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Löhr NA, Urban MC, Eisen F, Platz L, Hüttel W, Gressler M, Müller M, Hoffmeister D. The Ketosynthase Domain Controls Chain Length in Mushroom Oligocyclic Polyketide Synthases. Chembiochem 2023; 24:e202200649. [PMID: 36507600 PMCID: PMC10108026 DOI: 10.1002/cbic.202200649] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
The nonreducing iterative type I polyketide synthases (NR-PKSs) CoPKS1 and CoPKS4 of the webcap mushroom Cortinarius odorifer share 88 % identical amino acids. CoPKS1 almost exclusively produces a tricyclic octaketide product, atrochrysone carboxylic acid, whereas CoPKS4 shows simultaneous hepta- and octaketide synthase activity and also produces the bicyclic heptaketide 6-hydroxymusizin. To identify the region(s) controlling chain length, four chimeric enzyme variants were constructed and assayed for activity in Aspergillus niger as heterologous expression platform. We provide evidence that the β-ketoacyl synthase (KS) domain determines chain length in these mushroom NR-PKSs, even though their KS domains differ in only ten amino acids. A unique proline-rich linker connecting the acyl carrier protein with the thioesterase domain varies most between these two enzymes but is not involved in chain length control.
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Affiliation(s)
- Nikolai A Löhr
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Maximilian C Urban
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Frederic Eisen
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Lukas Platz
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Wolfgang Hüttel
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Markus Gressler
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Dirk Hoffmeister
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
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2
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Cox RJ. Curiouser and curiouser: progress in understanding the programming of iterative highly-reducing polyketide synthases. Nat Prod Rep 2023; 40:9-27. [PMID: 35543313 DOI: 10.1039/d2np00007e] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 1996-2022Investigations over the last 2 decades have begun to reveal how fungal iterative highly-reducing polyketide synthases are programmed. Both in vitro and in vivo experiments have revealed the interplay of intrinsic and extrinsic selectivity of the component catalytic domains of these systems. Structural biology has begun to provide high resolution structures of hr-PKS that can be used as the basis for their engineering and reprogramming, but progress to-date remains rudimentary. However, significant opportunities exist for translating the current level of understanding into the ability to rationally re-engineer these highly efficient systems for the production of important biologically active compounds through biotechnology.
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Affiliation(s)
- Russell J Cox
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167, Hannover, Germany.
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4
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Wang C, Wang X, Zhang L, Yue Q, Liu Q, Xu YM, Gunatilaka AAL, Wei X, Xu Y, Molnár I. Intrinsic and Extrinsic Programming of Product Chain Length and Release Mode in Fungal Collaborating Iterative Polyketide Synthases. J Am Chem Soc 2020; 142:17093-17104. [PMID: 32833442 DOI: 10.1021/jacs.0c07050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Combinatorial biosynthesis with fungal polyketide synthases (PKSs) promises to produce unprecedented bioactive "unnatural" natural products (uNPs) for drug discovery. Genome mining of the dothideomycete Rhytidhysteron rufulum uncovered a collaborating highly reducing PKS (hrPKS)-nonreducing PKS (nrPKS) pair. These enzymes produce trace amounts of rare S-type benzenediol macrolactone congeners with a phenylacetate core in a heterologous host. However, subunit shuffling and domain swaps with voucher enzymes demonstrated that all PKS domains are highly productive. This contradiction led us to reveal novel programming layers exerted by the starter unit acyltransferase (SAT) and the thioesterase (TE) domains on the PKS system. First, macrocyclic vs linear product formation is dictated by the intrinsic biosynthetic program of the TE domain. Next, the chain length of the hrPKS product is strongly influenced in trans by the off-loading preferences of the nrPKS SAT domain. Last, TE domains are size-selective filters that facilitate or obstruct product formation from certain priming units. Thus, the intrinsic programs of the SAT and TE domains are both part of the extrinsic program of the hrPKS subunit and modulate the observable metaprogram of the whole PKS system. Reconstruction of SAT and TE phylogenies suggests that these domains travel different evolutionary trajectories, with the resulting divergence creating potential conflicts in the PKS metaprogram. Such conflicts often emerge in chimeric PKSs created by combinatorial biosynthesis, reducing biosynthetic efficiency or even incapacitating the system. Understanding the points of failure for such engineered biocatalysts is pivotal to advance the biosynthetic production of uNPs.
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Affiliation(s)
- Chen Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.,Southwest Center for Natural Products Research, University of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United States
| | - Xiaojing Wang
- Microbial Pharmacology Laboratory, Shanghai University of Medicine and Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai 201318, P. R. China
| | - Liwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Qun Yue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Qingpei Liu
- Southwest Center for Natural Products Research, University of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United States.,School of Pharmaceutical Sciences, South-Central University for Nationalities, 182 Minyuan Road, Hongshan District, Wuhan 430074, P. R. China
| | - Ya-Ming Xu
- Southwest Center for Natural Products Research, University of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United States
| | - A A Leslie Gunatilaka
- Southwest Center for Natural Products Research, University of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United States
| | - Xiaoyi Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, P. R. China
| | - Yuquan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, 250 East Valencia Road, Tucson, Arizona 85706, United States
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5
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Yang XL, Friedrich S, Yin S, Piech O, Williams K, Simpson TJ, Cox RJ. Molecular basis of methylation and chain-length programming in a fungal iterative highly reducing polyketide synthase. Chem Sci 2019; 10:8478-8489. [PMID: 31803427 PMCID: PMC6839510 DOI: 10.1039/c9sc03173a] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/28/2019] [Indexed: 12/28/2022] Open
Abstract
Exchange of 32 different sub-fragments of the C-methyltransferase (C-MeT), pseudo-ketoreductase (ΨKR) and ketoreductase (KR) catalytic domains of the tenellin iterative Type I polyketide synthase non ribosomal peptide synthetase (PKS-NRPS) TENS by homologous fragments from the desmethylbassianin (DMBS) and militarinone (MILS) PKS-NRPS led to the creation of chimeric synthetases in which programming fidelity was altered, resulting in the production of mixtures of products with different methylation patterns and chain lengths. Swap of KR domain subfragments with the homologous fragments from the KR of the heptaketide militarinone synthetase resulted in the synthesis of penta, hexa and heptaketides. The results of these and previous experiments are rationalised by considering the existence of competition for acyl-carrier protein (ACP) bound substrates between different catalytic domains of the PKS. In particular, competition between the C-MeT and ketoreductase domains (KR) can account for methylation programming, and competition between the KR and the off-loading NRPS accounts for chain-length selectivity.
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Affiliation(s)
- Xiao-Long Yang
- Institute for Organic Chemistry , Leibniz University of Hannover , Schneiderberg 1B , 30167 , Hannover , Germany . .,BMWZ , Leibniz University of Hannover , Schneiderberg 38 , 30167 , Hannover , Germany
| | - Steffen Friedrich
- Institute for Organic Chemistry , Leibniz University of Hannover , Schneiderberg 1B , 30167 , Hannover , Germany . .,BMWZ , Leibniz University of Hannover , Schneiderberg 38 , 30167 , Hannover , Germany
| | - Sen Yin
- Institute for Organic Chemistry , Leibniz University of Hannover , Schneiderberg 1B , 30167 , Hannover , Germany . .,BMWZ , Leibniz University of Hannover , Schneiderberg 38 , 30167 , Hannover , Germany
| | - Oliver Piech
- Institute for Organic Chemistry , Leibniz University of Hannover , Schneiderberg 1B , 30167 , Hannover , Germany . .,BMWZ , Leibniz University of Hannover , Schneiderberg 38 , 30167 , Hannover , Germany
| | - Katherine Williams
- Institute for Organic Chemistry , Leibniz University of Hannover , Schneiderberg 1B , 30167 , Hannover , Germany . .,BMWZ , Leibniz University of Hannover , Schneiderberg 38 , 30167 , Hannover , Germany.,School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | - Thomas J Simpson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | - Russell J Cox
- Institute for Organic Chemistry , Leibniz University of Hannover , Schneiderberg 1B , 30167 , Hannover , Germany . .,BMWZ , Leibniz University of Hannover , Schneiderberg 38 , 30167 , Hannover , Germany
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Evolution of chemical diversity by coordinated gene swaps in type II polyketide gene clusters. Proc Natl Acad Sci U S A 2015; 112:13952-7. [PMID: 26499248 DOI: 10.1073/pnas.1511688112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Natural product biosynthetic pathways generate molecules of enormous structural complexity and exquisitely tuned biological activities. Studies of natural products have led to the discovery of many pharmaceutical agents, particularly antibiotics. Attempts to harness the catalytic prowess of biosynthetic enzyme systems, for both compound discovery and engineering, have been limited by a poor understanding of the evolution of the underlying gene clusters. We developed an approach to study the evolution of biosynthetic genes on a cluster-wide scale, integrating pairwise gene coevolution information with large-scale phylogenetic analysis. We used this method to infer the evolution of type II polyketide gene clusters, tracing the path of evolution from the single ancestor to those gene clusters surviving today. We identified 10 key gene types in these clusters, most of which were swapped in from existing cellular processes and subsequently specialized. The ancestral type II polyketide gene cluster likely comprised a core set of five genes, a roster that expanded and contracted throughout evolution. A key C24 ancestor diversified into major classes of longer and shorter chain length systems, from which a C20 ancestor gave rise to the majority of characterized type II polyketide antibiotics. Our findings reveal that (i) type II polyketide structure is predictable from its gene roster, (ii) only certain gene combinations are compatible, and (iii) gene swaps were likely a key to evolution of chemical diversity. The lessons learned about how natural selection drives polyketide chemical innovation can be applied to the rational design and guided discovery of chemicals with desired structures and properties.
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7
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Liu T, Sanchez JF, Chiang YM, Oakley BR, Wang CCC. Rational domain swaps reveal insights about chain length control by ketosynthase domains in fungal nonreducing polyketide synthases. Org Lett 2014; 16:1676-9. [PMID: 24593241 PMCID: PMC3993715 DOI: 10.1021/ol5003384] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
A facile
genetic methodology in the filamentous fungus Aspergillus
nidulans allowed exchange of the starter unit ACP transacylase
(SAT) domain
in the nonreduced polyketide synthase (NR-PKS) AfoE of the asperfuranone
pathway with the SAT domains from 10 other NR-PKSs. The newly created
hybrid with the NR-PKS AN3386 is able to accept a longer starter unit
in place of the native substrate to create a novel aromatic polyketide in vivo.
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Affiliation(s)
- Ting Liu
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy , Los Angeles, California 90089, United States
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8
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Analysis of the ketosynthase-chain length factor heterodimer from the fredericamycin polyketide synthase. ACTA ACUST UNITED AC 2011; 18:1021-31. [PMID: 21867917 DOI: 10.1016/j.chembiol.2011.07.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 05/01/2011] [Accepted: 05/03/2011] [Indexed: 11/24/2022]
Abstract
The pentadecaketide fredericamycin has the longest carbon chain backbone among polycyclic aromatic polyketide antibiotics whose biosynthetic genes have been sequenced. This backbone is synthesized by the bimodular fdm polyketide synthase (PKS). Here, we demonstrate that the bimodular fdm PKS as well as its elongation module alone synthesize undecaketides and dodecaketides. Thus, unlike other homologs, the fdm ketosynthase-chain length factor (KS-CLF) heterodimer does not exclusively control the backbone length of its natural product. Using sequence- and structure-based approaches, 48 CLF multiple mutants were engineered and analyzed. Unexpectedly, the I134F mutant was unable to turn over but could initiate and partially elongate the polyketide chain. This unprecedented mutant suggests that the KS-CLF heterodimer harbors an as yet uncharacterized chain termination mechanism. Together, our findings reveal fundamental mechanistic differences between the fdm PKS and its well-studied homologs.
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Das A, Szu PH, Fitzgerald JT, Khosla C. Mechanism and engineering of polyketide chain initiation in fredericamycin biosynthesis. J Am Chem Soc 2010; 132:8831-3. [PMID: 20540492 PMCID: PMC2904946 DOI: 10.1021/ja102517q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ability to incorporate atypical primer units through the use of dedicated initiation polyketide synthase (PKS) modules offers opportunities to expand the molecular diversity of polyketide natural products. Here we identify the initiation PKS module responsible for hexadienyl priming of the antibiotic fredericamycin and investigate its biochemical properties. We also exploit this PKS module for the design and in vivo biosynthesis of unusually primed analogues of a representative polyketide product, thereby emphasizing its utility to the metabolic engineer.
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Affiliation(s)
- Abhirup Das
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Ping-Hui Szu
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Jay T. Fitzgerald
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, California 94305
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
- Department of Biochemistry, Stanford University, Stanford, California 94305
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10
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Abe I, Morita H. Structure and function of the chalcone synthase superfamily of plant type III polyketide synthases. Nat Prod Rep 2010; 27:809-38. [PMID: 20358127 DOI: 10.1039/b909988n] [Citation(s) in RCA: 194] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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11
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Das A, Khosla C. In vivo and in vitro analysis of the hedamycin polyketide synthase. ACTA ACUST UNITED AC 2010; 16:1197-207. [PMID: 19942143 DOI: 10.1016/j.chembiol.2009.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 10/19/2009] [Accepted: 11/02/2009] [Indexed: 11/25/2022]
Abstract
Hedamycin is an antitumor polyketide antibiotic with unusual biosynthetic features. Earlier sequence analysis of the hedamycin biosynthetic gene cluster implied a role for type I and type II polyketide synthases (PKSs). We demonstrate that the hedamycin minimal PKS can synthesize a dodecaketide backbone. The ketosynthase (KS) subunit of this PKS has specificity for both type I and type II acyl carrier proteins (ACPs) with which it collaborates during chain initiation and chain elongation, respectively. The KS receives a C(6) primer unit from the terminal ACP domain of HedU (a type I PKS protein) directly and subsequently interacts with the ACP domain of HedE (a type II PKS protein) during the process of chain elongation. HedE is a bifunctional protein with both ACP and aromatase activity. Its aromatase domain can modulate the chain length specificity of the minimal PKS. Chain length can also be influenced by HedA, the C-9 ketoreductase. While co-expression of the hedamycin minimal PKS and a chain-initiation module from the R1128 PKS yields an isobutyryl-primed decaketide, the orthologous PKS subunits from the hedamycin gene cluster itself are unable to prime the minimal PKS with a nonacetyl starter unit. Our findings provide new insights into the mechanism of chain initiation and elongation by type II PKSs.
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Affiliation(s)
- Abhirup Das
- Department of Chemistry, Stanford University, CA 94305-5025, USA
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12
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Wang M, Zhou H, Wirz M, Tang Y, Boddy CN. A thioesterase from an iterative fungal polyketide synthase shows macrocyclization and cross coupling activity and may play a role in controlling iterative cycling through product offloading. Biochemistry 2009; 48:6288-90. [PMID: 19530704 PMCID: PMC2722786 DOI: 10.1021/bi9009049] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Zearalenone, a fungal macrocyclic polyketide, is a member of the resorcylic acid lactone family. Herein, we characterize in vitro the thioesterase from PKS13 in zearalenone biosynthesis (Zea TE). The excised Zea TE catalyzes macrocyclization of a linear thioester-activated model of zearalenone. Zea TE also catalyzes the cross coupling of a benzoyl thioester with alcohols and amines. Kinetic characterization of the cross coupling is consistent with a ping-pong bi-bi mechanism, confirming an acyl-enzyme intermediate. Finally, the substrate specificity of the Zea TE indicates the TE may help control iterative cycling on PKS13 by rapidly offloading the final resorcylate-containing product.
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Affiliation(s)
- Meng Wang
- Department of Chemistry, University of Ottawa, Ottawa, ON, T1N 6N5
- Department of Chemistry, Syracuse University, Syracuse, NY 13244
| | - Hui Zhou
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095
| | - Monica Wirz
- Department of Chemistry, University of Ottawa, Ottawa, ON, T1N 6N5
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095
| | - Christopher N. Boddy
- Department of Chemistry, University of Ottawa, Ottawa, ON, T1N 6N5
- Department of Chemistry, Syracuse University, Syracuse, NY 13244
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14
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15
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Evans SE, Williams C, Arthur CJ, Płoskoń E, Wattana-amorn P, Cox RJ, Crosby J, Willis CL, Simpson TJ, Crump MP. Probing the Interactions of Early Polyketide Intermediates with the Actinorhodin ACP from S. coelicolor A3(2). J Mol Biol 2009; 389:511-28. [DOI: 10.1016/j.jmb.2009.03.072] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 03/25/2009] [Accepted: 03/25/2009] [Indexed: 10/20/2022]
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Abstract
Natural products, produced chiefly by microorganisms and plants, can be large and structurally complex molecules. These molecules are manufactured by cellular assembly lines, in which enzymes construct the molecules in a stepwise fashion. The means by which enzymes interact and work together in a modular fashion to create diverse structural features has been an active area of research; the work has provided insight into the fine details of biosynthesis. A number of polycyclic aromatic natural products--including several noteworthy anticancer, antibacterial, antifungal, antiviral, antiparasitic, and other medicinally significant substances--are synthesized by polyketide synthases (PKSs) in soil-borne bacteria called actinomycetes. Concerted biosynthetic, enzymological, and structural biological investigations into these modular enzyme systems have yielded interesting mechanistic insights. A core module called the minimal PKS is responsible for synthesizing a highly reactive, protein-bound poly-beta-ketothioester chain. In the absence of other enzymes, the minimal PKS also catalyzes chain initiation and release, yielding an assortment of polycyclic aromatic compounds. In the presence of an initiation PKS module, polyketide backbones bearing additional alkyl, alkenyl, or aryl primer units are synthesized, whereas a range of auxiliary PKS enzymes and tailoring enzymes convert the product of the minimal PKS into the final natural product. In this Account, we summarize the knowledge that has been gained regarding this family of PKSs through recent investigations into the biosynthetic pathways of two natural products, actinorhodin and R1128 (A-D). We also discuss the practical relevance of these fundamental insights for the engineered biosynthesis of new polycyclic aromatic compounds. With a deeper understanding of the biosynthetic process in hand, we can assert control at various stages of molecular construction and thus introduce unnatural functional groups in the process. The metabolic engineer affords a number of new avenues for creating novel molecular structures that will likely have properties akin to their fully natural cousins.
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Affiliation(s)
| | - Chaitan Khosla
- Department of Chemistry
- Department of Chemical Engineering
- Department of Biochemistry, Stanford University, Stanford, California 94305-5025
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17
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Shi SP, Wanibuchi K, Morita H, Endo K, Noguchi H, Abe I. Enzymatic formation of unnatural novel chalcone, stilbene, and benzophenone scaffolds by plant type III polyketide synthase. Org Lett 2009; 11:551-4. [PMID: 19123789 DOI: 10.1021/ol802606w] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A C(19) hexaketide stilbene and a C(21) heptaketide chalcone were synthesized by Aloe arborescens octaketide synthase (OKS), a plant-specific type III polyketide synthase (PKS). Remarkably, the C(21) chalcone-forming activity was dramatically increased in a structure-guided OKS N222G mutant that produces a C(20) decaketide SEK15 from 10 molecules of malonyl-CoA. The findings suggested further strategies for production of unnatural polyketides by combination of the precursor-directed biosynthesis and the structure-guided engineering of type III PKS.
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Affiliation(s)
- She-Po Shi
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
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Beltran-Alvarez P, Arthur CJ, Cox RJ, Crosby J, Crump MP, Simpson TJ. Preliminary kinetic analysis of acyl carrier protein–ketoacylsynthase interactions in the actinorhodin minimal polyketide synthase. MOLECULAR BIOSYSTEMS 2009; 5:511-8. [DOI: 10.1039/b821844g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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19
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Abstract
Fungi produce a wide variety of biologically active compounds, a large proportion of which are produced by the polyketide biosynthetic pathway. Fungal polyketides comprise a very large and structurally very diverse group, and many display important biological activities, including lovastatin, aflatoxins, and strobilurins. These are produced by very large multifunctional iterative enzymes, the iterative type I polyketide synthases (PKSs) whose closest structural and functional analogues are the mammalian fatty acid synthases. Although fungal polyketides were one of the first classes of secondary metabolites to be subject to extensive biosynthetic studies, they remain the least studied and understood at the enzyme level. This chapter presents an overview of methodologies that have been applied to in vivo and in vitro genetic and biochemical studies on the PKSs responsible for both aromatic and highly reduced polyketide metabolites, and which are providing an improved insight into how these highly complex enzymes function.
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Affiliation(s)
- Russell J Cox
- School of Chemistry, University of Bristol, Bristol, United Kingdom
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Hong H, Spiteller D, Spencer JB. Incorporation of fluoroacetate into an aromatic polyketide and its influence on the mode of cyclization. Angew Chem Int Ed Engl 2008; 47:6028-32. [PMID: 18613185 DOI: 10.1002/anie.200801100] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hui Hong
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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Hong H, Spiteller D, Spencer J. Incorporation of Fluoroacetate into an Aromatic Polyketide and Its Influence on the Mode of Cyclization. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Ma Y, Smith LH, Cox RJ, Beltran-Alvarez P, Arthur CJ, Simpson F R S TJ. Catalytic relationships between type I and type II iterative polyketide synthases: The Aspergillus parasiticus norsolorinic acid synthase. Chembiochem 2007; 7:1951-8. [PMID: 17086560 DOI: 10.1002/cbic.200600341] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Norsolorinic acid synthase (NSAS) is a type I iterative polyketide synthase that occurs in the filamentous fungus Aspergillus parasiticus. PCR was used to clone fragments of NSAS corresponding to the acyl carrier protein (ACP), acyl transferase (AT) and beta-ketoacyl-ACP synthase (KS) catalytic domains. Expression of these gene fragments in Escherichia coli led to the production of soluble ACP and AT proteins. Coexpression of ACP with E. coli holo-ACP synthase (ACPS) let to production of NSAS holo-ACP, which could also be formed in vitro by using Streptomyces coelicolor ACPS. Analysis by mass spectrometry showed that, as with other type I carrier proteins, self-malonylation is not observed in the presence of malonyl CoA alone. However, the NSAS holo-ACP serves as substrate for S. coelicolor MCAT, S. coelicolor actinorhodin holo-ACP and NSAS AT domain-catalysed malonate transfer from malonyl CoA. The AT domain could transfer malonate from malonyl CoA to NSAS holo-ACP, but not hexanoate or acetate from either the cognate CoA or FAS ACP species to NSAS holo-ACP. The NSAS holo-ACP was also active in actinorhodin minimal PKS assays, but only in the presence of exogenous malonyl transferases.
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Affiliation(s)
- Yue Ma
- School of Chemistry, University of Bristol, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
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Cox RJ. Polyketides, proteins and genes in fungi: programmed nano-machines begin to reveal their secrets. Org Biomol Chem 2007; 5:2010-26. [PMID: 17581644 DOI: 10.1039/b704420h] [Citation(s) in RCA: 352] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fungi produce a wide variety of biologically active compounds. Among these, the polyketides form a large and structurally diverse group. These compounds are synthesised by highly programmed and very large iterative multifunctional proteins, the polyketide synthases, with nm dimensions. This review outlines the current state of knowledge regarding the links between gene sequence, protein architecture and biosynthetic programming for fungal polyketide synthases.
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Affiliation(s)
- Russell J Cox
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, UK BS8 1TS.
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Izumikawa M, Cheng Q, Moore BS. Priming type II polyketide synthases via a type II nonribosomal peptide synthetase mechanism. J Am Chem Soc 2006; 128:1428-9. [PMID: 16448095 PMCID: PMC2531066 DOI: 10.1021/ja0559707] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Benzoic acid priming of the enterocin and actinorhodin type II polyketide synthase complexes was accomplished in vitro via an unprecedented type II nonribosomal peptide synthetase-like mechanism involving the benzoate:acyl carrier protein (ACP) ligase EncN and the ACP EncC. The transfer of the aryl acid to the ACP is ATP-dependent, yet coenzyme A-independent, as characterized with radiolabeled substrates and protein mass spectrometry. Subsequent transport of the ACP-bound aryl group to the native enterocin and the aberrant actinorhodin ketosynthase chain length factor heterodimers was further demonstrated, thereby demonstrating the potential of this biocatalyst for engineering diverse aryl-primed aromatic polyketide agents.
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Affiliation(s)
- Miho Izumikawa
- College of Pharmacy, University of Arizona, Tucson, AZ, 85721
| | - Qian Cheng
- College of Pharmacy, University of Arizona, Tucson, AZ, 85721
| | - Bradley S. Moore
- College of Pharmacy, University of Arizona, Tucson, AZ, 85721
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
- E-mail:
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Peric-Concha N, Borovicka B, Long PF, Hranueli D, Waterman PG, Hunter IS. Ablation of the otcC Gene Encoding a Post-polyketide Hydroxylase from the Oxytetracyline Biosynthetic Pathway in Streptomyces rimosus Results in Novel Polyketides with Altered Chain Length. J Biol Chem 2005; 280:37455-60. [PMID: 16148009 DOI: 10.1074/jbc.m503191200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oxytetracycline (OTC) is a 19-carbon polyketide antibiotic made by Streptomyces rimosus. The otcC gene encodes an anhydrotetracycline oxygenase that catalyzes a hydroxylation of the anthracycline structure at position C-6 after biosynthesis of the polyketide backbone is completed. A recombinant strain of S. rimosus that was disrupted in the genomic copy of otcC synthesized a novel C-17 polyketide. This result indicates that the absence of the otcC gene product significantly influences the ability of the OTC "minimal" polyketide synthase to make a polyketide product of the correct chain length. A mutant copy of otcC was made by site-directed mutagenesis of three essential glycine codons located within the putative NADPH-binding domain. The mutant gene was expressed in Escherichia coli, and biochemical analysis confirmed that the gene product was catalytically inactive. When the mutant gene replaced the ablated gene in the chromosome of S. rimosus, the ability to make a 19-carbon backbone was restored, indicating that OtcC is an essential partner in the quaternary structure of the synthase complex.
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Bode HB, Müller R. Der Einfluss bakterieller Genomik auf die Naturstoff-Forschung. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501080] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
"There's life in the old dog yet!" This adage also holds true for natural product research. After the era of natural products was declared to be over, because of the introduction of combinatorial synthesis techniques, natural product research has taken a surprising turn back towards a major field of pharmaceutical research. Current challenges, such as emerging multidrug-resistant bacteria, might be overcome by developments which combine genomic knowledge with applied biology and chemistry to identify, produce, and alter the structure of new lead compounds. Significant biological activity is reported much less frequently for synthetic compounds, a fact reflected in the large proportion of natural products and their derivatives in clinical use. This Review describes the impact of microbial genomics on natural products research, in particularly the search for new lead structures and their optimization. The limitations of this research are also discussed, thus allowing a look into future developments.
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Affiliation(s)
- Helge B Bode
- Institut für Pharmazeutische Biotechnologie, Universität des Saarlandes, Postfach 151150, 66041 Saarbrücken, Germany
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Korman TP, Hill JA, Vu TN, Tsai SC. Structural analysis of actinorhodin polyketide ketoreductase: cofactor binding and substrate specificity. Biochemistry 2005; 43:14529-38. [PMID: 15544323 PMCID: PMC2263080 DOI: 10.1021/bi048133a] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aromatic polyketides are a class of natural products that include many pharmaceutically important aromatic compounds. Understanding the structure and function of PKS will provide clues to the molecular basis of polyketide biosynthesis specificity. Polyketide chain reduction by ketoreductase (KR) provides regio- and stereochemical diversity. Two cocrystal structures of actinorhodin polyketide ketoreductase (act KR) were solved to 2.3 A with either the cofactor NADP(+) or NADPH bound. The monomer fold is a highly conserved Rossmann fold. Subtle differences between structures of act KR and fatty acid KRs fine-tune the tetramer interface and substrate binding pocket. Comparisons of the NADP(+)- and NADPH-bound structures indicate that the alpha6-alpha7 loop region is highly flexible. The intricate proton-relay network in the active site leads to the proposed catalytic mechanism involving four waters, NADPH, and the active site tetrad Asn114-Ser144-Tyr157-Lys161. Acyl carrier protein and substrate docking models shed light on the molecular basis of KR regio- and stereoselectivity, as well as the differences between aromatic polyketide and fatty acid biosyntheses. Sequence comparison indicates that the above features are highly conserved among aromatic polyketide KRs. The structures of act KR provide an important step toward understanding aromatic PKS and will enhance our ability to design novel aromatic polyketide natural products with different reduction patterns.
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Affiliation(s)
| | | | | | - Shiou-Chuan Tsai
- * Address correspondence to this author. E-mail: . Phone: 949-824-4486. Fax: 949-824-8552
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Olano C, Wilkinson B, Moss SJ, Braña AF, Méndez C, Leadlay PF, Salas JA. Evidence from engineered gene fusions for the repeated use of a module in a modular polyketide synthase. Chem Commun (Camb) 2003:2780-2. [PMID: 14651102 DOI: 10.1039/b310648a] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Functional evidence for programmed loss of co-linearity on the borrelidin modular polyketide synthase (PKS) is presented.
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Affiliation(s)
- Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncologia del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
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