansion upon canonical polyketide synthase extension that allows for the installation of diverse chemical moieties in several natural products. Several of these moieties are unique among natural products, including the two vinyl methylesters found in the core structure of bryostatins. This family of molecules is derived from an obligate bacterial symbiont of a sessile marine bryozoan, Bugula neritina. Within this family, bryostatin 1 has been investigated as an anticancer, neuroprotective, and immunomodulatory compound. We have turned to the biosynthetic gene cluster within the bacterial symbiont to investigate the biosynthesis of bryostatins. Recent sequencing efforts resulted in the annotation of two missing genes: bryT and bryU. Using novel chemoenzymatic techniques, we have validated these as the missing enoyl-CoA hydratase and donor acyl carrier protein, essential components of the β-branching cassette of the bryostatin pathway. Together, this cassette installs the vinyl methylester moieties essential to the activity of bryostatins.
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Affiliation(s)
- Samuel T Slocum
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Andrew N Lowell
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - Vikram V Shende
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Chemistry, University of Michigan, Ann Arbor, MI, United States; Life Sciences Institute, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, United States.
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10
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Skiba MA, Maloney FP, Dan Q, Fraley AE, Aldrich CC, Smith JL, Brown WC. PKS-NRPS Enzymology and Structural Biology: Considerations in Protein Production. Methods Enzymol 2018; 604:45-88. [PMID: 29779664 PMCID: PMC5992914 DOI: 10.1016/bs.mie.2018.01.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The structural diversity and complexity of marine natural products have made them a rich and productive source of new bioactive molecules for drug development. The identification of these new compounds has led to extensive study of the protein constituents of the biosynthetic pathways from the producing microbes. Essential processes in the dissection of biosynthesis have been the elucidation of catalytic functions and the determination of 3D structures for enzymes of the polyketide synthases and nonribosomal peptide synthetases that carry out individual reactions. The size and complexity of these proteins present numerous difficulties in the process of going from gene to structure. Here, we review the problems that may be encountered at the various steps of this process and discuss some of the solutions devised in our and other labs for the cloning, production, purification, and structure solution of complex proteins using Escherichia coli as a heterologous host.
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Affiliation(s)
| | | | - Qingyun Dan
- University of Michigan, Ann Arbor, MI, United States
| | - Amy E Fraley
- University of Michigan, Ann Arbor, MI, United States
| | | | - Janet L Smith
- University of Michigan, Ann Arbor, MI, United States.
| | - W Clay Brown
- University of Michigan, Ann Arbor, MI, United States.
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11
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Abstract
The recent breakthroughs in assembling long error-prone reads were based on the overlap-layout-consensus (OLC) approach and did not utilize the strengths of the alternative de Bruijn graph approach to genome assembly. Moreover, these studies often assume that applications of the de Bruijn graph approach are limited to short and accurate reads and that the OLC approach is the only practical paradigm for assembling long error-prone reads. We show how to generalize de Bruijn graphs for assembling long error-prone reads and describe the ABruijn assembler, which combines the de Bruijn graph and the OLC approaches and results in accurate genome reconstructions.
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12
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Newman DJ. Predominately Uncultured Microbes as Sources of Bioactive Agents. Front Microbiol 2016; 7:1832. [PMID: 27917159 PMCID: PMC5114300 DOI: 10.3389/fmicb.2016.01832] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/01/2016] [Indexed: 12/15/2022] Open
Abstract
In this short review, I am discussing the relatively recent awareness of the role of symbionts in plant, marine-invertebrates and fungal areas. It is now quite obvious that in marine-invertebrates, a majority of compounds found are from either as yet unculturable or poorly culturable microbes, and techniques involving “state of the art” genomic analyses and subsequent computerized analyses are required to investigate these interactions. In the plant kingdom evidence is amassing that endophytes (mainly fungal in nature) are heavily involved in secondary metabolite production and that mimicking the microbial interactions of fermentable microbes leads to involvement of previously unrecognized gene clusters (cryptic clusters is one name used), that when activated, produce previously unknown bioactive molecules.
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13
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Heine D, Sundaram S, Bretschneider T, Hertweck C. Twofold polyketide branching by a stereoselective enzymatic Michael addition. Chem Commun (Camb) 2016; 51:9872-5. [PMID: 25994388 DOI: 10.1039/c5cc03085d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The versatility of the branching module of the rhizoxin polyketide synthase was tested in an in vitro enzyme assay with a polyketide mimic and branched (di)methylmalonyl-CoA extender units. Comparison of the products with synthetic reference compounds revealed that the module is able to stereoselectively introduce two branches in one step by a Michael addition-lactonisation sequence, thus expanding the scope of previously studied PKS systems.
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Affiliation(s)
- Daniel Heine
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany.
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14
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Genetic engineering and heterologous expression of the disorazol biosynthetic gene cluster via Red/ET recombineering. Sci Rep 2016; 6:21066. [PMID: 26875499 PMCID: PMC4753468 DOI: 10.1038/srep21066] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/18/2016] [Indexed: 11/08/2022] Open
Abstract
Disorazol, a macrocyclic polykitide produced by the myxobacterium Sorangium cellulosum So ce12 and it is reported to have potential cytotoxic activity towards several cancer cell lines, including multi-drug resistant cells. The disorazol biosynthetic gene cluster (dis) from Sorangium cellulosum (So ce12) was identified by transposon mutagenesis and cloned in a bacterial artificial chromosome (BAC) library. The 58-kb dis core gene cluster was reconstituted from BACs via Red/ET recombineering and expressed in Myxococcus xanthus DK1622. For the first time ever, a myxobacterial trans-AT polyketide synthase has been expressed heterologously in this study. Expression in M. xanthus allowed us to optimize the yield of several biosynthetic products using promoter engineering. The insertion of an artificial synthetic promoter upstream of the disD gene encoding a discrete acyl transferase (AT), together with an oxidoreductase (Or), resulted in 7-fold increase in disorazol production. The successful reconstitution and expression of the genetic sequences encoding for these promising cytotoxic compounds will allow combinatorial biosynthesis to generate novel disorazol derivatives for further bioactivity evaluation.
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15
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Abstract
This highlight provides an overview of recent advances in understanding the diversity of polyketide synthase (PKS) substrate building blocks. Substrates functioning as starter units and extender units contribute significantly to the chemical complexity and structural diversity exhibited by this class of natural products. This article complements and extends upon the current comprehensive reviews that have been published on these two topics (Moore and Hertweck, Nat. Prod. Rep., 2002, 19, 70; Chan et al., Nat. Prod. Rep., 2009, 1, 90; Wilson and Moore, Nat. Prod. Rep., 2012, 29, 72).
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Affiliation(s)
- Lauren Ray
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093-0204, USA
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16
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Bertin MJ, Vulpanovici A, Monroe EA, Korobeynikov A, Sherman DH, Gerwick L, Gerwick WH. The Phormidolide Biosynthetic Gene Cluster: A trans-AT PKS Pathway Encoding a Toxic Macrocyclic Polyketide. Chembiochem 2016; 17:164-73. [PMID: 26769357 PMCID: PMC4878910 DOI: 10.1002/cbic.201500467] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Indexed: 11/09/2022]
Abstract
Phormidolide is a polyketide produced by a cultured filamentous marine cyanobacterium and incorporates a 16-membered macrolactone. Its complex structure is recognizably derived from a polyketide synthase pathway, but possesses unique and intriguing structural features that prompted interest in investigating its biosynthetic origin. Stable isotope incorporation experiments confirmed the polyketide nature of this compound. We further characterized the phormidolide gene cluster (phm) through genome sequencing followed by bioinformatic analysis. Two discrete trans-type acyltransferase (trans-AT) ORFs along with KS-AT adaptor regions (ATd) within the polyketide synthase (PKS) megasynthases, suggest that the phormidolide gene cluster is a trans-AT PKS. Insights gained from analysis of the mode of acetate incorporation and ensuing keto reduction prompted our reevaluation of the stereochemistry of phormidolide hydroxy groups located along the linear polyketide chain.
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Affiliation(s)
- Matthew J Bertin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, MC 0212, La Jolla, CA, 92093, USA
| | - Alexandra Vulpanovici
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences, 2750 SW Campus Way, Corvallis, OR, 97331, USA
| | - Emily A Monroe
- Department of Biology, William Paterson University, 300 Pompton Road, Wayne, NJ, 07470, USA
| | - Anton Korobeynikov
- The Center for Algorithmic Biotechnology, Department of Statistical Modeling, St. Petersburg State University, Universitetskiy 28, Stary Peterhof, St. Petersburg, 198504, Russia
| | - David H Sherman
- Life Sciences Institute, Department of Medicinal Chemistry, Department of Chemistry, Department of Microbiology and Immunology, University of Michigan, 4008 Life Sciences Institute, 210 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, MC 0212, La Jolla, CA, 92093, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, MC 0212, La Jolla, CA, 92093, USA) address.
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17
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Weissman KJ. Genetic engineering of modular PKSs: from combinatorial biosynthesis to synthetic biology. Nat Prod Rep 2016; 33:203-30. [DOI: 10.1039/c5np00109a] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This reviews covers on-going efforts at engineering the gigantic modular polyketide synthases (PKSs), highlighting both notable successes and failures.
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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
- 54505 Vandœuvre-lès-Nancy Cedex
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18
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Abstract
Polyketides are a structurally and functionally diverse family of bioactive natural products that have found widespread application as pharmaceuticals, agrochemicals, and veterinary medicines. In bacteria complex polyketides are biosynthesized by giant multifunctional megaenzymes, termed modular polyketide synthases (PKSs), which construct their products in a highly coordinated assembly line-like fashion from a pool of simple precursor substrates. Not only is the multifaceted enzymology of PKSs a fascinating target for study, but it also presents considerable opportunities for the reengineering of these systems affording access to functionally optimized unnatural natural products. Here we provide an introductory primer to modular polyketide synthase structure and function, and highlight recent advances in the characterization and exploitation of these systems.
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Affiliation(s)
- Marisa Till
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
- BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Paul R Race
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
- BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
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19
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The LINKS motif zippers trans-acyltransferase polyketide synthase assembly lines into a biosynthetic megacomplex. J Struct Biol 2015; 193:196-205. [PMID: 26724270 DOI: 10.1016/j.jsb.2015.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 12/04/2015] [Accepted: 12/22/2015] [Indexed: 11/21/2022]
Abstract
Polyketides such as the clinically-valuable antibacterial agent mupirocin are constructed by architecturally-sophisticated assembly lines known as trans-acyltransferase polyketide synthases. Organelle-sized megacomplexes composed of several copies of trans-acyltransferase polyketide synthase assembly lines have been observed by others through transmission electron microscopy to be located at the Bacillus subtilis plasma membrane, where the synthesis and export of the antibacterial polyketide bacillaene takes place. In this work we analyze ten crystal structures of trans-acyltransferase polyketide synthases ketosynthase domains, seven of which are reported here for the first time, to characterize a motif capable of zippering assembly lines into a megacomplex. While each of the three-helix LINKS (Laterally-INteracting Ketosynthase Sequence) motifs is observed to similarly dock with a spatially-reversed copy of itself through hydrophobic and ionic interactions, the amino acid sequences of this motif are not conserved. Such a code is appropriate for mediating homotypic contacts between assembly lines to ensure the ordered self-assembly of a noncovalent, yet tightly-knit, enzymatic network. LINKS-mediated lateral interactions would also have the effect of bolstering the vertical association of the polypeptides that comprise a polyketide synthase assembly line.
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20
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Contemporary molecular tools in microbial ecology and their application to advancing biotechnology. Biotechnol Adv 2015; 33:1755-73. [DOI: 10.1016/j.biotechadv.2015.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 09/19/2015] [Accepted: 09/20/2015] [Indexed: 12/30/2022]
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21
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Matilla MA, Leeper FJ, Salmond GPC. Biosynthesis of the antifungal haterumalide, oocydin A, in Serratia, and its regulation by quorum sensing, RpoS and Hfq. Environ Microbiol 2015; 17:2993-3008. [PMID: 25753587 PMCID: PMC4552970 DOI: 10.1111/1462-2920.12839] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 02/02/2023]
Abstract
Polyketides represent an important class of bioactive natural products with a broad range of biological activities. We identified recently a large trans-acyltransferase (AT) polyketide synthase gene cluster responsible for the biosynthesis of the antifungal, anti-oomycete and antitumor haterumalide, oocydin A (ooc). Using genome sequencing and comparative genomics, we show that the ooc gene cluster is widespread within biocontrol and phytopathogenic strains of the enterobacteria, Serratia and Dickeya. The analysis of in frame deletion mutants confirmed the role of a hydroxymethylglutaryl-coenzyme A synthase cassette, three flavin-dependent tailoring enzymes, a free-standing acyl carrier protein and two hypothetical proteins in oocydin A biosynthesis. The requirement of the three trans-acting AT domains for the biosynthesis of the macrolide was also demonstrated. Expression of the ooc gene cluster was shown to be positively regulated by an N-acyl-L-homoserine lactone-based quorum sensing system, but operating in a strain-dependent manner. At a post-transcriptional level, the RNA chaperone, Hfq, plays a key role in oocydin A biosynthesis. The Hfq-dependent regulation is partially mediated by the stationary phase sigma factor, RpoS, which was also shown to positively regulate the synthesis of the macrolide. Our results reveal differential regulation of the divergently transcribed ooc transcriptional units, highlighting the complexity of oocydin A production.
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Affiliation(s)
- Miguel A Matilla
- Department of Biochemistry, University of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK
| | - Finian J Leeper
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW, UK
| | - George P C Salmond
- Department of Biochemistry, University of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK,*For correspondence. E-mail ; Tel. +44 (0)1223 333650; Fax +44 (0)1223 766108
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22
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Choi H, Oh DC. Considerations of the chemical biology of microbial natural products provide an effective drug discovery strategy. Arch Pharm Res 2015; 38:1591-605. [PMID: 26231248 DOI: 10.1007/s12272-015-0639-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 07/17/2015] [Indexed: 11/24/2022]
Abstract
Conventional approaches to natural product drug discovery rely mainly on random searches for bioactive compounds using bioassays. These traditional approaches do not incorporate a chemical biology perspective. Searching for bioactive molecules using a chemical and biological rationale constitutes a powerful search paradigm. Here, the authors review recent examples of the discovery of bioactive natural products based on chemical and biological interactions between hosts and symbionts, and propose this method provides a more effective means of exploring natural chemical diversity and eventually of discovering new drugs.
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Affiliation(s)
- Hyukjae Choi
- College of Pharmacy, Yeungnam University, 280 Daehak-ro, Gyeongsan, 712-749, Republic of Korea.
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742, Republic of Korea.
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23
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Flórez LV, Biedermann PHW, Engl T, Kaltenpoth M. Defensive symbioses of animals with prokaryotic and eukaryotic microorganisms. Nat Prod Rep 2015; 32:904-36. [DOI: 10.1039/c5np00010f] [Citation(s) in RCA: 233] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Many organisms team up with symbiotic microbes for defense against predators, parasites, parasitoids, or pathogens. Here we review the known defensive symbioses in animals and the microbial secondary metabolites responsible for providing protection to the host.
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Affiliation(s)
- Laura V. Flórez
- Max Planck Institute for Chemical Ecology
- Insect Symbiosis Research Group
- 07745 Jena
- Germany
| | - Peter H. W. Biedermann
- Max Planck Institute for Chemical Ecology
- Insect Symbiosis Research Group
- 07745 Jena
- Germany
| | - Tobias Engl
- Max Planck Institute for Chemical Ecology
- Insect Symbiosis Research Group
- 07745 Jena
- Germany
| | - Martin Kaltenpoth
- Max Planck Institute for Chemical Ecology
- Insect Symbiosis Research Group
- 07745 Jena
- Germany
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24
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Microbial communities and bioactive compounds in marine sponges of the family irciniidae-a review. Mar Drugs 2014; 12:5089-122. [PMID: 25272328 PMCID: PMC4210886 DOI: 10.3390/md12105089] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/12/2014] [Accepted: 09/16/2014] [Indexed: 11/16/2022] Open
Abstract
Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species—the vast majority of which are difficult to cultivate—and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed.
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25
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Dunn BJ, Watts KR, Robbins T, Cane DE, Khosla C. Comparative analysis of the substrate specificity of trans- versus cis-acyltransferases of assembly line polyketide synthases. Biochemistry 2014; 53:3796-806. [PMID: 24871074 PMCID: PMC4067149 DOI: 10.1021/bi5004316] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Due
to their pivotal role in extender unit selection during polyketide
biosynthesis, acyltransferase (AT) domains are important engineering
targets. A subset of assembly line polyketide synthases (PKSs) are
serviced by discrete, trans-acting ATs. Theoretically,
these trans-ATs can complement an inactivated cis-AT, promoting introduction of a noncognate extender
unit. This approach requires a better understanding of the substrate
specificity and catalytic mechanism of naturally occurring trans-ATs. We kinetically analyzed trans-ATs from the disorazole and kirromycin synthases and compared them
to a representative cis-AT from the 6-deoxyerythronolide
B synthase (DEBS). During transacylation, the disorazole AT favored
malonyl-CoA over methylmalonyl-CoA by >40000-fold, whereas the
kirromycin
AT favored ethylmalonyl-CoA over methylmalonyl-CoA by 20-fold. Conversely,
the disorazole AT had broader specificity than its kirromycin counterpart
for acyl carrier protein (ACP) substrates. The presence of the ACP
had little effect on the specificity (kcat/KM) of the cis-AT domain
for carboxyacyl-CoA substrates but had a marked influence on the corresponding
specificity parameters for the trans-ATs, suggesting
that these enzymes do not act strictly by a canonical ping-pong mechanism.
To investigate the relevance of the kinetic analysis of isolated ATs
in the context of intact PKSs, we complemented an in vitro AT-null DEBS assembly line with either trans-AT.
Whereas the disorazole AT efficiently complemented the mutant PKS
at substoichiometric protein ratios, the kirromycin AT was considerably
less effective. Our findings suggest that knowledge of both carboxyacyl-CoA
and ACP specificity is critical to the choice of a trans-AT in combination with a mutant PKS to generate novel polyketides.
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Affiliation(s)
- Briana J Dunn
- Department of Chemical Engineering, ‡Department of Chemistry, and ∥Department of Biochemistry, Stanford University , Stanford, California 94305, United States
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26
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Till M, Race PR. Progress challenges and opportunities for the re-engineering of trans-AT polyketide synthases. Biotechnol Lett 2014; 36:877-88. [PMID: 24557077 DOI: 10.1007/s10529-013-1449-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 12/23/2013] [Indexed: 12/13/2022]
Abstract
Polyketides are a structurally and functionally diverse family of bioactive natural products that are used extensively as pharmaceuticals and agrochemicals. In bacteria these molecules are biosynthesized by giant, multi-functional enzymatic complexes, termed modular polyketide synthases (PKSs), that function in assembly-line like fashion to fuse and tailor simple carboxylic acid monomers into a vast array of elaborate chemical scaffolds. Modifying PKSs through targeted synthase re-engineering is a promising approach for accessing functionally-optimized polyketides. Due to their highly mosaic architectures the recently identified trans-AT family of modular synthases appear inherently more amenable to re-engineering than their well studied cis-AT counterparts. Here, we review recent progress in the re-engineering of trans-AT PKSs, summarize opportunities for harnessing the biosynthetic potential of these systems, and highlight challenges that such re-engineering approaches present.
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Affiliation(s)
- M Till
- School of Biochemistry, Medical Sciences, University of Bristol, Bristol, BS8 1TD, UK
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27
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Irie K, Yanagita RC. Synthesis and Biological Activities of Simplified Analogs of the Natural PKC Ligands, Bryostatin-1 and Aplysiatoxin. CHEM REC 2014; 14:251-67. [DOI: 10.1002/tcr.201300036] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Kazuhiro Irie
- Division of Food Science and Biotechnology; Graduate School of Agriculture; Kyoto University; Kyoto 606-8502 Japan
| | - Ryo C. Yanagita
- Department of Applied Biological Science; Faculty of Agriculture, Kagawa University; Kagawa 761-0795 Japan
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28
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Microbial natural products: molecular blueprints for antitumor drugs. J Ind Microbiol Biotechnol 2013; 40:1181-210. [PMID: 23999966 DOI: 10.1007/s10295-013-1331-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 08/07/2013] [Indexed: 12/18/2022]
Abstract
Microbes from two of the three domains of life, the Prokarya, and Eukarya, continue to serve as rich sources of structurally complex chemical scaffolds that have proven to be essential for the development of anticancer therapeutics. This review describes only a handful of exemplary natural products and their derivatives as well as those that have served as elegant blueprints for the development of novel synthetic structures that are either currently in use or in clinical or preclinical trials together with some of their earlier analogs in some cases whose failure to proceed aided in the derivation of later compounds. In every case, a microbe has been either identified as the producer of secondary metabolites or speculated to be involved in the production via symbiotic associations. Finally, rapidly evolving next-generation sequencing technologies have led to the increasing availability of microbial genomes. Relevant examples of genome mining and genetic manipulation are discussed, demonstrating that we have only barely scratched the surface with regards to harnessing the potential of microbes as sources of new pharmaceutical leads/agents or biological probes.
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29
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Affiliation(s)
- Nicole B. Lopanik
- Department of Biology; Georgia State University; Atlanta Georgia 30303 USA
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30
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Sucipto H, Wenzel SC, Müller R. Exploring Chemical Diversity of α-Pyrone Antibiotics: Molecular Basis of Myxopyronin Biosynthesis. Chembiochem 2013; 14:1581-9. [DOI: 10.1002/cbic.201300289] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Indexed: 01/30/2023]
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31
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Musiol EM, Greule A, Härtner T, Kulik A, Wohlleben W, Weber T. The AT₂ domain of KirCI loads malonyl extender units to the ACPs of the kirromycin PKS. Chembiochem 2013; 14:1343-52. [PMID: 23828654 DOI: 10.1002/cbic.201300211] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Indexed: 11/06/2022]
Abstract
The antibiotic kirromycin is assembled by a hybrid modular polyketide synthases (PKSs)/nonribosomal peptide synthetases (NRPSs). Five of six PKSs of this complex assembly line do not have acyltransferase (AT) and have to recruit this activity from discrete AT enzymes. Here, we show that KirCI is a discrete AT which is involved in kirromycin production and displays a rarely found three-domain architecture (AT₁-AT₂-ER). We demonstrate that the second AT domain, KirCI-AT₂, but not KirCI-AT₁, is the malonyl-CoA-specific AT which utilizes this precursor for loading the acyl carrier proteins (ACPs) of the trans-AT PKS in vitro. In the kirromycin biosynthetic pathway, ACP5 is exclusively loaded with ethylmalonate by the enzyme KirCII and is not recognized as a substrate by KirCI. Interestingly, the excised KirCI-AT₂ can also transfer malonate to ACP5 and thus has a relaxed ACP-specificity compared to the entire KirCI protein. The ability of KirCI-AT₂ to load different ACPs provides opportunities for AT engineering as a potential strategy for polyketide diversification.
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Affiliation(s)
- Ewa Maria Musiol
- Mikrobiologie/Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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32
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Dunn BJ, Khosla C. Engineering the acyltransferase substrate specificity of assembly line polyketide synthases. J R Soc Interface 2013; 10:20130297. [PMID: 23720536 DOI: 10.1098/rsif.2013.0297] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Polyketide natural products act as a broad range of therapeutics, including antibiotics, immunosuppressants and anti-cancer agents. This therapeutic diversity stems from the structural diversity of these small molecules, many of which are produced in an assembly line manner by modular polyketide synthases. The acyltransferase (AT) domains of these megasynthases are responsible for selection and incorporation of simple monomeric building blocks, and are thus responsible for a large amount of the resulting polyketide structural diversity. The substrate specificity of these domains is often targeted for engineering in the generation of novel, therapeutically active natural products. This review outlines recent developments that can be used in the successful engineering of these domains, including AT sequence and structural data, mechanistic insights and the production of a diverse pool of extender units. It also provides an overview of previous AT domain engineering attempts, and concludes with proposed engineering approaches that take advantage of current knowledge. These approaches may lead to successful production of biologically active 'unnatural' natural products.
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Affiliation(s)
- Briana J Dunn
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
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33
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Anand S, Mohanty D. Computational Methods for Identification of Novel Secondary Metabolite Biosynthetic Pathways by Genome Analysis. Bioinformatics 2013. [DOI: 10.4018/978-1-4666-3604-0.ch086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Secondary metabolites belonging to polyketide and nonribosomal peptide families constitute a major class of natural products with diverse biological functions and a variety of pharmaceutically important properties. Experimental studies have shown that the biosynthetic machinery for polyketide and nonribosomal peptides involves multi-functional megasynthases like Polyketide Synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) which utilize a thiotemplate mechanism similar to that for fatty acid biosynthesis. Availability of complete genome sequences for an increasing number of microbial organisms has provided opportunities for using in silico genome mining to decipher the secondary metabolite natural product repertoire encoded by these organisms. Therefore, in recent years there have been major advances in development of computational methods which can analyze genome sequences to identify genes involved in secondary metabolite biosynthesis and help in deciphering the putative chemical structures of their biosynthetic products based on analysis of the sequence and structural features of the proteins encoded by these genes. These computational methods for deciphering the secondary metabolite biosynthetic code essentially involve identification of various catalytic domains present in this PKS/NRPS family of enzymes; a prediction of various reactions in these enzymatic domains and their substrate specificities and also precise identification of the order in which these domains would catalyze various biosynthetic steps. Structural bioinformatics analysis of known secondary metabolite biosynthetic clusters has helped in formulation of predictive rules for deciphering domain organization, substrate specificity, and order of substrate channeling. In this chapter, the progress in development of various computational methods is discussed by different research groups, and specifically, the utility in identification of novel metabolites by genome mining and rational design of natural product analogs by biosynthetic engineering studies.
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34
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Koryakina I, McArthur J, Randall S, Draelos MM, Musiol EM, Muddiman DC, Weber T, Williams GJ. Poly specific trans-acyltransferase machinery revealed via engineered acyl-CoA synthetases. ACS Chem Biol 2013; 8:200-8. [PMID: 23083014 DOI: 10.1021/cb3003489] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polyketide synthases construct polyketides with diverse structures and biological activities via the condensation of extender units and acyl thioesters. Although a growing body of evidence suggests that polyketide synthases might be tolerant to non-natural extender units, in vitro and in vivo studies aimed at probing and utilizing polyketide synthase specificity are severely limited to only a small number of extender units, owing to the lack of synthetic routes to a broad variety of acyl-CoA extender units. Here, we report the construction of promiscuous malonyl-CoA synthetase variants that can be used to synthesize a broad range of malonyl-CoA extender units substituted at the C2-position, several of which contain handles for chemoselective ligation and are not found in natural biosynthetic systems. We highlighted utility of these enzymes by probing the acyl-CoA specificity of several trans-acyltransferases, leading to the unprecedented discovery of poly specificity toward non-natural extender units, several of which are not found in naturally occurring biosynthetic pathways. These results reveal that polyketide biosynthetic machinery might be more tolerant to non-natural substrates than previously established, and that mutant synthetases are valuable tools for probing the specificity of biosynthetic machinery. Our data suggest new synthetic biology strategies for harnessing this promiscuity and enabling the regioselective modification of polyketides.
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Affiliation(s)
| | | | | | | | - Ewa M. Musiol
- Eberhard-Karls-Universität Tübingen, Interfakultäres Institut für
Mikrobiologie und Infektionsmedizin, Mikrobiologie/Biotechnologie,
Tübingen, Germany
| | | | - Tilmann Weber
- Eberhard-Karls-Universität Tübingen, Interfakultäres Institut für
Mikrobiologie und Infektionsmedizin, Mikrobiologie/Biotechnologie,
Tübingen, Germany
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Boronated tartrolon antibiotic produced by symbiotic cellulose-degrading bacteria in shipworm gills. Proc Natl Acad Sci U S A 2013; 110:E295-304. [PMID: 23288898 DOI: 10.1073/pnas.1213892110] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Shipworms are marine wood-boring bivalve mollusks (family Teredinidae) that harbor a community of closely related Gammaproteobacteria as intracellular endosymbionts in their gills. These symbionts have been proposed to assist the shipworm host in cellulose digestion and have been shown to play a role in nitrogen fixation. The genome of one strain of Teredinibacter turnerae, the first shipworm symbiont to be cultivated, was sequenced, revealing potential as a rich source of polyketides and nonribosomal peptides. Bioassay-guided fractionation led to the isolation and identification of two macrodioloide polyketides belonging to the tartrolon class. Both compounds were found to possess antibacterial properties, and the major compound was found to inhibit other shipworm symbiont strains and various pathogenic bacteria. The gene cluster responsible for the synthesis of these compounds was identified and characterized, and the ketosynthase domains were analyzed phylogenetically. Reverse-transcription PCR in addition to liquid chromatography and high-resolution mass spectrometry and tandem mass spectrometry revealed the transcription of these genes and the presence of the compounds in the shipworm, suggesting that the gene cluster is expressed in vivo and that the compounds may fulfill a specific function for the shipworm host. This study reports tartrolon polyketides from a shipworm symbiont and unveils the biosynthetic gene cluster of a member of this class of compounds, which might reveal the mechanism by which these bioactive metabolites are biosynthesized.
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Matilla MA, Stöckmann H, Leeper FJ, Salmond GPC. Bacterial biosynthetic gene clusters encoding the anti-cancer haterumalide class of molecules: biogenesis of the broad spectrum antifungal and anti-oomycete compound, oocydin A. J Biol Chem 2012; 287:39125-38. [PMID: 23012376 PMCID: PMC3493953 DOI: 10.1074/jbc.m112.401026] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/05/2012] [Indexed: 01/16/2023] Open
Abstract
Haterumalides are halogenated macrolides with strong antitumor properties, making them attractive targets for chemical synthesis. Unfortunately, current synthetic routes to these molecules are inefficient. The potent haterumalide, oocydin A, was previously identified from two plant-associated bacteria through its high bioactivity against plant pathogenic fungi and oomycetes. In this study, we describe oocydin A (ooc) biosynthetic gene clusters identified by genome sequencing, comparative genomics, and chemical analysis in four plant-associated enterobacteria of the Serratia and Dickeya genera. Disruption of the ooc gene cluster abolished oocydin A production and bioactivity against fungi and oomycetes. The ooc gene clusters span between 77 and 80 kb and encode five multimodular polyketide synthase (PKS) proteins, a hydroxymethylglutaryl-CoA synthase cassette and three flavin-dependent tailoring enzymes. The presence of two free-standing acyltransferase proteins classifies the oocydin A gene cluster within the growing family of trans-AT PKSs. The amino acid sequences and organization of the PKS domains are consistent with the chemical predictions and functional peculiarities associated with trans-acyltransferase PKS. Based on extensive in silico analysis of the gene cluster, we propose a biosynthetic model for the production of oocydin A and, by extension, for other members of the haterumalide family of halogenated macrolides exhibiting anti-cancer, anti-fungal, and other interesting biological properties.
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Affiliation(s)
- Miguel A. Matilla
- From the Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW and
| | - Henning Stöckmann
- the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Finian J. Leeper
- the Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - George P. C. Salmond
- From the Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW and
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37
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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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38
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Jensen K, Niederkrüger H, Zimmermann K, Vagstad AL, Moldenhauer J, Brendel N, Frank S, Pöplau P, Kohlhaas C, Townsend CA, Oldiges M, Hertweck C, Piel J. Polyketide proofreading by an acyltransferase-like enzyme. ACTA ACUST UNITED AC 2012; 19:329-39. [PMID: 22444588 DOI: 10.1016/j.chembiol.2012.01.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 12/09/2011] [Accepted: 01/02/2012] [Indexed: 11/18/2022]
Abstract
Trans-acyltransferase polyketide synthases (trans-AT PKSs) are an important group of bacterial enzymes producing bioactive polyketides. One difference from textbook PKSs is the presence of one or more free-standing AT-like enzymes. While one homolog loads the PKS with malonyl units, the function of the second copy (AT2) was unknown. We studied the two ATs PedC and PedD involved in pederin biosynthesis in an uncultivated symbiont. PedD displayed malonyl- but not acetyltransferase activity toward various acyl carrier proteins (ACPs). In contrast, the AT2 PedC efficiently hydrolyzed acyl units bound to N-acetylcysteamine or ACP. It accepted substrates with various chain lengths and functionalizations but did not cleave malonyl-ACP. These data are consistent with the role of PedC in PKS proofreading, suggesting a similar function for other AT2 homologs and providing strategies for polyketide titer improvement and biosynthetic investigations.
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Affiliation(s)
- Katja Jensen
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, 53121 Bonn, Germany
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39
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Musiol EM, Weber T. Discrete acyltransferases involved in polyketide biosynthesis. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20048a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Rath CM, Janto B, Earl J, Ahmed A, Hu FZ, Hiller L, Dahlgren M, Kreft R, Yu F, Wolff JJ, Kweon HK, Christiansen MA, Håkansson K, Williams RM, Ehrlich GD, Sherman DH. Meta-omic characterization of the marine invertebrate microbial consortium that produces the chemotherapeutic natural product ET-743. ACS Chem Biol 2011; 6:1244-56. [PMID: 21875091 DOI: 10.1021/cb200244t] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In many macroorganisms, the ultimate source of potent biologically active natural products has remained elusive due to an inability to identify and culture the producing symbiotic microorganisms. As a model system for developing a meta-omic approach to identify and characterize natural product pathways from invertebrate-derived microbial consortia, we chose to investigate the ET-743 (Yondelis) biosynthetic pathway. This molecule is an approved anticancer agent obtained in low abundance (10(-4)-10(-5) % w/w) from the tunicate Ecteinascidia turbinata and is generated in suitable quantities for clinical use by a lengthy semisynthetic process. On the basis of structural similarities to three bacterial secondary metabolites, we hypothesized that ET-743 is the product of a marine bacterial symbiont. Using metagenomic sequencing of total DNA from the tunicate/microbial consortium, we targeted and assembled a 35 kb contig containing 25 genes that comprise the core of the NRPS biosynthetic pathway for this valuable anticancer agent. Rigorous sequence analysis based on codon usage of two large unlinked contigs suggests that Candidatus Endoecteinascidia frumentensis produces the ET-743 metabolite. Subsequent metaproteomic analysis confirmed expression of three key biosynthetic proteins. Moreover, the predicted activity of an enzyme for assembly of the tetrahydroisoquinoline core of ET-743 was verified in vitro. This work provides a foundation for direct production of the drug and new analogues through metabolic engineering. We expect that the interdisciplinary approach described is applicable to diverse host-symbiont systems that generate valuable natural products for drug discovery and development.
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Affiliation(s)
| | - Benjamin Janto
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania 15212, United States
| | - Josh Earl
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania 15212, United States
| | - Azad Ahmed
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania 15212, United States
| | - Fen Z. Hu
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania 15212, United States
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, Pennsylvania 15212, United States
- Department of Otolaryngology, Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, Pennsylvania 15212, United States
| | - Luisa Hiller
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania 15212, United States
| | - Meg Dahlgren
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania 15212, United States
| | - Rachael Kreft
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania 15212, United States
| | | | - Jeremy J. Wolff
- Bruker Daltonics, Billerica, Massachusetts 01821, United States
| | | | | | | | - Robert M. Williams
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania 15212, United States
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, Pennsylvania 15212, United States
- Department of Otolaryngology, Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, Pennsylvania 15212, United States
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41
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Musiol EM, Härtner T, Kulik A, Moldenhauer J, Piel J, Wohlleben W, Weber T. Supramolecular templating in kirromycin biosynthesis: the acyltransferase KirCII loads ethylmalonyl-CoA extender onto a specific ACP of the trans-AT PKS. ACTA ACUST UNITED AC 2011; 18:438-44. [PMID: 21513880 DOI: 10.1016/j.chembiol.2011.02.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 02/14/2011] [Accepted: 02/15/2011] [Indexed: 11/16/2022]
Abstract
In the biosynthesis of complex polyketides, acyltransferase domains (ATs) are key determinants of structural diversity. Their specificity and position in polyketide synthases (PKSs) usually controls the location and structure of building blocks in polyketides. Many bioactive polyketides, however, are generated by trans-AT PKSs lacking internal AT domains. They were previously believed to use mainly malonyl-specific free-standing ATs. Here, we report a mechanism of structural diversification, in which the trans-AT KirCII regiospecifically incorporates the unusual extender unit ethylmalonyl-CoA in kirromycin polyketide biosynthesis.
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Affiliation(s)
- Ewa M Musiol
- Eberhard-Karls-Universität Tübingen, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Mikrobiologie/Biotechnologie, 72076 Tübingen, Germany
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42
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Trindade-Silva AE, Lim-Fong GE, Sharp KH, Haygood MG. Bryostatins: biological context and biotechnological prospects. Curr Opin Biotechnol 2011; 21:834-42. [PMID: 20971628 DOI: 10.1016/j.copbio.2010.09.018] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 09/25/2010] [Accepted: 09/29/2010] [Indexed: 11/18/2022]
Abstract
Bryostatins are a family of protein kinase C modulators that have potential applications in biomedicine. Found in miniscule quantities in a small marine invertebrate, lack of supply has hampered their development. In recent years, bryostatins have been shown to have potent bioactivity in the central nervous system, an uncultivated marine bacterial symbiont has been shown to be the likely natural source of the bryostatins, the bryostatin biosynthetic genes have been identified and characterized, and bryostatin analogues with promising biological activity have been developed and tested. Challenges in the development of bryostatins for biomedical and biotechnological application include the cultivation of the bacterial symbiont and heterologous expression of bryostatin biosynthesis genes. Continued exploration of the biology as well as the symbiotic origin of the bryostatins presents promising opportunities for discovery of additional bryostatins, and new functions for bryostatins.
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Affiliation(s)
- Amaro E Trindade-Silva
- Instituto de Química de São Carlos, Universidade de São Paulo CP 780, CEP 13560-970, São Carlos, SP, Brazil
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43
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Buchholz TJ, Rath CM, Lopanik NB, Gardner NP, Håkansson K, Sherman DH. Polyketide β-branching in bryostatin biosynthesis: identification of surrogate acetyl-ACP donors for BryR, an HMG-ACP synthase. ACTA ACUST UNITED AC 2011; 17:1092-100. [PMID: 21035732 DOI: 10.1016/j.chembiol.2010.08.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 08/10/2010] [Accepted: 08/17/2010] [Indexed: 10/18/2022]
Abstract
In vitro analysis of natural product biosynthetic gene products isolated from unculturable symbiotic bacteria is necessary to probe the functionalities of these enzymes. Herein, we report the biochemical characterization of BryR, the 3-hydroxy-3-methylglutaryl (HMG)-CoA synthase (HMGS) homolog implicated in β-branching at C13 and C21 of the core ring system from the bryostatin metabolic pathway (Bry). We confirmed the activity of BryR using two complementary methods, radio-SDS PAGE, and Fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS). The activity of BryR depended on pairing of the native acetoacetyl-BryM3 acceptor acyl carrier protein (ACP) with an appropriate donor acetyl-ACP from a heterologous HMGS cassette. Additionally, the ability of BryR to discriminate between various ACPs was assessed using a surface plasmon resonance (SPR)-based protein-protein binding assay. Our data suggest that specificity for a protein-bound acyl group is a distinguishing feature between HMGS homologs found in PKS or PKS/NRPS biosynthetic pathways and those of primary metabolism. These findings reveal an important example of molecular recognition between protein components that are essential for biosynthetic fidelity in natural product assembly and modification.
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Affiliation(s)
- Tonia J Buchholz
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
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44
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Zhang F, He HY, Tang MC, Tang YM, Zhou Q, Tang GL. Cloning and Elucidation of the FR901464 Gene Cluster Revealing a Complex Acyltransferase-less Polyketide Synthase Using Glycerate as Starter Units. J Am Chem Soc 2011; 133:2452-62. [DOI: 10.1021/ja105649g] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Feng Zhang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Hai-Yan He
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Man-Cheng Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yu-Min Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Qiang Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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45
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Irschik H, Kopp M, Weissman KJ, Buntin K, Piel J, Müller R. Analysis of the sorangicin gene cluster reinforces the utility of a combined phylogenetic/retrobiosynthetic analysis for deciphering natural product assembly by trans-AT PKS. Chembiochem 2011; 11:1840-9. [PMID: 20715267 DOI: 10.1002/cbic.201000313] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Herbert Irschik
- Microbial Drugs, Helmholtz Center for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
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46
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Zimmermann K, Engeser M, Blunt JW, Munro MHG, Piel J. Pederin-type pathways of uncultivated bacterial symbionts: analysis of o-methyltransferases and generation of a biosynthetic hybrid. J Am Chem Soc 2010; 131:2780-1. [PMID: 19206228 DOI: 10.1021/ja808889k] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complex polyketide pederin is a potent antitumor agent isolated from Paederus spp. rove beetles. We have previously isolated a set of genes from a bacterial endosymbiont that are good candidates for pederin biosynthesis. To biochemically study this pathway, we expressed three methyltransferases from the putative pederin pathway and used the partially unmethylated analogue mycalamide A from the marine sponge Mycale hentscheli as test substrate. Analysis by high-resolution MS/MS and NMR revealed that PedO regiospecifically methylates the marine compound to generate the nonnatural hybrid compound 18-O-methylmycalamide A with increased cytotoxicity. To our knowledge, this is the first biochemical evidence that invertebrates can obtain defensive complex polyketides from bacterial symbionts.
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Affiliation(s)
- Katrin Zimmermann
- Kekule Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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47
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Chan YA, Thomas MG. Recognition of (2S)-aminomalonyl-acyl carrier protein (ACP) and (2R)-hydroxymalonyl-ACP by acyltransferases in zwittermicin A biosynthesis. Biochemistry 2010; 49:3667-77. [PMID: 20353188 DOI: 10.1021/bi100141n] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyketide synthases elongate a polyketide backbone by condensing carboxylic acid precursors that are thioesterified to either coenzyme A or an acyl carrier protein (ACP). Two of the three known ACP-linked extender units, (2S)-aminomalonyl-ACP and (2R)-hydroxymalonyl-ACP, are found in the biosynthesis of the agriculturally important antibiotic zwittermicin A. We previously reconstituted the formation of (2S)-aminomalonyl-ACP and (2R)-hydroxymalonyl-ACP from the primary metabolites l-serine and 1,3-bisphospho-d-glycerate. In this report, we characterize the two acyltransferases involved in the specific transfer of the (2S)-aminomalonyl and (2R)-hydroxymalonyl moieties from the ACPs associated with extender unit formation to the ACPs integrated into the polyketide synthase. This work establishes which acyltransferase recognizes each extender unit and also provides insight into the substrate selectivity of these enzymes. These are important step toward harnessing these rare polyketide synthase extender units for combinatorial biosynthesis.
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Affiliation(s)
- Yolande A Chan
- Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, Wisconsin 53706, USA
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48
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Abstract
This review discusses the biosynthesis of natural products that are generated by trans-AT polyketide synthases, a family of catalytically versatile enzymes that have recently been recognized as one of the major group of proteins involved in the production of bioactive polyketides. 436 references are cited.
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Affiliation(s)
- Jörn Piel
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Bonn, Germany.
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49
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La Clair JJ. Natural product mode of action (MOA) studies: a link between natural and synthetic worlds. Nat Prod Rep 2010; 27:969-95. [DOI: 10.1039/b909989c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Brady SF, Simmons L, Kim JH, Schmidt EW. Metagenomic approaches to natural products from free-living and symbiotic organisms. Nat Prod Rep 2009; 26:1488-503. [PMID: 19844642 DOI: 10.1039/b817078a] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Sean F Brady
- The Rockefeller University, New York, NY 10021, USA.
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