1
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Paulsel TQ, Williams GJ. Current State-of-the-Art Toward Chemoenzymatic Synthesis of Polyketide Natural Products. Chembiochem 2023; 24:e202300386. [PMID: 37615926 PMCID: PMC10964317 DOI: 10.1002/cbic.202300386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 08/25/2023]
Abstract
Polyketide natural products have significant promise as pharmaceutical targets for human health and as molecular tools to probe disease and complex biological systems. While the biosynthetic logic of polyketide synthases (PKS) is well-understood, biosynthesis of designer polyketides remains challenging due to several bottlenecks, including substrate specificity constraints, disrupted protein-protein interactions, and protein solubility and folding issues. Focusing on substrate specificity, PKSs are typically interrogated using synthetic thioesters. PKS assembly lines and their products offer a wealth of information when studied in a chemoenzymatic fashion. This review provides an overview of the past two decades of polyketide chemoenzymatic synthesis and their contributions to the field of chemical biology. These synthetic strategies have successfully yielded natural product derivatives while providing critical insights into enzymatic promiscuity and mechanistic activity.
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Affiliation(s)
- Thaddeus Q Paulsel
- Department of Chemistry, NC State University Dabney Hall, Room 208, Campus Box 8204, 2620 Yarbrough Dr., NC State University, Raleigh, NC 27695, USA
- Comparative Medicine Institute, NC State University, 1060 William Moore Dr., NC State University, Raleigh, NC 27607, USA
| | - Gavin J Williams
- Department of Chemistry, NC State University Dabney Hall, Room 208, Campus Box 8204, 2620 Yarbrough Dr., NC State University, Raleigh, NC 27695, USA
- Comparative Medicine Institute, NC State University, 1060 William Moore Dr., NC State University, Raleigh, NC 27607, USA
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2
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Schröder M, Roß T, Hemmerling F, Hahn F. Studying a Bottleneck of Multimodular Polyketide Synthase Processing: the Polyketide Structure-Dependent Performance of Ketoreductase Domains. ACS Chem Biol 2022; 17:1030-1037. [PMID: 35412301 DOI: 10.1021/acschembio.2c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ketoreductases (KRs) are canonical domains of type I polyketide synthases (PKSs). They stereoselectively reduce ACP-bound β-ketothioester intermediates and are responsible for a large part of the stereocenters in reduced polyketides. Albeit essential for the understanding and engineering of PKS, the specific effects of altering the polyketide part of KR precursors on their performance has rarely been studied. We present investigations on the substrate-dependent performance of six isolated KR domains using a library of structurally diverse surrogates for PKS thioester intermediates. A pronounced correlation between the polyketide structure and the KR performance was observed with activity and stereoselectivity diminishing with growing deviation from the natural KR precursor structure. The extent of this decrease and the profile of arising side products was characteristic for the individual KRs. Our results reinforce the importance of structure-KR performance relationships and suggest extended studies with isolated domains and whole PKS modules.
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Affiliation(s)
- Marius Schröder
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
- Biomolekulares Wirkstoffzentrum, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - Theresa Roß
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Franziska Hemmerling
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
- Biomolekulares Wirkstoffzentrum, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
- Biomolekulares Wirkstoffzentrum, Leibniz Universität Hannover, 30167 Hannover, Germany
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3
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Wunderlich J, Roß T, Schröder M, Hahn F. Step-Economic Synthesis of Biomimetic β-Ketopolyene Thioesters and Demonstration of Their Usefulness in Enzymatic Biosynthesis Studies. Org Lett 2020; 22:4955-4959. [PMID: 32610930 DOI: 10.1021/acs.orglett.0c01348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Studies on the biosynthetic processing of polyene thioester intermediates are complicated by limited access to appropriate substrate surrogates. We present a step-economic synthetic access to biomimetic β-ketopolyene thioesters that is based on an Ir-catalyzed reductive Horner-Wadsworth-Emmons olefination. New β-ketotriene and pentaenethioates of pantetheine and N-acetylcysteamine were exemplarily synthesized via short and concise routes. The usefulness of these compounds was demonstrated in an in vitro assay with the ketoreductase domain MycKRB from mycolactone biosynthesis.
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Affiliation(s)
- Johannes Wunderlich
- Fakultät Biologie, Chemie und Geologie, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Theresa Roß
- Fakultät Biologie, Chemie und Geologie, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Marius Schröder
- Fakultät Biologie, Chemie und Geologie, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Frank Hahn
- Fakultät Biologie, Chemie und Geologie, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
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4
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Drufva EE, Hix EG, Bailey CB. Site directed mutagenesis as a precision tool to enable synthetic biology with engineered modular polyketide synthases. Synth Syst Biotechnol 2020; 5:62-80. [PMID: 32637664 PMCID: PMC7327777 DOI: 10.1016/j.synbio.2020.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/04/2022] Open
Abstract
Modular polyketide synthases (PKSs) are a multidomain megasynthase class of biosynthetic enzymes that have great promise for the development of new compounds, from new pharmaceuticals to high value commodity and specialty chemicals. Their colinear biosynthetic logic has been viewed as a promising platform for synthetic biology for decades. Due to this colinearity, domain swapping has long been used as a strategy to introduce molecular diversity. However, domain swapping often fails because it perturbs critical protein-protein interactions within the PKS. With our increased level of structural elucidation of PKSs, using judicious targeted mutations of individual residues is a more precise way to introduce molecular diversity with less potential for global disruption of the protein architecture. Here we review examples of targeted point mutagenesis to one or a few residues harbored within the PKS that alter domain specificity or selectivity, affect protein stability and interdomain communication, and promote more complex catalytic reactivity.
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Key Words
- ACP, acyl carrier protein
- AT, acyltransferase
- DEBS, 6-deoxyerthronolide B synthase
- DH, dehydratase
- EI, enoylisomerase
- ER, enoylreductase
- KR, ketoreductase
- KS, ketosynthase
- LM, loading module
- MT, methyltransferase
- Mod, module
- PKS, polyketide synthase
- PS, pyran synthase
- Polyketide synthase
- Protein engineering
- Rational design
- SNAC, N-acetyl cysteamine
- Saturation mutagenesis
- Site directed mutagenesis
- Synthetic biology
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Affiliation(s)
- Erin E. Drufva
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| | - Elijah G. Hix
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| | - Constance B. Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
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5
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Hollmann T, Berkhan G, Wagner L, Sung KH, Kolb S, Geise H, Hahn F. Biocatalysts from Biosynthetic Pathways: Enabling Stereoselective, Enzymatic Cycloether Formation on a Gram Scale. ACS Catal 2020. [DOI: 10.1021/acscatal.9b05071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Tim Hollmann
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Gesche Berkhan
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
- Centre for Biomolecular Drug Research, Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Lisa Wagner
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Kwang Hoon Sung
- Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany
- Protein Facility, ILAb Co., Ltd. NP513, The Catholic University of Korea, 420-743 Bucheon, Republic of Korea
| | - Simon Kolb
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Hendrik Geise
- Centre for Biomolecular Drug Research, Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
- Centre for Biomolecular Drug Research, Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany
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6
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Bayly CL, Yadav VG. Towards Precision Engineering of Canonical Polyketide Synthase Domains: Recent Advances and Future Prospects. Molecules 2017; 22:molecules22020235. [PMID: 28165430 PMCID: PMC6155766 DOI: 10.3390/molecules22020235] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 01/09/2023] Open
Abstract
Modular polyketide synthases (mPKSs) build functionalized polymeric chains, some of which have become blockbuster therapeutics. Organized into repeating clusters (modules) of independently-folding domains, these assembly-line-like megasynthases can be engineered by introducing non-native components. However, poor introduction points and incompatible domain combinations can cause both unintended products and dramatically reduced activity. This limits the engineering and combinatorial potential of mPKSs, precluding access to further potential therapeutics. Different regions on a given mPKS domain determine how it interacts both with its substrate and with other domains. Within the assembly line, these interactions are crucial to the proper ordering of reactions and efficient polyketide construction. Achieving control over these domain functions, through precision engineering at key regions, would greatly expand our catalogue of accessible polyketide products. Canonical mPKS domains, given that they are among the most well-characterized, are excellent candidates for such fine-tuning. The current minireview summarizes recent advances in the mechanistic understanding and subsequent precision engineering of canonical mPKS domains, focusing largely on developments in the past year.
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Affiliation(s)
- Carmen L Bayly
- Department of Genome Sciences & Technology, The University of British Columbia, Vancouver, BC V5Z 4S6, Canada.
- Department of Chemical & Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Vikramaditya G Yadav
- Department of Chemical & Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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7
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Bailey CB, Pasman ME, Keatinge-Clay AT. Substrate structure-activity relationships guide rational engineering of modular polyketide synthase ketoreductases. Chem Commun (Camb) 2016; 52:792-5. [PMID: 26568113 PMCID: PMC4690787 DOI: 10.1039/c5cc07315d] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modular polyketide synthase ketoreductases can set two chiral centers through a single reduction. To probe the basis of stereocontrol, a structure-activity relationship study was performed with three α-methyl, β-ketothioester substrates and four ketoreductases. Since interactions with the β-ketoacyl moiety were found to be most critical, residues implicated in contacting this moiety were mutated. Two mutations were sufficient to completely reverse the stereoselectivity of the model ketoreductase EryKR1, converting it from an enzyme that generates (2S,3R)-products into one that yields (2S,3S)-products.
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Affiliation(s)
- Constance B Bailey
- Department of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, TX 78712, USA.
| | - Marjolein E Pasman
- Department of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, TX 78712, USA.
| | - Adrian T Keatinge-Clay
- Department of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, TX 78712, USA. and Department of Molecular Biosciences, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712, USA
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8
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9
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Li Y, Fiers WD, Bernard S, Smith JL, Aldrich CC, Fecik RA. Polyketide intermediate mimics as probes for revealing cryptic stereochemistry of ketoreductase domains. ACS Chem Biol 2014; 9:2914-22. [PMID: 25299319 PMCID: PMC4273979 DOI: 10.1021/cb5006883] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 10/09/2014] [Indexed: 12/27/2022]
Abstract
Among natural product families, polyketides have shown the most promise for combinatorial biosynthesis of natural product-like libraries. Though recent research in the area has provided many mechanistic revelations, a basic-level understanding of kinetic and substrate tolerability is still needed before the full potential of combinatorial biosynthesis can be realized. We have developed a novel set of chemical probes for the study of ketoreductase domains of polyketide synthases. This chemical tool-based approach was validated using the ketoreductase of pikromycin module 2 (PikKR2) as a model system. Triketide substrate mimics 12 and 13 were designed to increase stability (incorporating a nonhydrolyzable thioether linkage) and minimize nonessential functionality (truncating the phosphopantetheinyl arm). PikKR2 reduction product identities as well as steady-state kinetic parameters were determined by a combination of LC-MS/MS analysis of synthetic standards and a NADPH consumption assay. The d-hydroxyl product is consistent with bioinformatic analysis and results from a complementary biochemical and molecular biological approach. When compared to widely employed substrates in previous studies, diketide 63 and trans-decalone 64, substrates 12 and 13 showed 2-10 fold lower K(M) values (2.4 ± 0.8 and 7.8 ± 2.7 mM, respectively), indicating molecular recognition of intermediate-like substrates. Due to an abundance of the nonreducable enol-tautomer, the k(cat) values were attenuated by as much as 15-336 fold relative to known substrates. This study reveals the high stereoselectivity of PikKR2 in the face of gross substrate permutation, highlighting the utility of a chemical probe-based approach in the study of polyketide ketoreductases.
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Affiliation(s)
- Yang Li
- Department
of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - William D. Fiers
- Department
of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Steffen
M. Bernard
- Chemical Biology Program, Department of Biological
Chemistry,
and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Janet L. Smith
- Chemical Biology Program, Department of Biological
Chemistry,
and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Courtney C. Aldrich
- Department
of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Robert A. Fecik
- Department
of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
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10
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He HY, Yuan H, Tang MC, Tang GL. An Unusual Dehydratase Acting on Glycerate and a Ketoreducatse Stereoselectively Reducing α-Ketone in Polyketide Starter Unit Biosynthesis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Abstract
Natural products are important sources of pharmaceuticals, in part owing to their diverse biological activities. Enzymes from natural product biosynthetic pathways have become attractive candidates as biocatalysts for modifying the structures and bioactivities of these complex compounds. Numerous enzymes have been harvested to generate innovative scaffolds, large-scale synthesis of chiral building blocks, and semisynthesis of medicinally relevant natural product derivatives. This review discusses recent examples from three areas: (a) polyketide catalytic domain engineering geared toward synthesis of new polyketides, (b) engineering of tailoring enzymes (other than oxidative enzymes) as biocatalysts, and (c) in vitro total synthesis of natural products using purified enzyme components. With the availability of exponentially increasing genomic information and new genome mining tools, many new and powerful biocatalysts tailored for pharmaceutical synthesis will likely emerge from secondary metabolism.
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12
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Piasecki SK, Zheng J, Axelrod AJ, Detelich M, Keatinge-Clay AT. Structural and functional studies of a trans-acyltransferase polyketide assembly line enzyme that catalyzes stereoselective α- and β-ketoreduction. Proteins 2014; 82:2067-77. [PMID: 24634061 PMCID: PMC4142079 DOI: 10.1002/prot.24561] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/19/2014] [Accepted: 03/06/2014] [Indexed: 11/06/2022]
Abstract
While the cis-acyltransferase modular polyketide synthase assembly lines have largely been structurally dissected, enzymes from within the recently discovered trans-acyltransferase polyketide synthase assembly lines are just starting to be observed crystallographically. Here we examine the ketoreductase (KR) from the first polyketide synthase module of the bacillaene nonribosomal peptide synthetase/polyketide synthase at 2.35-Å resolution. This KR naturally reduces both α- and β-keto groups and is the only KR known to do so during the biosynthesis of a polyketide. The isolated KR not only reduced an N-acetylcysteamine-bound β-keto substrate to a D-β-hydroxy product, but also an N-acetylcysteamine-bound α-keto substrate to an L-α-hydroxy product. That the substrates must enter the active site from opposite directions to generate these stereochemistries suggests that the acyl-phosphopantetheine moiety is capable of accessing very different conformations despite being anchored to a serine residue of a docked acyl carrier protein. The features enabling stereocontrolled α-ketoreduction may not be extensive since a KR that naturally reduces a β-keto group within a cis-acyltransferase polyketide synthase was identified that performs a completely stereoselective reduction of the same α-keto substrate to generate the D-α-hydroxy product. A sequence analysis of trans-acyltransferase KRs reveals that a single residue, rather than a three-residue motif found in cis-acyltransferase KRs, is predictive of the orientation of the resulting β-hydroxyl group.
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Affiliation(s)
- Shawn K. Piasecki
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Jianting Zheng
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Abram J. Axelrod
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Madeline Detelich
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Adrian T. Keatinge-Clay
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
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13
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He HY, Yuan H, Tang MC, Tang GL. An unusual dehydratase acting on glycerate and a ketoreducatse stereoselectively reducing α-ketone in polyketide starter unit biosynthesis. Angew Chem Int Ed Engl 2014; 53:11315-9. [PMID: 25160004 DOI: 10.1002/anie.201406602] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Indexed: 11/06/2022]
Abstract
Polyketide synthases (PKSs) usually employ a ketoreductase (KR) to catalyze the reduction of a β-keto group, followed by a dehydratase (DH) that drives the dehydration to form a double bond between the α- and β-carbon atoms. Herein, a DH*-KR* involved in FR901464 biosynthesis was characterized: DH* acts on glyceryl-S-acyl carrier protein (ACP) to yield ACP-linked pyruvate; subsequently KR* reduces α-ketone that yields L-lactyl-S-ACP as starter unit for polyketide biosynthesis. Genetic and biochemical evidence was found to support a similar pathway that is involved in the biosynthesis of lankacidins. These results not only identified new PKS domains acting on different substrates, but also provided additional options for engineering the PKS starter pathway or biocatalysis.
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Affiliation(s)
- Hai-Yan He
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032 (China)
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14
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Xu Y, Zhou T, Espinosa-Artiles P, Tang Y, Zhan J, Molnár I. Insights into the biosynthesis of 12-membered resorcylic acid lactones from heterologous production in Saccharomyces cerevisiae. ACS Chem Biol 2014; 9:1119-27. [PMID: 24597618 PMCID: PMC4033647 DOI: 10.1021/cb500043g] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
The phytotoxic fungal polyketides
lasiodiplodin and resorcylide
inhibit human blood coagulation factor XIIIa, mineralocorticoid receptors,
and prostaglandin biosynthesis. These secondary metabolites belong
to the 12-membered resorcylic acid lactone (RAL12) subclass
of the benzenediol lactone (BDL) family. Identification of genomic
loci for the biosynthesis of lasiodiplodin from Lasiodiplodia
theobromae and resorcylide from Acremonium zeae revealed collaborating iterative polyketide synthase (iPKS) pairs
whose efficient heterologous expression in Saccharomyces cerevisiae provided a convenient access to the RAL12 scaffolds desmethyl-lasiodiplodin
and trans-resorcylide, respectively. Lasiodiplodin
production was reconstituted in the heterologous host by co-expressing
an O-methyltransferase also encoded in the lasiodiplodin
cluster, while a glutathione-S-transferase was found
not to be necessary for heterologous production. Clarification of
the biogenesis of known resorcylide congeners in the heterologous
host helped to disentangle the roles that biosynthetic irregularities
and chemical interconversions play in generating chemical diversity.
Observation of 14-membered RAL homologues during in vivo heterologous biosynthesis of RAL12 metabolites revealed
“stuttering” by fungal iPKSs. The close global and domain-level
sequence similarities of the orthologous BDL synthases across different
structural subclasses implicate repeated horizontal gene transfers
and/or cluster losses in different fungal lineages. The absence of
straightforward correlations between enzyme sequences and product
structural features (the size of the macrocycle, the conformation
of the exocyclic methyl group, or the extent of reduction by the hrPKS)
suggest that BDL structural variety is the result of a select few
mutations in key active site cavity positions.
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Affiliation(s)
- Yuquan Xu
- Biotechnology
Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun
South St., Beijing 100081, People’s Republic of China
- Natural
Products Center, School of Natural Resources and the Environment,
College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Rd., Tucson, Arizona 85706, United States
| | - Tong Zhou
- Department
of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, Utah 84322, United States
| | - Patricia Espinosa-Artiles
- Natural
Products Center, School of Natural Resources and the Environment,
College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Rd., Tucson, Arizona 85706, United States
| | - Ying Tang
- Natural
Products Center, School of Natural Resources and the Environment,
College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Rd., Tucson, Arizona 85706, United States
- College
of Sciences, Sichuan University, Chengdu, Sichuan 610064, People’s Republic of China
| | - Jixun Zhan
- Department
of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, Utah 84322, United States
| | - István Molnár
- Natural
Products Center, School of Natural Resources and the Environment,
College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Rd., Tucson, Arizona 85706, United States
- Bio5
Institute, The University of Arizona, 1657 E. Helen St., Tucson, Arizona 85721, United States
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15
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Soehano I, Yang L, Ding F, Sun H, Low ZJ, Liu X, Liang ZX. Insights into the programmed ketoreduction of partially reducing polyketide synthases: stereo- and substrate-specificity of the ketoreductase domain. Org Biomol Chem 2014; 12:8542-9. [DOI: 10.1039/c4ob01777c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Evidence are provided to support that partially reducing polyketide synthases achieve programmed ketoreduction by differential recognition of polyketide intermediates.
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Affiliation(s)
- Ishin Soehano
- School of Biological Sciences Nanyang Technological University
- , Singapore
| | - Lifeng Yang
- School of Biological Sciences Nanyang Technological University
- , Singapore
| | - Feiqing Ding
- School of Mathematics and Physics
- Nanyang Technological University
- , Singapore
| | - Huihua Sun
- School of Biological Sciences Nanyang Technological University
- , Singapore
| | - Zhen Jie Low
- School of Biological Sciences Nanyang Technological University
- , Singapore
| | - Xuewei Liu
- School of Mathematics and Physics
- Nanyang Technological University
- , Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences Nanyang Technological University
- , Singapore
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Kitsche A, Kalesse M. Configurational Assignment of Secondary Hydroxyl Groups and Methyl Branches in Polyketide Natural Products through Bioinformatic Analysis of the Ketoreductase Domain. Chembiochem 2013; 14:851-61. [DOI: 10.1002/cbic.201300063] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Indexed: 12/17/2022]
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17
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Zou Y, Yin H, Kong D, Deng Z, Lin S. ATrans-Acting Ketoreductase in Biosynthesis of a Symmetric Polyketide Dimer SIA7248. Chembiochem 2013; 14:679-83. [DOI: 10.1002/cbic.201300068] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Indexed: 11/07/2022]
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18
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Characterization of the biosynthetic genes for 10,11-dehydrocurvularin, a heat shock response-modulating anticancer fungal polyketide from Aspergillus terreus. Appl Environ Microbiol 2013; 79:2038-47. [PMID: 23335766 DOI: 10.1128/aem.03334-12] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
10,11-Dehydrocurvularin is a prevalent fungal phytotoxin with heat shock response and immune-modulatory activities. It features a dihydroxyphenylacetic acid lactone polyketide framework with structural similarities to resorcylic acid lactones like radicicol or zearalenone. A genomic locus was identified from the dehydrocurvularin producer strain Aspergillus terreus AH-02-30-F7 to reveal genes encoding a pair of iterative polyketide synthases (A. terreus CURS1 [AtCURS1] and AtCURS2) that are predicted to collaborate in the biosynthesis of 10,11-dehydrocurvularin. Additional genes in this locus encode putative proteins that may be involved in the export of the compound from the cell and in the transcriptional regulation of the cluster. 10,11-Dehydrocurvularin biosynthesis was reconstituted in Saccharomyces cerevisiae by heterologous expression of the polyketide synthases. Bioinformatic analysis of the highly reducing polyketide synthase AtCURS1 and the nonreducing polyketide synthase AtCURS2 highlights crucial biosynthetic programming differences compared to similar synthases involved in resorcylic acid lactone biosynthesis. These differences lead to the synthesis of a predicted tetraketide starter unit that forms part of the 12-membered lactone ring of dehydrocurvularin, as opposed to the penta- or hexaketide starters in the 14-membered rings of resorcylic acid lactones. Tetraketide N-acetylcysteamine thioester analogues of the starter unit were shown to support the biosynthesis of dehydrocurvularin and its analogues, with yeast expressing AtCURS2 alone. Differential programming of the product template domain of the nonreducing polyketide synthase AtCURS2 results in an aldol condensation with a different regiospecificity than that of resorcylic acid lactones, yielding the dihydroxyphenylacetic acid scaffold characterized by an S-type cyclization pattern atypical for fungal polyketides.
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19
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Caffrey P. Dissecting complex polyketide biosynthesis. Comput Struct Biotechnol J 2012; 3:e201210010. [PMID: 24688670 PMCID: PMC3962154 DOI: 10.5936/csbj.201210010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 12/17/2022] Open
Abstract
Numerous bioactive natural products are synthesised by modular polyketide synthases. These compounds can be made in high yield by native multienzyme assembly lines. However, formation of analogues by genetically engineered systems is often considerably less efficient. Biochemical studies on intact polyketide synthase proteins have amassed a body of knowledge that is substantial but still incomplete. Recently, the constituent enzymes have been structurally characterised as discrete domains or didomains. These recombinant proteins have been used to reconstitute single extension cycles in vitro. This has given further insights into how the final stereochemistry of chiral centres in polyketides is determined. In addition, this approach has revealed how domains co-operate to ensure efficient transfer of growing intermediates along the assembly line. This work is leading towards more effective re-programming of these enzymes for use in synthesis of new medicinal compounds.
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Affiliation(s)
- Patrick Caffrey
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
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20
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Piasecki SK, Taylor CA, Detelich JF, Liu J, Zheng J, Komsoukaniants A, Siegel DR, Keatinge-Clay AT. Employing modular polyketide synthase ketoreductases as biocatalysts in the preparative chemoenzymatic syntheses of diketide chiral building blocks. ACTA ACUST UNITED AC 2012; 18:1331-40. [PMID: 22035802 DOI: 10.1016/j.chembiol.2011.07.021] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 07/18/2011] [Accepted: 07/19/2011] [Indexed: 11/19/2022]
Abstract
Chiral building blocks are valuable intermediates in the syntheses of natural products and pharmaceuticals. A scalable chemoenzymatic route to chiral diketides has been developed that includes the general synthesis of α-substituted, β-ketoacyl N-acetylcysteamine thioesters followed by a biocatalytic cycle in which a glucose-fueled NADPH-regeneration system drives reductions catalyzed by isolated modular polyketide synthase (PKS) ketoreductases (KRs). To identify KRs that operate as active, stereospecific biocatalysts, 11 isolated KRs were incubated with 5 diketides and their products were analyzed by chiral chromatography. KRs that naturally reduce small polyketide intermediates were the most active and stereospecific toward the panel of diketides. Several biocatalytic reactions were scaled up to yield more than 100 mg of product. These syntheses demonstrate the ability of PKS enzymes to economically and greenly generate diverse chiral building blocks on a preparative scale.
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Affiliation(s)
- Shawn K Piasecki
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
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21
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Javidpour P, Korman TP, Shakya G, Tsai SC. Structural and biochemical analyses of regio- and stereospecificities observed in a type II polyketide ketoreductase. Biochemistry 2011; 50:4638-49. [PMID: 21506596 DOI: 10.1021/bi200335f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Type II polyketides include antibiotics such as tetracycline and chemotherapeutics such as daunorubicin. Type II polyketides are biosynthesized by the type II polyketide synthase (PKS) that consists of 5-10 stand-alone domains. In many type II PKSs, the type II ketoreductase (KR) specifically reduces the C9-carbonyl group. How the type II KR achieves such a high regiospecificity and the nature of stereospecificity are not well understood. Sequence alignment of KRs led to a hypothesis that a well-conserved 94-XGG-96 motif may be involved in controlling the stereochemistry. The stereospecificity of single-, double-, and triple-mutant combinations of P94L, G95D, and G96D were analyzed in vitro and in vivo for the actinorhodin KR (actKR). The P94L mutation is sufficient to change the stereospecificity of actKR. Binary and ternary crystal structures of both wild-type and P94L actKR were determined. Together with assay results, docking simulations, and cocrystal structures, a model for stereochemical control is presented herein that elucidates how type II polyketides are introduced into the substrate pocket such that the C9-carbonyl can be reduced with high regio- and stereospecificities. The molecular features of actKR important for regio- and stereospecificities can potentially be applied in biosynthesizing new polyketides via protein engineering that rationally controls polyketide keto reduction.
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Affiliation(s)
- Pouya Javidpour
- Department of Molecular Biology and Biochemistry, University of California-Irvine, CA 92697, USA
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22
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Kwan DH, Tosin M, Schläger N, Schulz F, Leadlay PF. Insights into the stereospecificity of ketoreduction in a modular polyketide synthase. Org Biomol Chem 2011; 9:2053-6. [DOI: 10.1039/c1ob00022e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Valenzano CR, Lawson RJ, Chen AY, Khosla C, Cane DE. The biochemical basis for stereochemical control in polyketide biosynthesis. J Am Chem Soc 2009; 131:18501-11. [PMID: 19928853 PMCID: PMC3699857 DOI: 10.1021/ja908296m] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One of the most striking features of complex polyketides is the presence of numerous methyl- and hydroxyl-bearing stereogenic centers. To investigate the biochemical basis for the control of polyketide stereochemistry and to establish the timing and mechanism of the epimerization at methyl-bearing centers, a series of incubations was carried out using reconstituted components from a variety of modular polyketide synthases. In all cases the stereochemistry of the product was directly correlated with the intrinsic stereospecificity of the ketoreductase domain, independent of the particular chain elongation domains that were used, thereby establishing that methyl group epimerization, when it does occur, takes place after ketosynthase-catalyzed chain elongation. The finding that there were only minor differences in the rates of product formation observed for parallel incubations using an epimerizing ketoreductase domain and the nonepimerizing ketoreductase domain supports the proposal that the epimerization is catalyzed by the ketoreductase domain itself.
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Affiliation(s)
- Chiara R. Valenzano
- Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108
| | - Rachel J. Lawson
- Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108
| | - Alice Y. Chen
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
| | - Chaitan Khosla
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
- Department of Chemistry, Stanford University, Stanford, California 94305
- Department of Biochemistry, Stanford University, Stanford, California 94305
| | - David E. Cane
- Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108
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24
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Chen AY, Cane DE, Khosla C. Structure-based dissociation of a type I polyketide synthase module. ACTA ACUST UNITED AC 2007; 14:784-92. [PMID: 17656315 PMCID: PMC1978548 DOI: 10.1016/j.chembiol.2007.05.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 05/23/2007] [Accepted: 05/31/2007] [Indexed: 11/25/2022]
Abstract
Individual modules of modular polyketide synthases (PKSs) such as 6-deoxyerythronolide B synthase (DEBS) consist of conserved, covalently linked domains separated by unconserved intervening linker sequences. To better understand the protein-protein and enzyme-substrate interactions in modular catalysis, we have exploited recent structural insights to prepare stand-alone domains of selected DEBS modules. When combined in vitro, ketosynthase (KS), acyl transferase (AT), and acyl carrier protein (ACP) domains of DEBS module 3 catalyzed methylmalonyl transfer and diketide substrate elongation. When added to a minimal PKS, ketoreductase domains from DEBS modules 1, 2, and 6 showed specificity for the beta-ketoacylthioester substrate, but not for either the ACP domain carrying the polyketide substrate or the KS domain that synthesized the substrate. With insights into catalytic efficiency and specificity of PKS modules, our results provide guidelines for constructing optimal hybrid PKS systems.
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Affiliation(s)
- Alice Y. Chen
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
| | - David E. Cane
- Department of Chemistry, Brown University, Providence RI 02912-9108
| | - Chaitan Khosla
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Department of Biochemistry, Stanford University, Stanford, CA 94305
- To whom correspondence should be addressed. E-mail:
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25
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Castonguay R, He W, Chen AY, Khosla C, Cane DE. Stereospecificity of ketoreductase domains of the 6-deoxyerythronolide B synthase. J Am Chem Soc 2007; 129:13758-69. [PMID: 17918944 PMCID: PMC2547127 DOI: 10.1021/ja0753290] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
6-Deoxyerythronolide B synthase (DEBS) is a modular polyketide synthase (PKS) responsible for the biosynthesis of 6-dEB (1), the parent aglycone of the broad spectrum macrolide antibiotic erythromycin. Individual DEBS modules, which contain the catalytic domains necessary for each step of polyketide chain elongation and chemical modification, can be deconstructed into constituent domains. To better understand the intrinsic stereospecificity of the ketoreductase (KR) domains, an in vitro reconstituted system has been developed involving combinations of ketosynthase (KS)-acyl transferase (AT) didomains with acyl-carrier protein (ACP) and KR domains from different DEBS modules. Incubations with (2S,3R)-2-methyl-3-hydroxypentanoic acid N-acetylcysteamine thioester (2) and methylmalonyl-CoA plus NADPH result in formation of a reduced, ACP-bound triketide that is converted to the corresponding triketide lactone 4 by either base- or enzyme-catalyzed hydrolysis/cyclization. A sensitive and robust GC-MS technique has been developed to assign the stereochemistry of the resulting triketide lactones, on the basis of direct comparison with synthetic standards of each of the four possible diasteromers 4a-4d. Using the [KS][AT] didomains from either DEBS module 3 or module 6 in combination with KR domains from modules 2 or 6 gave in all cases exclusively (2R,3S,4R,5R)-3,5-dihydroxy-2,4-dimethyl-n-heptanoic acid-delta-lactone (4a). The same product was also generated by a chimeric module in which [KS3][AT3] was fused to [KR5][ACP5] and the DEBS thioesterase [TE] domain. Reductive quenching of the ACP-bound 2-methyl-3-ketoacyl triketide intermediate with sodium borohydride confirmed that in each case the triketide intermediate carried only an unepimerized d-2-methyl group. The results confirm the predicted stereospecificity of the individual KR domains, while revealing an unexpected configurational stability of the ACP-bound 2-methyl-3-ketoacyl thioester intermediate. The methodology should be applicable to the study of any combination of heterologous [KS][AT] and [KR] domains.
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Affiliation(s)
- Roselyne Castonguay
- Contribution from the Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108
| | - Weiguo He
- Contribution from the Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108
| | - Alice Y. Chen
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
| | - Chaitan Khosla
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
- Department of Chemistry, Stanford University, Stanford, California 94305
- Department of Biochemistry, Stanford University, Stanford, California 94305
| | - David E. Cane
- Contribution from the Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108
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26
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Abstract
6-Deoxyerythronolide B, the macrocyclic aglycone of the antibiotic erythromycin, is synthesized by a polyketide synthase (PKS) that has emerged as the prototypical modular megasynthase. A variety of molecular biological, protein chemical, and biosynthetic experiments over the past two decades have yielded insights into its mechanistic features. More recently, high-resolution structural images of portions of the 6-deoxyerythronolide B synthase have provided a platform for interpreting this wealth of biochemical data, while at the same time presenting a fundamentally new basis for the design of more detailed investigations into this remarkable enzyme. For example, the critical roles of domain-domain interactions and nonconserved linkers, as well as large interdomain movements in the structure and function of modular PKSs, have been highlighted. In turn, these insights point the way forward for more sophisticated and efficient biosynthetic engineering of complex polyketide natural products.
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Affiliation(s)
- Chaitan Khosla
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA.
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27
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Bali S, Weissman KJ. Ketoreduction in mycolactone biosynthesis: insight into substrate specificity and stereocontrol from studies of discrete ketoreductase domains in vitro. Chembiochem 2007; 7:1935-42. [PMID: 17031885 DOI: 10.1002/cbic.200600285] [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
Mycolactone, a polyketide toxin responsible for the extensive tissue destruction seen in Buruli ulcer, is assembled on a modular polyketide synthase (PKS). Despite operating on structurally different intermediates during synthesis, many of the ketoreductase (KR) domains of the mycolactone (MLS) PKS have identical sequences. This suggests that these enzymes might exhibit an unusually high level of substrate promiscuity. However, we show here that when recombinant mycolactone KR domains are tested with a range of surrogate substrates, their specificity closely matches that of KR domains derived from other PKS systems. In addition, our findings reinforce the role of substrate tethering for achieving stereochemical control in modular PKSs by affecting the delicate energetics of ketoreduction.
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Affiliation(s)
- Shilpa Bali
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
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29
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Weissman KJ. Single Amino Acid Substitutions Alter the Efficiency of Docking in Modular Polyketide Biosynthesis. Chembiochem 2006; 7:1334-42. [PMID: 16871615 DOI: 10.1002/cbic.200600185] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kira J Weissman
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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