1
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Drufva EE, Spengler NR, Hix EG, Bailey CB. Site-Directed Mutagenesis of Modular Polyketide Synthase Ketoreductase Domains for Altered Stereochemical Control. Chembiochem 2020; 22:1122-1150. [PMID: 33185924 DOI: 10.1002/cbic.202000613] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/12/2020] [Indexed: 12/18/2022]
Abstract
Bacterial modular type I polyketide synthases (PKSs) are complex multidomain assembly line proteins that produce a range of pharmaceutically relevant molecules with a high degree of stereochemical control. Due to their colinear properties, they have been considerable targets for rational biosynthetic pathway engineering. Among the domains harbored within these complex assembly lines, ketoreductase (KR) domains have been extensively studied with the goal of altering their stereoselectivity by site-directed mutagenesis, as they confer much of the stereochemical complexity present in pharmaceutically active reduced polyketide scaffolds. Here we review all efforts to date to perform site-directed mutagenesis on PKS KRs, most of which have been done in the context of excised KR domains on model diffusible substrates such as β-keto N-acetyl cysteamine thioesters. We also discuss the challenges around translating the findings of these studies to alter stereocontrol in the context of a complex multidomain enzymatic assembly line.
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Affiliation(s)
- Erin E Drufva
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
| | - Nolan R Spengler
- 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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2
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Kalkreuter E, CroweTipton JM, Lowell AN, Sherman DH, Williams GJ. Engineering the Substrate Specificity of a Modular Polyketide Synthase for Installation of Consecutive Non-Natural Extender Units. J Am Chem Soc 2019; 141:1961-1969. [PMID: 30676722 DOI: 10.1021/jacs.8b10521] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There is significant interest in diversifying the structures of polyketides to create new analogues of these bioactive molecules. This has traditionally been done by focusing on engineering the acyltransferase (AT) domains of polyketide synthases (PKSs) responsible for the incorporation of malonyl-CoA extender units. Non-natural extender units have been utilized by engineered PKSs previously; however, most of the work to date has been accomplished with ATs that are either naturally promiscuous and/or located in terminal modules lacking downstream bottlenecks. These limitations have prevented the engineering of ATs with low native promiscuity and the study of any potential gatekeeping effects by domains downstream of an engineered AT. In an effort to address this gap in PKS engineering knowledge, the substrate preferences of the final two modules of the pikromycin PKS were compared for several non-natural extender units and through active site mutagenesis. This led to engineering of the methylmalonyl-CoA specificity of both modules and inversion of their selectivity to prefer consecutive non-natural derivatives. Analysis of the product distributions of these bimodular reactions revealed unexpected metabolites resulting from gatekeeping by the downstream ketoreductase and ketosynthase domains. Despite these new bottlenecks, AT engineering provided the first full-length polyketide products incorporating two non-natural extender units. Together, this combination of tandem AT engineering and the identification of previously poorly characterized bottlenecks provides a platform for future advancements in the field.
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Affiliation(s)
- Edward Kalkreuter
- Department of Chemistry , NC State University , Raleigh , North Carolina 27695 , United States.,Comparative Medicine Institute , NC State University , Raleigh , North Carolina 27695 , United States
| | - Jared M CroweTipton
- Department of Chemistry , NC State University , Raleigh , North Carolina 27695 , United States
| | - Andrew N Lowell
- Life Sciences Institute, Department of Medicinal Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - David H Sherman
- Life Sciences Institute, Department of Medicinal Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Chemistry and Department of Microbiology & Immunology , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Gavin J Williams
- Department of Chemistry , NC State University , Raleigh , North Carolina 27695 , United States.,Comparative Medicine Institute , NC State University , Raleigh , North Carolina 27695 , United States
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3
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Moretto L, Vance S, Heames B, Broadhurst RW. Dissecting how modular polyketide synthase ketoreductases interact with acyl carrier protein-attached substrates. Chem Commun (Camb) 2017; 53:11457-11460. [PMID: 28980673 PMCID: PMC6038798 DOI: 10.1039/c7cc04625a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 06/29/2017] [Indexed: 11/21/2022]
Abstract
Interaction studies using fragments excised from the modular mycolactone polyketide synthase show that ketoreductase domains possess a generic binding site for acyl carrier protein domains and provide evidence that the pendant 5'-phosphopantetheine prosthetic group plays a key role in delivering acyl substrates to the active site in the correct orientation.
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Affiliation(s)
- Luisa Moretto
- Department of Molecular Biosciences
, The University of Texas at Austin
,
Austin
, TX 78712
, USA
| | - Steven Vance
- Crescendo Biologics Ltd
,
Meditrina Building 260
, Babraham Research Campus
, Cambridge CB22 3AT
, UK
| | - Brennan Heames
- Department of Biochemistry
, University of Cambridge
,
80 Tennis Court Road
, Cambridge CB2 1GA
, UK
.
| | - R. William Broadhurst
- Department of Biochemistry
, University of Cambridge
,
80 Tennis Court Road
, Cambridge CB2 1GA
, UK
.
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4
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Weissman KJ. Polyketide stereocontrol: a study in chemical biology. Beilstein J Org Chem 2017; 13:348-371. [PMID: 28326145 PMCID: PMC5331325 DOI: 10.3762/bjoc.13.39] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/01/2017] [Indexed: 11/23/2022] Open
Abstract
The biosynthesis of reduced polyketides in bacteria by modular polyketide synthases (PKSs) proceeds with exquisite stereocontrol. As the stereochemistry is intimately linked to the strong bioactivity of these molecules, the origins of stereochemical control are of significant interest in attempts to create derivatives of these compounds by genetic engineering. In this review, we discuss the current state of knowledge regarding this key aspect of the biosynthetic pathways. Given that much of this information has been obtained using chemical biology tools, work in this area serves as a showcase for the power of this approach to provide answers to fundamental biological questions.
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Affiliation(s)
- Kira J Weissman
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, Avenue de la Forêt de Haye, BP 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
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5
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Xie X, Garg A, Khosla C, Cane DE. Mechanism and Stereochemistry of Polyketide Chain Elongation and Methyl Group Epimerization in Polyether Biosynthesis. J Am Chem Soc 2017; 139:3283-3292. [PMID: 28157306 DOI: 10.1021/jacs.7b00278] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The polyketide synthases responsible for the biosynthesis of the polyether antibiotics nanchangmycin (1) and salinomycin (4) harbor a number of redox-inactive ketoreductase (KR0) domains that are implicated in the generation of C2-epimerized (2S)-2-methyl-3-ketoacyl-ACP intermediates. Evidence that the natural substrate for the polyether KR0 domains is, as predicted, a (2R)-2-methyl-3-ketoacyl-ACP intermediate, came from a newly developed coupled ketosynthase (KS)-ketoreductase (KR) assay that established that the decarboxylative condensation of methylmalonyl-CoA with S-propionyl-N-acetylcysteamine catalyzed by the Nan[KS1][AT1] didomain from module 1 of the nanchangmycin synthase generates exclusively the corresponding (2R)-2-methyl-3-ketopentanoyl-ACP (7a) product. In tandem equilibrium isotope exchange experiments, incubation of [2-2H]-(2R,3S)-2-methyl-3-hydroxypentanoyl-ACP (6a) with redox-active, epimerase-inactive EryKR6 from module 6 of the 6-deoxyerythronolide B synthase and catalytic quantities of NADP+ in the presence of redox-inactive, recombinant NanKR10 or NanKR50, from modules 1 and 5 of the nanchangmycin synthase, or recombinant SalKR70 from module 7 of the salinomycin synthase, resulted in first-order, time-dependent washout of deuterium from 6a. Control experiments confirmed that this washout was due to KR0-catalyzed isotope exchange of the reversibly generated, transiently formed oxidation product [2-2H]-(2R)-2-methyl-3-ketopentanoyl-ACP (7a), consistent with the proposed epimerase activity of each of the KR0 domains. Although they belong to the superfamily of short chain dehydrogenase-reductases, the epimerase-active KR0 domains from polyether synthases lack one or both residues of the conserved Tyr-Ser dyad that has previously been implicated in KR-catalyzed epimerizations.
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Affiliation(s)
- Xinqiang Xie
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
| | - Ashish Garg
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
| | - Chaitan Khosla
- Departments of Chemical Engineering, Chemistry, and Biochemistry, Stanford University , Stanford, California 94305, United States
| | - David E Cane
- Department of Chemistry, Brown University , Box H, Providence, Rhode Island 02912-9108, United States
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6
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Liddle E, Scott A, Han LC, Ivison D, Simpson TJ, Willis CL, Cox RJ. In vitro kinetic study of the squalestatin tetraketide synthase dehydratase reveals the stereochemical course of a fungal highly reducing polyketide synthase. Chem Commun (Camb) 2017; 53:1727-1730. [PMID: 28106181 DOI: 10.1039/c6cc10172k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Six potential diketide substrates for the squalestatin tetraketide synthase (SQTKS) dehydratase (DH) domain were synthesised as N-acetyl cysteamine thiolesters (SNAC) and tested in kinetic assays as substrates with an isolated DH domain. 3R-3-hydroxybutyryl SNAC 3R-16 was turned over by the enzyme, but its enantiomer was not. Of the four 2-methyl substrates only 2R,3R-2-methyl-3-hydroxybutyryl SNAC 2R,3R-8 was a substrate. Combined with stereochemical information from the isolated SQTKS enoyl reductase (ER) domain, our results provide a near complete stereochemical description of the first cycle of beta-modification reactions of a fungal highly reducing polyketide synthase (HR-PKS). The results emphasise the close relationship between fungal HR-PKS and vertebrate fatty acid synthases (vFAS).
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Affiliation(s)
- Emma Liddle
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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7
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Essig S, Schmalzbauer B, Bretzke S, Scherer O, Koeberle A, Werz O, Müller R, Menche D. Predictive Bioinformatic Assignment of Methyl-Bearing Stereocenters, Total Synthesis, and an Additional Molecular Target of Ajudazol B. J Org Chem 2016; 81:1333-57. [DOI: 10.1021/acs.joc.5b02844] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Sebastian Essig
- Institut
für Organische Chemie, Ruprecht-Karls Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Björn Schmalzbauer
- Kekulé-Institut
für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Sebastian Bretzke
- Institut
für Organische Chemie, Ruprecht-Karls Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Olga Scherer
- Institute
of Pharmacy, Friedrich Schiller Universität Jena, Philosophenweg
14, 07743 Jena, Germany
| | - Andreas Koeberle
- Institute
of Pharmacy, Friedrich Schiller Universität Jena, Philosophenweg
14, 07743 Jena, Germany
| | - Oliver Werz
- Institute
of Pharmacy, Friedrich Schiller Universität Jena, Philosophenweg
14, 07743 Jena, Germany
| | - Rolf Müller
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS) and Institut
for Pharmaceutical Biotechnology, Universität des Saarlandes, C 2.3, 66123 Saarbrücken, Germany
| | - Dirk Menche
- Kekulé-Institut
für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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8
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The structural biology of biosynthetic megaenzymes. Nat Chem Biol 2015; 11:660-70. [PMID: 26284673 DOI: 10.1038/nchembio.1883] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/02/2015] [Indexed: 01/27/2023]
Abstract
The modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) are among the largest and most complicated enzymes in nature. In these biosynthetic systems, independently folding protein domains, which are organized into units called 'modules', operate in assembly-line fashion to construct polymeric chains and tailor their functionalities. Products of PKSs and NRPSs include a number of blockbuster medicines, and this has motivated researchers to understand how they operate so that they can be modified by genetic engineering. Beginning in the 1990s, structural biology has provided a number of key insights. The emerging picture is one of remarkable dynamics and conformational programming in which the chemical states of individual catalytic domains are communicated to the others, configuring the modules for the next stage in the biosynthesis. This unexpected level of complexity most likely accounts for the low success rate of empirical genetic engineering experiments and suggests ways forward for productive megaenzyme synthetic biology.
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9
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Annaval T, Paris C, Leadlay PF, Jacob C, Weissman KJ. Evaluating Ketoreductase Exchanges as a Means of Rationally Altering Polyketide Stereochemistry. Chembiochem 2015; 16:1357-64. [DOI: 10.1002/cbic.201500113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Indexed: 12/22/2022]
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10
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Garg A, Khosla C, Cane DE. Coupled methyl group epimerization and reduction by polyketide synthase ketoreductase domains. Ketoreductase-catalyzed equilibrium isotope exchange. J Am Chem Soc 2013; 135:16324-7. [PMID: 24161343 DOI: 10.1021/ja408944s] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Incubation of [2-(2)H]-(2S,3R)-2-methyl-3-hydroxypentanoyl-SACP ([2-(2)H]-1a) with the epimerizing ketoreductase domain EryKR1 in the presence of a catalytic amount NADP(+) (0.05 equiv) resulted in time- and cofactor-dependent washout of deuterium from 1a, as a result of equilibrium isotope exchange of transiently generated [2-(2)H]-2-methyl-3-ketopentanoyl-ACP. Incubations of [2-(2)H]-(2S,3S)-2-methyl-3-hydroxy-pentanoyl-SACP with RifKR7 and with NysKR1 also resulted in time-dependent loss of deuterium. By contrast, incubations of [2-(2)H]-(2R,3S)-2-methyl-3-hydroxypentanoyl-SACP and [2-(2)H]-(2R,3R)-2-methyl-3-hydroxypentanoyl-SACP with the non-epimerizing ketoreductase domains EryKR6 and TylKR1, respectively, did not result in any significant washout of deuterium. The isotope exchange assay directly establishes that specific polyketide synthase ketoreductase domains also have an intrinsic epimerase activity, thus enabling mechanistic analysis of a key determinant of polyketide stereocomplexity.
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Affiliation(s)
- Ashish Garg
- Department of Chemistry, Brown University , Providence, Rhode Island 02912-9108, United States
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11
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Javidpour P, Bruegger J, Srithahan S, Korman TP, Crump MP, Crosby J, Burkart MD, Tsai SC. The determinants of activity and specificity in actinorhodin type II polyketide ketoreductase. ACTA ACUST UNITED AC 2013; 20:1225-34. [PMID: 24035284 DOI: 10.1016/j.chembiol.2013.07.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 06/28/2013] [Accepted: 07/07/2013] [Indexed: 11/17/2022]
Abstract
In the actinorhodin type II polyketide synthase, the first polyketide modification is a regiospecific C9-carbonyl reduction, catalyzed by the ketoreductase (actKR). Our previous studies identified the actKR 94-PGG-96 motif as a determinant of stereospecificity. The molecular basis for reduction regiospecificity is, however, not well understood. In this study, we examined the activities of 20 actKR mutants through a combination of kinetic studies, PKS reconstitution, and structural analyses. Residues have been identified that are necessary for substrate interaction, and these observations have suggested a structural model for this reaction. Polyketides dock at the KR surface and are steered into the enzyme pocket where C7-C12 cyclization is mediated by the KR before C9-ketoreduction can occur. These molecular features can potentially serve as engineering targets for the biosynthesis of novel, reduced polyketides.
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Affiliation(s)
- Pouya Javidpour
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
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12
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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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13
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Kwan DH, Schulz F. The stereochemistry of complex polyketide biosynthesis by modular polyketide synthases. Molecules 2011; 16:6092-115. [PMID: 21775938 PMCID: PMC6264292 DOI: 10.3390/molecules16076092] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 07/06/2011] [Accepted: 07/18/2011] [Indexed: 11/24/2022] Open
Abstract
Polyketides are a diverse class of medically important natural products whose biosynthesis is catalysed by polyketide synthases (PKSs), in a fashion highly analogous to fatty acid biosynthesis. In modular PKSs, the polyketide chain is assembled by the successive condensation of activated carboxylic acid-derived units, where chain extension occurs with the intermediates remaining covalently bound to the enzyme, with the growing polyketide tethered to an acyl carrier domain (ACP). Carboxylated acyl-CoA precursors serve as activated donors that are selected by the acyltransferase domain (AT) providing extender units that are added to the growing chain by condensation catalysed by the ketosynthase domain (KS). The action of ketoreductase (KR), dehydratase (DH), and enoylreductase (ER) activities can result in unreduced, partially reduced, or fully reduced centres within the polyketide chain depending on which of these enzymes are present and active. The PKS-catalysed assembly process generates stereochemical diversity, because carbon–carbon double bonds may have either cis- or trans- geometry, and because of the chirality of centres bearing hydroxyl groups (where they are retained) and branching methyl groups (the latter arising from use of propionate extender units). This review shall cover the studies that have determined the stereochemistry in many of the reactions involved in polyketide biosynthesis by modular PKSs.
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Affiliation(s)
- David H. Kwan
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver B.C., V6T 1Z1, Canada
- Authors to whom correspondence should be addressed; (D.H.K.); (F.S.); Tel.: +1-604-822-9300 (D.H.K.); +49-231-133-2429 (F.S.); Fax: +1-604-822-9126 (D.H.K.); +49-231-133-2498 (F.S.)
| | - Frank Schulz
- Fakultät für Chemie, Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
- Max-Planck-Institut für Molekulare Physiologie, Abteilung für Chemische Biologie, Otto-Hahn- Straße 11, 44227 Dortmund, Germany
- Authors to whom correspondence should be addressed; (D.H.K.); (F.S.); Tel.: +1-604-822-9300 (D.H.K.); +49-231-133-2429 (F.S.); Fax: +1-604-822-9126 (D.H.K.); +49-231-133-2498 (F.S.)
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14
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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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15
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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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16
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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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17
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Hong H, Leadlay PF, Staunton J. The changing patterns of covalent active site occupancy during catalysis on a modular polyketide synthase multienzyme revealed by ion-trap mass spectrometry. FEBS J 2009; 276:7057-69. [PMID: 19860832 DOI: 10.1111/j.1742-4658.2009.07418.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A catalytically competent, homodimeric diketide synthase comprising the first extension module of the erythromycin polyketide synthase was analysed using MS, after limited proteolysis to release functional domains, to determine the pattern of covalent attachment of substrates and intermediates to active sites during catalysis. Using the natural substrates, the acyltransferase and acylcarrier protein of the loading module were found to be heavily loaded with propionyl starter groups, while the ketosynthase was fully propionylated. The acylcarrier protein of the extension module was partly occupied by the product diketide, and the adjacent chain-releasing thioesterase domain was vacant, implying that the rate-limiting step is transfer of the diketide from the acylcarrier protein to the thioesterase domain. The data suggest an attractive model for preventing iterative chain extension by efficient repriming of the ketosynthase domain after condensation. Use of the alternative starter unit valeryl-CoA produced an altered pattern, in which a significant proportion of the extension acylcarrier protein was loaded with methylmalonate, not diketide, consistent with the condensation step having become an additional slow step. Strikingly, when NADPH was omitted, the extension acylcarrier protein contained methylmalonate and none of the expected keto diketide, in contrast to results obtained previously by mixing individual recombinant domains, showing the importance of also studying intact modules. The detailed patterns of loading of the extension acylcarrier protein (of which there are two in the homodimer) also provided the first evidence for simultaneous loading of both acylcarrier proteins and for the coordination of timing between the two active centres for chain extension.
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Affiliation(s)
- Hui Hong
- Department of Chemistry, University of Cambridge, UK.
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18
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Kellenberger L, Galloway IS, Sauter G, Böhm G, Hanefeld U, Cortés J, Staunton J, Leadlay PF. A polylinker approach to reductive loop swaps in modular polyketide synthases. Chembiochem 2009; 9:2740-9. [PMID: 18937219 DOI: 10.1002/cbic.200800332] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Multiple versions of the DEBS 1-TE gene, which encodes a truncated bimodular polyketide synthase (PKS) derived from the erythromycin-producing PKS, were created by replacing the DNA encoding the ketoreductase (KR) domain in the second extension module by either of two synthetic oligonucleotide linkers. This made available a total of nine unique restriction sites for engineering. The DNA for donor "reductive loops," which are sets of contiguous domains comprising either KR or KR and dehydratase (DH), or KR, DH and enoylreductase (ER) domains, was cloned from selected modules of five natural PKS multienzymes and spliced into module 2 of DEBS 1-TE using alternative polylinker sites. The resulting hybrid PKSs were tested for triketide production in vivo. Most of the hybrid multienzymes were active, vindicating the treatment of the reductive loop as a single structural unit, but yields were dependent on the restriction sites used. Further, different donor reductive loops worked optimally with different splice sites. For those reductive loops comprising DH, ER and KR domains, premature TE-catalysed release of partially reduced intermediates was sometimes seen, which provided further insight into the overall stereochemistry of reduction in those modules. Analysis of loops containing KR only, which should generate stereocentres at both C-2 and C-3, revealed that the 3-hydroxy configuration (but not the 2-methyl configuration) could be altered by appropriate choice of a donor loop. The successful swapping of reductive loops provides an interesting parallel to a recently suggested pathway for the natural evolution of modular PKSs by recombination.
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Affiliation(s)
- Laurenz Kellenberger
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB21GA, United Kingdom
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19
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Korman TP, Tan YH, Wong J, Luo R, Tsai SC. Inhibition kinetics and emodin cocrystal structure of a type II polyketide ketoreductase. Biochemistry 2008; 47:1837-47. [PMID: 18205400 DOI: 10.1021/bi7016427] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Type II polyketides are a class of natural products that include pharmaceutically important aromatic compounds such as the antibiotic tetracycline and antitumor compound doxorubicin. The type II polyketide synthase (PKS) is a complex consisting of 5-10 standalone domains homologous to fatty acid synthase (FAS). Polyketide ketoreductase (KR) provides regio- and stereochemical diversity during the reduction. How the type II polyketide KR specifically reduces only the C9 carbonyl group is not well understood. The cocrystal structures of actinorhodin polyketide ketoreductase (actKR) bound with NADPH or NADP+ and the inhibitor emodin were solved with the wild type and P94L mutant of actKR, revealing the first observation of a bent p-quinone in an enzyme active site. Molecular dynamics simulation help explain the origin of the bent geometry. Extensive screening for in vitro substrates shows that unlike FAS KR, the actKR prefers bicyclic substrates. Inhibition kinetics indicate that actKR follows an ordered Bi Bi mechanism. Together with docking simulations that identified a potential phosphopantetheine binding groove, the structural and functional studies reveal that the C9 specificity is a result of active site geometry and substrate ring constraints. The results lay the foundation for the design of novel aromatic polyketide natural products with different reduction patterns.
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Affiliation(s)
- Tyler Paz Korman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
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20
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Sattely ES, Fischbach MA, Walsh CT. Total biosynthesis: in vitro reconstitution of polyketide and nonribosomal peptide pathways. Nat Prod Rep 2008; 25:757-93. [DOI: 10.1039/b801747f] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Keatinge-Clay AT. A tylosin ketoreductase reveals how chirality is determined in polyketides. ACTA ACUST UNITED AC 2007; 14:898-908. [PMID: 17719489 DOI: 10.1016/j.chembiol.2007.07.009] [Citation(s) in RCA: 233] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2007] [Revised: 06/09/2007] [Accepted: 07/09/2007] [Indexed: 10/22/2022]
Abstract
Because it controls the majority of polyketide stereocenters, the ketoreductase (KR) is a central target in engineering polyketide synthases (PKSs). To elucidate the mechanisms of stereocontrol, the structure of KR from the first module of the tylosin PKS was determined. A comparison with a recently solved erythromycin KR that operates on the same substrate explains why their products have opposite alpha-substituent chiralities. The structure reveals how polyketides are guided into the active site by key residues in different KR types. There are four types of reductase-competent KRs, each capable of fixing a unique combination of alpha-substituent and beta-hydroxyl group chiralities, as well as two types of reductase-incompetent KRs that control alpha-substituent chirality alone. A protocol to assign how a module will enforce substituent chirality based on its sequence is presented.
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Affiliation(s)
- Adrian T Keatinge-Clay
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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22
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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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23
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Abstract
This review chronicles the synergistic growth of the fields of fatty acid and polyketide synthesis over the last century. In both animal fatty acid synthases and modular polyketide synthases, similar catalytic elements are covalently linked in the same order in megasynthases. Whereas in fatty acid synthases the basic elements of the design remain immutable, guaranteeing the faithful production of saturated fatty acids, in the modular polyketide synthases, the potential of the basic design has been exploited to the full for the elaboration of a wide range of secondary metabolites of extraordinary structural diversity.
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Affiliation(s)
- Stuart Smith
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, California 94609, USA.
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24
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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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25
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Starcevic A, Jaspars M, Cullum J, Hranueli D, Long PF. Predicting the nature and timing of epimerisation on a modular polyketide synthase. Chembiochem 2007; 8:28-31. [PMID: 17133646 DOI: 10.1002/cbic.200600399] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Antonio Starcevic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
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26
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Alhamadsheh MM, Palaniappan N, DasChouduri S, Reynolds KA. Modular polyketide synthases and cis double bond formation: establishment of activated cis-3-cyclohexylpropenoic acid as the diketide intermediate in phoslactomycin biosynthesis. J Am Chem Soc 2007; 129:1910-1. [PMID: 17256943 PMCID: PMC2553709 DOI: 10.1021/ja068818t] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - Kevin A. Reynolds
- Department of Chemistry, Portland State University, Portland, OR 97207
- E-mail:
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27
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Sudek S, Lopanik NB, Waggoner LE, Hildebrand M, Anderson C, Liu H, Patel A, Sherman DH, Haygood MG. Identification of the putative bryostatin polyketide synthase gene cluster from "Candidatus Endobugula sertula", the uncultivated microbial symbiont of the marine bryozoan Bugula neritina. JOURNAL OF NATURAL PRODUCTS 2007; 70:67-74. [PMID: 17253852 DOI: 10.1021/np060361d] [Citation(s) in RCA: 206] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The bryostatins are protein kinase C modulators with unique structural features and potential anticancer and neurological activities. These complex polyketides were isolated from the marine bryozoan Bugula neritina, but recent studies indicate that they are produced by the uncultured symbiotic bacterium "Candidatus Endobugula sertula" ("E. sertula"). Here we present the putative biosynthetic genes: five modular polyketide synthase (PKS) genes, a discrete acyltransferase, a beta-ketosynthase, a hydroxy-methyl-glutaryl CoA synthase (HMG-CS), and a methyltransferase. The cluster was sequenced in two closely related "E. sertula" strains from different host species. In one strain the gene cluster is contiguous, while in the other strain it is split into two loci, with one locus containing the PKS genes and the other containing the accessory genes. Here, we propose a hypothesis for the biosynthesis of the bryostatins. Thirteen PKS modules form the core macrolactone ring, and the pendent methyl ester groups are added by the HMG-CS gene cassette. The resulting hypothetical compound bryostatin 0 is the common basis for the 20 known bryostatins. As "E. sertula" is to date uncultured, heterologous expression of this biosynthetic gene cluster has the potential of producing the bioactive bryostatins in large enough quantities for development into a pharmaceutical.
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Affiliation(s)
- Sebastian Sudek
- Scripps Institution of Oceanography, Marine Biology Research Division, and Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, California 92093-0202, USA
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28
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Baerga-Ortiz A, Popovic B, Siskos AP, O'Hare HM, Spiteller D, Williams MG, Campillo N, Spencer JB, Leadlay PF. Directed Mutagenesis Alters the Stereochemistry of Catalysis by Isolated Ketoreductase Domains from the Erythromycin Polyketide Synthase. ACTA ACUST UNITED AC 2006; 13:277-85. [PMID: 16638533 DOI: 10.1016/j.chembiol.2006.01.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Revised: 01/10/2006] [Accepted: 01/10/2006] [Indexed: 11/18/2022]
Abstract
The ketoreductase (KR) domains eryKR(1) and eryKR(2) from the erythromycin-producing polyketide synthase (PKS) reduce 3-ketoacyl-thioester intermediates with opposite stereospecificity. Modeling of eryKR(1) and eryKR(2) showed that conserved amino acids previously correlated with production of alternative alcohol configurations lie in the active site. eryKR(1) domains mutated at these positions showed an altered stereochemical outcome in reduction of (2R, S)-2-methyl-3-oxopentanoic acid N-acetylcysteamine thioester. The wild-type eryKR(1) domain exclusively gave the (2S, 3R)-3-hydroxy-2-methylpentanoic acid N-acetylcysteamine thioester, while the double mutant (F141W, P144G) gave only the (2S, 3S) isomer, a switch of the alcohol stereochemistry. Mutation of the eryKR(2) domain, in contrast, greatly increased the proportion of the wild-type (2R, 3S)-alcohol product. These data confirm the role of key residues in stereocontrol and suggest an additional way to make rational alterations in polyketide antibiotic structure.
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Affiliation(s)
- Abel Baerga-Ortiz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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29
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O'Hare HM, Baerga-Ortiz A, Popovic B, Spencer JB, Leadlay PF. High-Throughput Mutagenesis to Evaluate Models of Stereochemical Control in Ketoreductase Domains from the Erythromycin Polyketide Synthase. ACTA ACUST UNITED AC 2006; 13:287-96. [PMID: 16638534 DOI: 10.1016/j.chembiol.2006.01.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Revised: 12/21/2005] [Accepted: 01/06/2006] [Indexed: 11/25/2022]
Abstract
Ketoreductase (KR) activities help determine the stereochemistry of the products of modular polyketide synthases (PKSs). For example, domains eryKR(1) and eryKR(2), contained, respectively, in the first and second extension modules of the erythromycin-producing PKS, reduce 3-ketoacyl-thioester intermediates with opposite stereospecificity. Amino acid motifs that correlate with stereochemical outcome have been identified in KRs. We have used saturation mutagenesis of these motifs in eryKR(1) and eryKR(2), and a microplate-based screen of such mutants for activity against (9R, S)-trans-1-decalone, to identify candidate enzymes potentially altered in stereocontrol. Active mutants were reassayed with (2R, S)-2-methyl-3-oxopentanoic acid N-acetylcysteamine thioester, and the alcohol products were analyzed by chiral HPLC. Variant enzymes were found with either altered substrate selectivity for the (2R) or (2S) substrate or altered stereospecificity of reduction, or both, further highlighting the importance of these motifs in stereochemical control.
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Affiliation(s)
- Helen M O'Hare
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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30
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Abstract
In this issue of Chemistry & Biology, Leadlay and coworkers report overproduction of a number of ketoreductase domains from modular polyketide synthases. These discrete enzymes allow the stereochemistry of polyketide ketoreduction to be studied in isolation.
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Affiliation(s)
- Patrick Caffrey
- School of Biomolecular and Biomedical Science and Centre for Synthesis and Chemical Biology, University College Dublin, Ireland
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31
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Hill AM. The biosynthesis, molecular genetics and enzymology of the polyketide-derived metabolites. Nat Prod Rep 2005; 23:256-320. [PMID: 16572230 DOI: 10.1039/b301028g] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This review covers the biosynthesis of aliphatic and aromatic polyketides as well as mixed polyketide/NRPS metabolites, and discusses the molecular genetics and enzymology of the proteins responsible for their formation.
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32
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Abstract
The bacterial multienzyme polyketide synthases (PKSs) produce a diverse array of products that have been developed into medicines, including antibiotics and anticancer agents. The modular genetic architecture of these PKSs suggests that it might be possible to engineer the enzymes to produce novel drug candidates, a strategy known as 'combinatorial biosynthesis'. So far, directed engineering of modular PKSs has resulted in the production of more than 200 new polyketides, but key challenges remain before the potential of combinatorial biosynthesis can be fully realized.
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Affiliation(s)
- Kira J Weissman
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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33
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Siskos AP, Baerga-Ortiz A, Bali S, Stein V, Mamdani H, Spiteller D, Popovic B, Spencer JB, Staunton J, Weissman KJ, Leadlay PF. Molecular Basis of Celmer's Rules: Stereochemistry of Catalysis by Isolated Ketoreductase Domains from Modular Polyketide Synthases. ACTA ACUST UNITED AC 2005; 12:1145-53. [PMID: 16242657 DOI: 10.1016/j.chembiol.2005.08.017] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Revised: 08/01/2005] [Accepted: 08/01/2005] [Indexed: 10/25/2022]
Abstract
A system is reported for the recombinant expression of individual ketoreductase (KR) domains from modular polyketide synthases (PKSs) and scrutiny of their intrinsic specificity and stereospecificity toward surrogate diketide substrates. The eryKR(1) and the tylKR(1) domains, derived from the first extension module of the erythromycin PKS and the tylosin PKS, respectively, both catalyzed reduction of (2R, S)-2-methyl-3-oxopentanoic acid N-acetylcysteamine thioester, with complete stereoselectivity and stereospecificity, even though the substrate is not tethered to an acyl carrier protein or an intact PKS multienzyme. In contrast, and to varying degrees, the isolated enzymes eryKR(2), eryKR(5), and eryKR(6) exercised poorer control over substrate selection and the stereochemical course of ketoreduction. These data, together with modeling of diketide binding to KR(1) and KR(2), demonstrate the fine energetic balance between alternative modes of presentation of ketoacylthioester substrates to KR active sites.
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34
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Weissman KJ. Polyketide synthases: mechanisms and models. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2005:43-78. [PMID: 15645716 DOI: 10.1007/3-540-27055-8_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Affiliation(s)
- K J Weissman
- Department of Biochemistry, University of Cambridge, UK.
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35
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Abstract
The polyketide vicenistatin has significant anticancer activity. In the January issue of Chemistry & Biology, Kakinuma and coworkers reported on the vicenistatin biosynthetic gene cluster and demonstrated in vitro glycosylation of its aglycone core, raising the possibility of producing analogs with altered sugar residues.
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Affiliation(s)
- Patrick Caffrey
- Department of Industrial Microbiology, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
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36
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Olano C, Wilkinson B, Sánchez C, Moss SJ, Sheridan R, Math V, Weston AJ, Braña AF, Martin CJ, Oliynyk M, Méndez C, Leadlay PF, Salas JA. Biosynthesis of the angiogenesis inhibitor borrelidin by Streptomyces parvulus Tü4055: cluster analysis and assignment of functions. ACTA ACUST UNITED AC 2004; 11:87-97. [PMID: 15112998 DOI: 10.1016/j.chembiol.2003.12.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2003] [Revised: 10/30/2003] [Accepted: 10/30/2003] [Indexed: 10/21/2022]
Abstract
The biosynthetic gene cluster for the angiogenesis inhibitor borrelidin has been cloned from Streptomyces parvulus Tü4055. Sequence analysis indicates that the macrolide ring of borrelidin is formed by a modular polyketide synthase (PKS) (borA1-A6), a result that was confirmed by disruption of borA3. The borrelidin PKS is striking because only seven rather than the nine modules expected for a nonaketide product are encoded by borA1-A6. The starter unit of the PKS has been verified as trans-cyclopentane-1,2-dicarboxylic acid (trans-1,2-CPDA), and the genes involved in its biosynthesis identified. Other genes responsible for biosynthesis of the nitrile moiety, regulation, and self-resistance were also identified.
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Affiliation(s)
- Carlos Olano
- Departamento de Biologá Funcional e Instituto Universitario de Oncologia del Principado de Asturias, Universidad de Oviedo, 33006 Oviedo, Spain
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37
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Abstract
Combinatorial biosynthesis involves the genetic manipulation of natural product biosynthetic enzymes to produce potential new drug candidates that would otherwise be difficult to obtain. In either a theoretical or practical sense, the number of combinations possible from different types of natural product pathways ranges widely. Enzymes that have been the most amenable to this technology synthesize the polyketides, nonribosomal peptides, and hybrids of the two. The number of polyketide or peptide natural products theoretically possible is huge, but considerable work remains before these large numbers can be realized. Nevertheless, many analogs have been created by this technology, providing useful structure-activity relationship data and leading to a few compounds that may reach the clinic in the next few years. In this review the focus is on recent advances in our understanding of how different enzymes for natural product biosynthesis can be used successfully in this technology.
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38
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Graziani EI, Overk CR, Carter GT. Purification, structure determination, and antimicrobial activity of neutramycins B-G. JOURNAL OF NATURAL PRODUCTS 2003; 66:1149-1153. [PMID: 14510587 DOI: 10.1021/np0301691] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Neutramycins B-G were purified from a historical sample of neutramycin in our antibiotic collection. The structures of the compounds were solved by 2D NMR spectroscopic analysis. Four of the compounds (2-5) are probable biosynthetic intermediates or shunt metabolites of neutramycin biosynthesis, while two (6, 7) are likely to be degradation products. Only one intermediate (5) showed weak Gram-positive activity.
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Affiliation(s)
- Edmund I Graziani
- Department of Chemical and Screening Sciences, Wyeth Research, 401 N. Middletown Road, Pearl River, New York 10965, USA.
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39
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Kumar P, Li Q, Cane DE, Khosla C. Intermodular communication in modular polyketide synthases: structural and mutational analysis of linker mediated protein-protein recognition. J Am Chem Soc 2003; 125:4097-102. [PMID: 12670230 DOI: 10.1021/ja0297537] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modular polyketide synthases (PKSs) present an attractive scaffold for the engineered biosynthesis of novel polyketide products via recombination of naturally occurring enzyme modules with desired catalytic properties. Recent studies have highlighted the pivotal role of short intermodular "linker pairs" in the selective channeling of biosynthetic intermediates between adjacent PKS modules. Using a combination of computer modeling, NMR spectroscopy, cross-linking, and site-directed mutagenesis, we have investigated the mechanism by which a linker pair from the 6-deoxyerythronolide B synthase promotes chain transfer. Our studies support a "coiled-coil" model in which the individual peptides comprising this linker pair adopt helical conformations that associate through a combination of hydrophobic and electrostatic interactions in an antiparallel fashion. Given the important contribution of such linker pair interactions to the kinetics of chain transfer between PKS modules, the ability to rationally modulate linker pair affinity by site-directed mutagenesis could be useful in the construction of optimized hybrid PKSs.
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Affiliation(s)
- Pawan Kumar
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
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40
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Abstract
Polyketides are a large class of structurally diverse, biologically active natural products. Recent experiments add evidence that many of the enzymes involved in the biosynthesis of these natural products are intrinsically tolerant of nonnatural substrates. In addition, an increasing understanding of structure-function relationships in various enzyme-substrate systems is aiding efforts to begin engineering these proteins for even greater synthetic utility.
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Affiliation(s)
- Nicola L Pohl
- Department of Chemistry and the Plant Sciences Institute, 2756 Gilman Hall, Iowa State University, Ames, IA 50011-3111, USA.
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