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Koch AA, Schmidt JJ, Lowell AN, Hansen DA, Coburn KM, Chemler JA, Sherman DH. Probing Selectivity and Creating Structural Diversity Through Hybrid Polyketide Synthases. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Aaron A. Koch
- Life Sciences Institute The University of Michigan (USA) 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
| | - Jennifer J. Schmidt
- Life Sciences Institute The University of Michigan (USA) 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
| | - Andrew N. Lowell
- Life Sciences Institute The University of Michigan (USA) 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
- Current address: Department of Chemistry Virginia Tech Blacksburg VA 24061 USA
| | - Douglas A. Hansen
- Life Sciences Institute The University of Michigan (USA) 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
| | - Katherine M. Coburn
- Life Sciences Institute The University of Michigan (USA) 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
| | - Joseph A. Chemler
- Life Sciences Institute The University of Michigan (USA) 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
| | - David H. Sherman
- Life Sciences Institute The University of Michigan (USA) 210 Washtenaw Avenue Ann Arbor MI 48109-2216 USA
- Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology The University of Michigan USA
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Koch AA, Schmidt JJ, Lowell AN, Hansen DA, Coburn KM, Chemler JA, Sherman DH. Probing Selectivity and Creating Structural Diversity Through Hybrid Polyketide Synthases. Angew Chem Int Ed Engl 2020; 59:13575-13580. [PMID: 32357274 DOI: 10.1002/anie.202004991] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Indexed: 11/09/2022]
Abstract
Engineering polyketide synthases (PKS) to produce new metabolites requires an understanding of catalytic points of failure during substrate processing. Growing evidence indicates the thioesterase (TE) domain as a significant bottleneck within engineered PKS systems. We created a series of hybrid PKS modules bearing exchanged TE domains from heterologous pathways and challenged them with both native and non-native polyketide substrates. Reactions pairing wildtype PKS modules with non-native substrates primarily resulted in poor conversions to anticipated macrolactones. Likewise, product formation with native substrates and hybrid PKS modules bearing non-cognate TE domains was severely reduced. In contrast, non-native substrates were converted by most hybrid modules containing a substrate compatible TE, directly implicating this domain as the major catalytic gatekeeper and highlighting its value as a target for protein engineering to improve analog production in PKS pathways.
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Affiliation(s)
- Aaron A Koch
- Life Sciences Institute, The University of Michigan (USA), 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - Jennifer J Schmidt
- Life Sciences Institute, The University of Michigan (USA), 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - Andrew N Lowell
- Life Sciences Institute, The University of Michigan (USA), 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA.,Current address: Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Douglas A Hansen
- Life Sciences Institute, The University of Michigan (USA), 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - Katherine M Coburn
- Life Sciences Institute, The University of Michigan (USA), 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - Joseph A Chemler
- Life Sciences Institute, The University of Michigan (USA), 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - David H Sherman
- Life Sciences Institute, The University of Michigan (USA), 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA.,Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, The University of Michigan, USA
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Dhakal D, Sohng JK, Pandey RP. Engineering actinomycetes for biosynthesis of macrolactone polyketides. Microb Cell Fact 2019; 18:137. [PMID: 31409353 PMCID: PMC6693128 DOI: 10.1186/s12934-019-1184-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/02/2019] [Indexed: 12/18/2022] Open
Abstract
Actinobacteria are characterized as the most prominent producer of natural products (NPs) with pharmaceutical importance. The production of NPs from these actinobacteria is associated with particular biosynthetic gene clusters (BGCs) in these microorganisms. The majority of these BGCs include polyketide synthase (PKS) or non-ribosomal peptide synthase (NRPS) or a combination of both PKS and NRPS. Macrolides compounds contain a core macro-lactone ring (aglycone) decorated with diverse functional groups in their chemical structures. The aglycon is generated by megaenzyme polyketide synthases (PKSs) from diverse acyl-CoA as precursor substrates. Further, post-PKS enzymes are responsible for allocating the structural diversity and functional characteristics for their biological activities. Macrolides are biologically important for their uses in therapeutics as antibiotics, anti-tumor agents, immunosuppressants, anti-parasites and many more. Thus, precise genetic/metabolic engineering of actinobacteria along with the application of various chemical/biological approaches have made it plausible for production of macrolides in industrial scale or generation of their novel derivatives with more effective biological properties. In this review, we have discussed versatile approaches for generating a wide range of macrolide structures by engineering the PKS and post-PKS cascades at either enzyme or cellular level in actinobacteria species, either the native or heterologous producer strains.
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Affiliation(s)
- Dipesh Dhakal
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, 31460 Chungnam Republic of Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, 31460 Chungnam Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, 31460 Chungnam Republic of Korea
| | - Ramesh Prasad Pandey
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, 31460 Chungnam Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, 31460 Chungnam Republic of Korea
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Hansen DA, Koch AA, Sherman DH. Identification of a Thioesterase Bottleneck in the Pikromycin Pathway through Full-Module Processing of Unnatural Pentaketides. J Am Chem Soc 2017; 139:13450-13455. [PMID: 28836772 DOI: 10.1021/jacs.7b06432] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Polyketide biosynthetic pathways have been engineered to generate natural product analogs for over two decades. However, manipulation of modular type I polyketide synthases (PKSs) to make unnatural metabolites commonly results in attenuated yields or entirely inactive pathways, and the mechanistic basis for compromised production is rarely elucidated since rate-limiting or inactive domain(s) remain unidentified. Accordingly, we synthesized and assayed a series of modified pikromycin (Pik) pentaketides that mimic early pathway engineering to probe the substrate tolerance of the PikAIII-TE module in vitro. Truncated pentaketides were processed with varying efficiencies to corresponding macrolactones, while pentaketides with epimerized chiral centers were poorly processed by PikAIII-TE and failed to generate 12-membered ring products. Isolation and identification of extended but prematurely offloaded shunt products suggested that the Pik thioesterase (TE) domain has limited substrate flexibility and functions as a gatekeeper in the processing of unnatural substrates. Synthesis of an analogous hexaketide with an epimerized nucleophilic hydroxyl group allowed for direct evaluation of the substrate stereoselectivity of the excised TE domain. The epimerized hexaketide failed to undergo cyclization and was exclusively hydrolyzed, confirming the TE domain as a key catalytic bottleneck. In an accompanying paper , we engineer the standalone Pik thioesterase to yield a thioesterase (TES148C) and module (PikAIII-TES148C) that display gain-of-function processing of substrates with inverted hydroxyl groups.
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Affiliation(s)
- Douglas A Hansen
- Life Sciences Institute, ‡Department of Medicinal Chemistry, §Cancer Biology Graduate Program, ⊥Department of Chemistry, and ∥Department of Microbiology & Immunology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Aaron A Koch
- Life Sciences Institute, ‡Department of Medicinal Chemistry, §Cancer Biology Graduate Program, ⊥Department of Chemistry, and ∥Department of Microbiology & Immunology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - David H Sherman
- Life Sciences Institute, ‡Department of Medicinal Chemistry, §Cancer Biology Graduate Program, ⊥Department of Chemistry, and ∥Department of Microbiology & Immunology, University of Michigan , Ann Arbor, Michigan 48109, United States
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Nigam A, Almabruk KH, Saxena A, Yang J, Mukherjee U, Kaur H, Kohli P, Kumari R, Singh P, Zakharov LN, Singh Y, Mahmud T, Lal R. Modification of rifamycin polyketide backbone leads to improved drug activity against rifampicin-resistant Mycobacterium tuberculosis. J Biol Chem 2015; 289:21142-52. [PMID: 24923585 DOI: 10.1074/jbc.m114.572636] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rifamycin B, a product of Amycolatopsis mediterranei S699, is the precursor of clinically used antibiotics that are effective against tuberculosis, leprosy, and AIDS-related mycobacterial infections. However, prolonged usage of these antibiotics has resulted in the emergence of rifamycin-resistant strains of Mycobacterium tuberculosis. As part of our effort to generate better analogs of rifamycin, we substituted the acyltransferase domain of module 6 of rifamycin polyketide synthase with that of module 2 of rapamycin polyketide synthase. The resulting mutants (rifAT6::rapAT2) of A. mediterranei S699 produced new rifamycin analogs, 24-desmethylrifamycin B and 24-desmethylrifamycin SV, which contained modification in the polyketide backbone. 24-Desmethylrifamycin B was then converted to 24-desmethylrifamycin S, whose structure was confirmed by MS, NMR, and X-ray crystallography. Subsequently, 24-desmethylrifamycin S was converted to 24-desmethylrifampicin, which showed excellent antibacterial activity against several rifampicin-resistant M. tuberculosis strains.
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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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Harvey CJB, Puglisi JD, Pande VS, Cane DE, Khosla C. Precursor directed biosynthesis of an orthogonally functional erythromycin analogue: selectivity in the ribosome macrolide binding pocket. J Am Chem Soc 2012; 134:12259-65. [PMID: 22741553 DOI: 10.1021/ja304682q] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The macrolide antibiotic erythromycin A and its semisynthetic analogues have been among the most useful antibacterial agents for the treatment of infectious diseases. Using a recently developed chemical genetic strategy for precursor-directed biosynthesis and colony bioassay of 6-deoxyerythromycin D analogues, we identified a new class of alkynyl- and alkenyl-substituted macrolides with activities comparable to that of the natural product. Further analysis revealed a marked and unexpected dependence of antibiotic activity on the size and degree of unsaturation of the precursor. Based on these leads, we also report the precursor-directed biosynthesis of 15-propargyl erythromycin A, a novel antibiotic that not only is as potent as erythromycin A with respect to its ability to inhibit bacterial growth and cell-free ribosomal protein biosynthesis but also harbors an orthogonal functional group that is capable of facile chemical modification.
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Affiliation(s)
- Colin J B Harvey
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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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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Lee HY, Harvey CJB, Cane DE, Khosla C. Improved precursor-directed biosynthesis in E. coli via directed evolution. J Antibiot (Tokyo) 2010; 64:59-64. [PMID: 21081955 PMCID: PMC3030684 DOI: 10.1038/ja.2010.129] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Erythromycin and related macrolide antibiotics are widely used polyketide natural products. We have evolved an engineered biosynthetic pathway in Escherichia coli that yields erythromycin analogs from simple synthetic precursors. Multiple rounds of mutagenesis and screening led to the identification of new mutant strains with improved efficiency for precursor directed biosynthesis. Genetic and biochemical analysis suggested that the phenotypically relevant alterations in these mutant strains were localized exclusively to the host-vector system, and not to the polyketide synthase. We also demonstrate the utility of this improved system through engineered biosynthesis of a novel alkynyl erythromycin derivative with comparable antibacterial activity to its natural counterpart. In addition to reinforcing the power of directed evolution for engineering macrolide biosynthesis, our studies have identified a new lead substance for investigating structure-function relationships in the bacterial ribosome.
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Affiliation(s)
- Ho Young Lee
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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Gemma S, Gabellieri E, Sanna Coccone S, Martí F, Taglialatela-Scafati O, Novellino E, Campiani G, Butini S. Synthesis of Dihydroplakortin, 6-epi-Dihydroplakortin, and Their C10-Desethyl Analogues. J Org Chem 2010; 75:2333-40. [DOI: 10.1021/jo1001559] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sandra Gemma
- Dipartimento Farmaco Chimico Tecnologico (DFCT)
- European Research Centre for Drug Discovery and Development (NatSynDrugs)
| | - Emanuele Gabellieri
- Dipartimento Farmaco Chimico Tecnologico (DFCT)
- European Research Centre for Drug Discovery and Development (NatSynDrugs)
| | - Salvatore Sanna Coccone
- Dipartimento Farmaco Chimico Tecnologico (DFCT)
- European Research Centre for Drug Discovery and Development (NatSynDrugs)
| | - Francesc Martí
- Dipartimento Farmaco Chimico Tecnologico (DFCT)
- European Research Centre for Drug Discovery and Development (NatSynDrugs)
| | - Orazio Taglialatela-Scafati
- European Research Centre for Drug Discovery and Development (NatSynDrugs)
- Dipartimento di Chimica delle Sostanze Naturali (DCSN)
| | - Ettore Novellino
- European Research Centre for Drug Discovery and Development (NatSynDrugs)
- Dipartimento di Chimica Farmaceutica e Tossicologica (DCFT)
| | - Giuseppe Campiani
- Dipartimento Farmaco Chimico Tecnologico (DFCT)
- European Research Centre for Drug Discovery and Development (NatSynDrugs)
| | - Stefania Butini
- Dipartimento Farmaco Chimico Tecnologico (DFCT)
- European Research Centre for Drug Discovery and Development (NatSynDrugs)
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Magarvey NA, Fortin PD, Thomas PM, Kelleher NL, Walsh CT. Gatekeeping versus promiscuity in the early stages of the andrimid biosynthetic assembly line. ACS Chem Biol 2008; 3:542-54. [PMID: 18652473 DOI: 10.1021/cb800085g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The antibiotic andrimid, a nanomolar inhibitor of bacterial acetyl coenzyme A carboxylase, is generated on an unusual polyketide/nonribosomal peptide enzyme assembly line in that all thiolation (T) domains/small-molecule building stations are on separate proteins. In addition, a transglutaminase homologue is used to condense andrimid building blocks together on the andrimid assembly line. The first two modules of the andrimid assembly line yields an octatrienoyl-beta-Phe-thioester tethered to the AdmI T domain, with amide bond formation carried out by a free-standing transglutaminase homologue AdmF. Analysis of the aminomutase AdmH reveals its specific conversion from l-Phe to (S)-beta-Phe, which in turn is activated by AdmJ and ATP to form (S)-beta-Phe-aminoacyl-AMP. AdmJ then transfers the (S)-beta-Phe moiety to one of the free-standing T domains, AdmI, but not AdmA, which instead gets loaded with an octatrienoyl group by other enzymes. AdmF, the amide synthase, will accept a variety of acyl groups in place of the octatrienoyl donor if presented on either AdmA or AdmI. AdmF will also use either stereoisomer of phenylalanine or beta-Phe when presented on AdmA and AdmI, but not when placed on noncognate T domains. Further, we show the polyketide synthase proteins responsible for the polyunsaturated acyl cap can be bypassed in vitro with N-acetylcysteamine as a low-molecular-weight acyl donor to AdmF and also in vivo in an Escherichia coli strain bearing the andrimid biosynthetic gene cluster with a knockout in admA.
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Affiliation(s)
- Nathan A. Magarvey
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Pascal D. Fortin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Paul M. Thomas
- Department of Chemistry, University of Illinois, Urbana−Champaign, Illinois 61801
| | - Neil L. Kelleher
- Department of Chemistry, University of Illinois, Urbana−Champaign, Illinois 61801
| | - Christopher T. Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
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Gupta S, Lakshmanan V, Kim BS, Fecik R, Reynolds KA. Generation of novel pikromycin antibiotic products through mutasynthesis. Chembiochem 2008; 9:1609-16. [PMID: 18512859 DOI: 10.1002/cbic.200700635] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The pikromycin polyketide synthase (PKS) of S. venezuelae, which consists of one loading module and six extension modules, is responsible for the formation of the hexaketide narbonolide, a key intermediate in the biosynthesis of the antibiotic pikromycin. S. venezuelae strains in which PikAI, which houses the loading domain and first two modules of the PKS, is either absent or catalytically inactive, produce no pikromycin product. When these strains are grown in the presence of a synthetically prepared triketide product, activated as the N-acetylcysteamine thioester, pikromycin yields are restored to as much as 11 % of that seen in the wild-type strain. Feeding analogues of the triketide intermediate provides pikromycin analogues bearing different alkyl substituents at C13 and C14. One of these analogues, Delta(15,16)-dehydropikromycin, exhibits improved antimicrobial activity relative to pikromycin.
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Affiliation(s)
- Shuchi Gupta
- Department of Chemistry, Portland State University, Portland, OR 97201, USA
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Kirschning A, Taft F, Knobloch T. Total synthesis approaches to natural product derivatives based on the combination of chemical synthesis and metabolic engineering. Org Biomol Chem 2007; 5:3245-59. [PMID: 17912378 DOI: 10.1039/b709549j] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Secondary metabolites are an extremely diverse and important group of natural products with industrial and biomedical implications. Advances in metabolic engineering of both native and heterologous secondary metabolite producing organisms have allowed the directed synthesis of desired novel products by exploiting their biosynthetic potentials. Metabolic engineering utilises knowledge of cellular metabolism to alter biosynthetic pathways. An important technique that combines chemical synthesis with metabolic engineering is mutasynthesis (mutational biosynthesis; MBS), which advanced from precursor-directed biosynthesis (PDB). Both techniques are based on the cellular uptake of modified biosynthetic intermediates and their incorporation into complex secondary metabolites. Mutasynthesis utilises genetically engineered organisms in conjunction with feeding of chemically modified intermediates. From a synthetic chemist's point of view the concept of mutasynthesis is highly attractive, as the method combines chemical expertise with Nature's synthetic machinery and thus can be exploited to rapidly create small libraries of secondary metabolites. However, in each case, the method has to be critically compared with semi- and total synthesis in terms of practicability and efficiency. Recent developments in metabolic engineering promise to further broaden the scope of outsourcing chemically demanding steps to biological systems.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, and Center of Biomolecular Drug Research (BMWZ), Schneiderberg 1b, 30167 Hannover, Germany.
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Watts K, Mijts B, Schmidt-Dannert C. Current and Emerging Approaches for Natural Product Biosynthesis in Microbial Cells. Adv Synth Catal 2005. [DOI: 10.1002/adsc.200505062] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Affiliation(s)
- Leonard Katz
- Kosan Biosciences, Incorporated, 3832 Bay Center Place, Hayward, California 94545, USA.
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16
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Kaneko T, McArthur H, Sutcliffe J. Recent developments in the area of macrolide antibiotics. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.10.4.403] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Weist S, Süssmuth RD. Mutational biosynthesis—a tool for the generation of structural diversity in the biosynthesis of antibiotics. Appl Microbiol Biotechnol 2005; 68:141-50. [PMID: 15702315 DOI: 10.1007/s00253-005-1891-8] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2004] [Revised: 12/17/2004] [Accepted: 12/19/2004] [Indexed: 10/25/2022]
Abstract
Natural products represent an important source of drugs in a number of therapeutic fields, e.g. antiinfectives and cancer therapy. Natural products are considered as biologically validated lead structures, and evolution of compounds with novel or enhanced biological properties is expected from the generation of structural diversity in natural product libraries. However, natural products are often structurally complex, thus precluding reasonable synthetic access for further structure-activity relationship studies. As a consequence, natural product research involves semisynthetic or biotechnological approaches. Among the latter are mutasynthesis (also known as mutational biosynthesis) and precursor-directed biosynthesis, which are based on the cellular uptake and incorporation into complex antibiotics of relatively simple biosynthetic building blocks. This appealing idea, which has been applied almost exclusively to bacteria and fungi as producing organisms, elegantly circumvents labourious total chemical synthesis approaches and exploits the biosynthetic machinery of the microorganism. The recent revitalization of mutasynthesis is based on advancements in both chemical syntheses and molecular biology, which have provided a broader available substrate range combined with the generation of directed biosynthesis mutants. As an important tool in supporting combinatorial biosynthesis, mutasynthesis will further impact the future development of novel secondary metabolite structures.
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Affiliation(s)
- S Weist
- Biologische Chemie/Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
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Affiliation(s)
- Robert McDaniel
- Kosan Biosciences, 3832 Bay Center Place, Hayward, California 94545, USA.
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Wong D, Robertson G. Applying combinatorial chemistry and biology to food research. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2004; 52:7187-7198. [PMID: 15563194 DOI: 10.1021/jf040140i] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In the past decade combinatorial chemistry has become a major focus of research activity in the pharmaceutical industry for accelerating the development of novel therapeutic compounds. The same combinatorial strategies could be applied to a broad spectrum of areas in agricultural and food research, including food safety and nutrition, development of product ingredients, and processing and conversion of natural products. In contrast to "rational design", the combinatorial approach relies on molecular diversity and high-throughput screening. The capability of exploring the structural and functional limits of a vast population of diverse chemical and biochemical molecules makes it possible to expedite the creation and isolation of compounds of desirable and useful properties. Several studies in recent years have demonstrated the utility of combinatorial methods for food research. These include the discovery of synthetic antimicrobial, antioxidative, and aflatoxin-binding peptides, the identification and analysis of unique flavor compounds, the generation of new enzyme inhibitors, the development of therapeutic antibodies for botulinum neurotoxins, the synthesis of unnatural polyketides and carotenoids, and the modification of food enzymes with novel properties. The results of such activities could open a large area of applications with potential benefits to the food industry. This review describes the current techniques of combinatorial chemistry and their applications, with emphasis on examples in food science research.
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Affiliation(s)
- Dominic Wong
- Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA.
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Abstract
Metabolic engineering is the science that combines systematic analysis of metabolic and other pathways with molecular biological techniques to improve cellular properties by designing and implementing rational genetic modifications. As such, metabolic engineering deals with the measurement of metabolic fluxes and elucidation of their control as determinants of metabolic function and cell physiology. A novel aspect of metabolic engineering is that it departs from the traditional reductionist paradigm of cellular metabolism, taking instead a holistic view. In this sense, metabolic engineering is well suited as a framework for the analysis of genome-wide differential gene expression data, in combination with data on protein content and in vivo metabolic fluxes. The insights of the integrated view of metabolism generated by metabolic engineering will have profound implications in biotechnological applications, as well as in devising rational strategies for target selection for screening candidate drugs or designing gene therapies. In this article we review basic concepts of metabolic engineering and provide examples of applications in the production of primary and secondary metabolites, improving cellular properties, and biomedical engineering.
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Affiliation(s)
- M Koffas
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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21
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Tsai SC, Miercke LJ, Krucinski J, Gokhale R, Chen JC, Foster PG, Cane DE, Khosla C, Stroud RM. Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: versatility from a unique substrate channel. Proc Natl Acad Sci U S A 2001; 98:14808-13. [PMID: 11752428 PMCID: PMC64940 DOI: 10.1073/pnas.011399198] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As the first structural elucidation of a modular polyketide synthase (PKS) domain, the crystal structure of the macrocycle-forming thioesterase (TE) domain from the 6-deoxyerythronolide B synthase (DEBS) was solved by a combination of multiple isomorphous replacement and multiwavelength anomalous dispersion and refined to an R factor of 24.1% to 2.8-A resolution. Its overall tertiary architecture belongs to the alpha/beta-hydrolase family, with two unusual features unprecedented in this family: a hydrophobic leucine-rich dimer interface and a substrate channel that passes through the entire protein. The active site triad, comprised of Asp-169, His-259, and Ser-142, is located in the middle of the substrate channel, suggesting the passage of the substrate through the protein. Modeling indicates that the active site can accommodate and orient the 6-deoxyerythronolide B precursor uniquely, while at the same time shielding the active site from external water and catalyzing cyclization by macrolactone formation. The geometry and organization of functional groups explain the observed substrate specificity of this TE and offer strategies for engineering macrocycle biosynthesis. Docking of a homology model of the upstream acyl carrier protein (ACP6) against the TE suggests that the 2-fold axis of the TE dimer may also be the axis of symmetry that determines the arrangement of domains in the entire DEBS. Sequence conservation suggests that all TEs from modular polyketide synthases have a similar fold, dimer 2-fold axis, and substrate channel geometry.
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Affiliation(s)
- S C Tsai
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
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22
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Wu N, Tsuji SY, Cane DE, Khosla C. Assessing the balance between protein-protein interactions and enzyme-substrate interactions in the channeling of intermediates between polyketide synthase modules. J Am Chem Soc 2001; 123:6465-74. [PMID: 11439032 DOI: 10.1021/ja010219t] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.4] [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 the modular polyketide synthase (PKS) that catalyzes the biosynthesis of 6-deoxyerythronolide B (6-dEB), the aglycon precursor of the antibiotic erythromycin. The biosynthesis of 6-dEB exemplifies the extraordinary substrate- and stereo-selectivity of this family of multifunctional enzymes. Paradoxically, DEBS has been shown to be an attractive scaffold for combinatorial biosynthesis, indicating that its constituent modules are also very tolerant of unnatural substrates. By interrogating individual modules of DEBS with a panel of diketides activated as N-acetylcysteamine (NAC) thioesters, it was recently shown that individual modules have a marked ability to discriminate among certain diastereomeric diketides. However, since free NAC thioesters were used as substrates in these studies, the modules were primed by a diffusive process, which precluded involvement of the covalent, substrate-channeling mechanism by which enzyme-bound intermediates are directly transferred from one module to the next in a multimodular PKS. Recent evidence pointing to a pivotal role for protein-protein interactions in the substrate-channeling mechanism has prompted us to develop novel assays to reassess the steady-state kinetic parameters of individual DEBS modules when primed in a more "natural" channeling mode by the same panel of diketide substrates used earlier. Here we describe these assays and use them to quantify the kinetic benefit of linker-mediated substrate channeling in a modular PKS. This benefit can be substantial, especially for intrinsically poor substrates. Examples are presented where the k(cat) of a module for a given diketide substrate increases >100-fold when the substrate is presented to the module in a channeling mode as opposed to a diffusive mode. However, the substrate specificity profiles for individual modules are conserved regardless of the mode of presentation. By highlighting how substrate channeling can allow PKS modules to effectively accept and process intrinsically poor substrates, these studies provide a rational basis for examining the enormous untapped potential for combinatorial biosynthesis via module rearrangement.
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Affiliation(s)
- N Wu
- Departments of Chemistry, Chemical Engineering, and Biochemistry, Stanford University, Stanford California 94305, USA
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23
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Abstract
Metabolic engineering of natural products is a science that has been built on the goals of traditional strain improvement with the availability of modern molecular biological technologies. In the past 15 years, the state of the art in metabolic engineering of natural products has advanced from the first proof-of-principle experiment based on minimal known genetics to a commonplace event using highly specific and sophisticated gene manipulation methods. With the availability of genes, host organisms, vector systems, and standard molecular biological tools, it is expected that metabolic engineering will be translated into industrial reality.
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Affiliation(s)
- W R Strohl
- Natural Products Drug Discovery-Microbiology, Merck Research Labs, Rahway, New Jersey 07065, USA.
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Wu N, Kudo F, Cane DE, Khosla C. Analysis of the Molecular Recognition Features of Individual Modules Derived from the Erythromycin Polyketide Synthase. J Am Chem Soc 2000. [DOI: 10.1021/ja000023d] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nicholas Wu
- Contribution from the Departments of Chemical Engineering, Chemistry, and Biochemistry, Stanford University, Stanford, California 94305-5025, and Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108
| | - Fumitaka Kudo
- Contribution from the Departments of Chemical Engineering, Chemistry, and Biochemistry, Stanford University, Stanford, California 94305-5025, and Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108
| | - David E. Cane
- Contribution from the Departments of Chemical Engineering, Chemistry, and Biochemistry, Stanford University, Stanford, California 94305-5025, and Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108
| | - Chaitan Khosla
- Contribution from the Departments of Chemical Engineering, Chemistry, and Biochemistry, Stanford University, Stanford, California 94305-5025, and Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108
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Hunziker D, Wu N, Kenoshita K, Cane DE, Khosla C. Precursor directed biosynthesis of novel 6-deoxyerythronolide B analogs containing non-natural oxygen substituents and reactive functionalities. Tetrahedron Lett 1999. [DOI: 10.1016/s0040-4039(98)02507-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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26
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Abstract
Polyketides and non-ribosomal peptides are two large families of complex natural products that are built from simple carboxylic acid or amino acid monomers, respectively, and that have important medicinal or agrochemical properties. Despite the substantial differences between these two classes of natural products, each is synthesized biologically under the control of exceptionally large, multifunctional proteins termed polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) that contain repeated, coordinated groups of active sites called modules, in which each module is responsible for catalysis of one complete cycle of polyketide or polypeptide chain elongation and associated functional group modifications. It has recently become possible to use molecular genetic methodology to alter the number, content, and order of such modules and, in so doing, to alter rationally the structure of the resultant products. This review considers the promise and challenges inherent in the combinatorial manipulation of PKS and NRPS structure in order to generate entirely "unnatural" products.
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Affiliation(s)
- D E Cane
- Department of Chemistry, Box H, Brown University, Providence, RI 02912-9108, USA
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