1
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McCullough TM, Choudhary V, Akey DL, Skiba MA, Bernard SM, Kittendorf JD, Schmidt JJ, Sherman DH, Smith JL. Substrate Trapping in Polyketide Synthase Thioesterase Domains: Structural Basis for Macrolactone Formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599880. [PMID: 38948807 PMCID: PMC11213023 DOI: 10.1101/2024.06.20.599880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Emerging antibiotic resistance requires continual improvement in the arsenal of antimicrobial drugs, especially the critical macrolide antibiotics. Formation of the macrolactone scaffold of these polyketide natural products is catalyzed by a modular polyketide synthase (PKS) thioesterase (TE). The TE accepts a linear polyketide substrate from the termina PKS acyl carrier protein to generate an acyl-enzyme adduct that is resolved by attack of a substrate hydroxyl group to form the macrolactone. Our limited mechanistic understanding of TE selectivity for a substrate nucleophile and/or water has hampered development of TEs as biocatalysts that accommodate a variety of natural and non-natural substrates. To understand how TEs direct the substrate nucleophile for macrolactone formation, acyl-enzyme intermediates were trapped as stable amides by substituting the natural serine OH with an amino group. Incorporation of the unnatural amino acid, 1,3-diaminopropionic acid (DAP), was tested with five PKS TEs. DAP-modified TEs (TE DAP ) from the pikromycin and erythromycin pathways were purified and tested with six full-length polyketide intermediates from three pathways. The erythromycin TE had permissive substrate selectivity, whereas the pikromycin TE was selective for its native hexaketide and heptaketide substrates. In a crystal structure of a native substrate trapped in pikromycin TE DAP , the linear heptaketide was curled in the active site with the nucleophilic hydroxyl group positioned 4 Å from the amide-enzyme linkage. The curled heptaketide displayed remarkable shape complementarity with the TE acyl cavity. The strikingly different shapes of acyl cavities in TEs of known structure, including those reported here for juvenimicin, tylosin and fluvirucin biosynthesis, provide new insights to facilitate TE engineering and optimization.
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2
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Li Z, Chai L, Tang Z, Zhu H, Xue P, Sun F, Lin H, Zhou Y, Lin X. Precursor-Directed Biosynthesis of Neoantimycin Derivatives with Selective Cytotoxicity. JOURNAL OF NATURAL PRODUCTS 2024; 87:1376-1383. [PMID: 38662398 DOI: 10.1021/acs.jnatprod.4c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
A precursor-directed biosynthesis approach led to the accumulation of seven new neoantimycin derivatives (1-7) from Streptomyces conglobatus RJ2. Structure elucidation was conducted using NMR and HRESIMS analysis, and the absolute configuration was determined by advanced Marfey's method, Mosher's analysis, and ECD analysis. The obtained compounds revealed selective and significant cytotoxicity, specifically against colorectal cancer cells bearing the K-ras mutation, with IC50 values ranging from 40 nM to 3.5 μM.
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Affiliation(s)
- Zhengyuan Li
- Institute of Marine Drugs, Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, People's Republic of China
| | - Ling Chai
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Chinese Medicine and Pharmaceutical Science, Nanning 530022, People's Republic of China
| | - Zhenzhou Tang
- Institute of Marine Drugs, Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, People's Republic of China
| | - Hongrui Zhu
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Peiying Xue
- Institute of Marine Drugs, Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, People's Republic of China
| | - Fan Sun
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Houwen Lin
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Yongjun Zhou
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Xiao Lin
- Institute of Marine Drugs, Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, People's Republic of China
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3
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Jian X, Pang F, Hobson C, Jenner M, Alkhalaf LM, Challis GL. Antibiotic Skeletal Diversification via Differential Enoylreductase Recruitment and Module Iteration in trans-Acyltransferase Polyketide Synthases. J Am Chem Soc 2024; 146:6114-6124. [PMID: 38389455 PMCID: PMC10921412 DOI: 10.1021/jacs.3c13667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Microorganisms are remarkable chemists capable of assembling complex molecular architectures that penetrate cells and bind biomolecular targets with exquisite selectivity. Consequently, microbial natural products have wide-ranging applications in medicine and agriculture. How the "blind watchmaker" of evolution creates skeletal diversity is a key question in natural products research. Comparative analysis of biosynthetic pathways to structurally related metabolites is an insightful approach to addressing this. Here, we report comparative biosynthetic investigations of gladiolin, a polyketide antibiotic from Burkholderia gladioli with promising activity against multidrug-resistant Mycobacterium tuberculosis, and etnangien, a structurally related antibiotic produced by Sorangium cellulosum. Although these metabolites have very similar macrolide cores, their C21 side chains differ significantly in both length and degree of saturation. Surprisingly, the trans-acyltransferase polyketide synthases (PKSs) that assemble these antibiotics are almost identical, raising intriguing questions about mechanisms underlying structural diversification in this important class of biosynthetic assembly line. In vitro reconstitution of key biosynthetic transformations using simplified substrate analogues, combined with gene deletion and complementation experiments, enabled us to elucidate the origin of all the structural differences in the C21 side chains of gladiolin and etnangien. The more saturated gladiolin side chain arises from a cis-acting enoylreductase (ER) domain in module 1 and in trans recruitment of a standalone ER to module 5 of the PKS. Remarkably, module 5 of the gladiolin PKS is intrinsically iterative in the absence of the standalone ER, accounting for the longer side chain in etnangien. These findings have important implications for biosynthetic engineering approaches to the creation of novel polyketide skeletons.
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Affiliation(s)
- Xinyun Jian
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Warwick
Integrative Synthetic Biology Centre, University
of Warwick, Coventry CV4 7AL, U.K.
- Department
of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- ARC
Centre of Excellence for Innovations in Protein and Peptide Science, Monash University, Clayton, VIC 3800, Australia
| | - Fang Pang
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Christian Hobson
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Matthew Jenner
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Warwick
Integrative Synthetic Biology Centre, University
of Warwick, Coventry CV4 7AL, U.K.
| | - Lona M. Alkhalaf
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | - Gregory L. Challis
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Warwick
Integrative Synthetic Biology Centre, University
of Warwick, Coventry CV4 7AL, U.K.
- Department
of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- ARC
Centre of Excellence for Innovations in Protein and Peptide Science, Monash University, Clayton, VIC 3800, Australia
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4
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Sood U, Müller M, Lan T, Garg G, Singhvi N, Hira P, Singh P, Nigam A, Verma M, Lata P, Kaur H, Kumar A, Rawat CD, Lal S, Aldrich C, Bechthold A, Lal R. Amycolatopsis mediterranei: A Sixty-Year Journey from Strain Isolation to Unlocking Its Potential of Rifamycin Analogue Production by Combinatorial Biosynthesis. JOURNAL OF NATURAL PRODUCTS 2024; 87:424-438. [PMID: 38289177 DOI: 10.1021/acs.jnatprod.3c00686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Ever since the isolation of Amycolatopsis mediterranei in 1957, this strain has been the focus of research worldwide. In the last 60 years or more, our understanding of the taxonomy, development of cloning vectors and conjugation system, physiology, genetics, genomics, and biosynthetic pathway of rifamycin B production in A. mediterranei has substantially increased. In particular, the development of cloning vectors, transformation system, characterization of the rifamycin biosynthetic gene cluster, and the regulation of rifamycin B production by the pioneering work of Heinz Floss have made the rifamycin polyketide biosynthetic gene cluster (PKS) an attractive target for extensive genetic manipulations to produce rifamycin B analogues which could be effective against multi-drug-resistant tuberculosis. Additionally, a better understanding of the regulation of rifamycin B production and the application of newer genomics tools, including CRISPR-assisted genome editing systems, might prove useful to overcome the limitations associated with low production of rifamycin analogues.
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Affiliation(s)
- Utkarsh Sood
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi-110007, India
| | - Moritz Müller
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany
| | - Tian Lan
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Gauri Garg
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi-110007, India
| | - Nirjara Singhvi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, Uttarakhand 248007, India
| | - Princy Hira
- Department of Zoology, Maitreyi College, University of Delhi, Delhi-110003, India
| | - Priya Singh
- Department of Zoology, Maitreyi College, University of Delhi, Delhi-110003, India
| | - Aeshna Nigam
- Department of Zoology, Shivaji College, University of Delhi, Delhi-110027, India
| | - Mansi Verma
- Department of Zoology, Hansraj College, University of Delhi, Delhi-110007, India
| | - Pushp Lata
- Department of Zoology, University of Delhi, Delhi-110007, India
| | - Hardeep Kaur
- Department of Zoology, Ramjas College, University of Delhi, Delhi-110007, India
| | - Abhilash Kumar
- Department of Zoology, Ramjas College, University of Delhi, Delhi-110007, India
| | - Charu Dogra Rawat
- Department of Zoology, Ramjas College, University of Delhi, Delhi-110007, India
| | - Sukanya Lal
- PhiXGen Private Limited, Gurugram, Haryana-122001, India
| | - Courtney Aldrich
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Andreas Bechthold
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany
| | - Rup Lal
- PhiXGen Private Limited, Gurugram, Haryana-122001, India
- Acharya Narendra Dev College, University of Delhi, Delhi-110019, India
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5
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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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6
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Lund S, Hall R, Williams GJ. An Artificial Pathway for Isoprenoid Biosynthesis Decoupled from Native Hemiterpene Metabolism. ACS Synth Biol 2019; 8:232-238. [PMID: 30648856 PMCID: PMC6556385 DOI: 10.1021/acssynbio.8b00383] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isoprenoids are constructed in nature using hemiterpene building blocks that are biosynthesized from lengthy enzymatic pathways with little opportunity to deploy precursor-directed biosynthesis. Here, an artificial alcohol-dependent hemiterpene biosynthetic pathway was designed and coupled to several isoprenoid biosynthetic systems, affording lycopene and a prenylated tryptophan in robust yields. This approach affords a potential route to diverse non-natural hemiterpenes and by extension isoprenoids modified with non-natural chemical functionality. Accordingly, the prototype chemo-enzymatic pathway is a critical first step toward the construction of engineered microbial strains for bioconversion of simple scalable building blocks into complex isoprenoid scaffolds.
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Affiliation(s)
- Sean Lund
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, United States
- Present address: Amyris, 5885 Hollis St Ste. 100, Emeryville, California 94608, United States
| | - Rachael Hall
- Department of Chemistry, NC State University, Raleigh, North Carolina 27695, 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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7
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Wang Y, Lazor KM, DeMeester KE, Liang H, Heiss TK, Grimes CL. Postsynthetic Modification of Bacterial Peptidoglycan Using Bioorthogonal N-Acetylcysteamine Analogs and Peptidoglycan O-Acetyltransferase B. J Am Chem Soc 2017; 139:13596-13599. [PMID: 28898061 PMCID: PMC5837961 DOI: 10.1021/jacs.7b06820] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Bacteria have the natural ability to install protective postsynthetic modifications onto its bacterial peptidoglycan (PG), the coat woven into bacterial cell wall. Peptidoglycan O-acetyltransferase B (PatB) catalyzes the O-acetylation of PG in Gram (-) bacteria, which aids in bacterial survival, as it prevents autolysins such as lysozyme from cleaving the PG. We explored the mechanistic details of PatB's acetylation function and determined that PatB has substrate specificity for bioorthgonal short N-acetyl cysteamine (SNAc) donors. A variety of functionality including azides and alkynes were installed on tri-N-acetylglucosamine (NAG)3, a PG mimic, as well as PG isolated from various Gram (+) and Gram (-) bacterial species. The bioorthogonal modifications protect the isolated PG against lysozyme degradation in vitro. We further demonstrate that this postsynthetic modification of PG can be extended to use click chemistry to fluorescently label the mature PG in whole bacterial cells of Bacillus subtilis. Modifying PG postsynthetically can aid in the development of antibiotics and immune modulators by expanding the understanding of how PG is processed by lytic enzymes.
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Affiliation(s)
- Yiben Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Klare M. Lazor
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Kristen E. DeMeester
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Hai Liang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Tyler K. Heiss
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Catherine L. Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
- Department of Biological Chemistry, University of Delaware, Newark, DE 19716, USA
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8
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Koch A, Hansen DA, Shende VV, Furan LR, Houk KN, Jiménez-Osés G, Sherman DH. A Single Active Site Mutation in the Pikromycin Thioesterase Generates a More Effective Macrocyclization Catalyst. J Am Chem Soc 2017; 139:13456-13465. [PMID: 28836768 PMCID: PMC5617804 DOI: 10.1021/jacs.7b06436] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Indexed: 11/28/2022]
Abstract
Macrolactonization of natural product analogs presents a significant challenge to both biosynthetic assembly and synthetic chemistry. In the preceding paper , we identified a thioesterase (TE) domain catalytic bottleneck processing unnatural substrates in the pikromycin (Pik) system, preventing the formation of epimerized macrolactones. Here, we perform molecular dynamics simulations showing the epimerized hexaketide was accommodated within the Pik TE active site; however, intrinsic conformational preferences of the substrate resulted in predominately unproductive conformations, in agreement with the observed hydrolysis. Accordingly, we engineered the stereoselective Pik TE to yield a variant (TES148C) with improved reaction kinetics and gain-of-function processing of an unnatural, epimerized hexaketide. Quantum mechanical comparison of model TES148C and TEWT reaction coordinate diagrams revealed a change in mechanism from a stepwise addition-elimination (TEWT) to a lower energy concerted acyl substitution (TES148C), accounting for the gain-of-function and improved reaction kinetics. Finally, we introduced the S148C mutation into a polyketide synthase module (PikAIII-TE) to impart increased substrate flexibility, enabling the production of diastereomeric macrolactones.
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Affiliation(s)
- Aaron
A. Koch
- Life
Sciences Institute, Cancer Biology Graduate Program, Department of Medicinal Chemistry, Program in Chemical
Biology, Department of Chemistry, and Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Douglas A. Hansen
- Life
Sciences Institute, Cancer Biology Graduate Program, Department of Medicinal Chemistry, Program in Chemical
Biology, Department of Chemistry, and Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vikram V. Shende
- Life
Sciences Institute, Cancer Biology Graduate Program, Department of Medicinal Chemistry, Program in Chemical
Biology, Department of Chemistry, and Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Lawrence R. Furan
- Life
Sciences Institute, Cancer Biology Graduate Program, Department of Medicinal Chemistry, Program in Chemical
Biology, Department of Chemistry, and Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Gonzalo Jiménez-Osés
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - David H. Sherman
- Life
Sciences Institute, Cancer Biology Graduate Program, Department of Medicinal Chemistry, Program in Chemical
Biology, Department of Chemistry, and Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
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9
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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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10
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Gil A, Albericio F, Álvarez M. Role of the Nozaki–Hiyama–Takai–Kishi Reaction in the Synthesis of Natural Products. Chem Rev 2017. [DOI: 10.1021/acs.chemrev.7b00144] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Alejandro Gil
- ChemBio Lab, Barcelona Science Park, Baldiri Reixac 10, E-08028 Barcelona, Spain
- CIBER-BBN,
Networking
Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Fernando Albericio
- ChemBio Lab, Barcelona Science Park, Baldiri Reixac 10, E-08028 Barcelona, Spain
- CIBER-BBN,
Networking
Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
- University of Kwa-Zulu-Natal, 4001, Durban, South Africa
| | - Mercedes Álvarez
- ChemBio Lab, Barcelona Science Park, Baldiri Reixac 10, E-08028 Barcelona, Spain
- CIBER-BBN,
Networking
Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
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11
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Gober CM, Joullié MM. Joining Forces: Fermentation and Organic Synthesis for the Production of Complex Heterocycles. J Org Chem 2016; 81:10136-10144. [PMID: 27427903 PMCID: PMC5096955 DOI: 10.1021/acs.joc.6b01308] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Commercial application of many promising heterocyclic natural products is limited by their natural abundance. While organic synthesis provides access to many natural products, total synthesis of numerous complex molecules is not economically feasible. In recent years, the combination of fermentation and organic synthesis has provided a new route for the production of complex heterocycles that are inaccessible by typical synthetic methods. This JOCSynopsis will review examples of how this union of disciplines has overcome obstacles in both academia and industry.
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Affiliation(s)
- Claire M. Gober
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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12
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Argyropoulos P, Bergeret F, Pardin C, Reimer JM, Pinto A, Boddy CN, Schmeing TM. Towards a characterization of the structural determinants of specificity in the macrocyclizing thioesterase for deoxyerythronolide B biosynthesis. Biochim Biophys Acta Gen Subj 2016; 1860:486-97. [DOI: 10.1016/j.bbagen.2015.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/13/2015] [Accepted: 11/20/2015] [Indexed: 12/12/2022]
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13
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Horsman ME, Hari TPA, Boddy CN. Polyketide synthase and non-ribosomal peptide synthetase thioesterase selectivity: logic gate or a victim of fate? Nat Prod Rep 2016; 33:183-202. [DOI: 10.1039/c4np00148f] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thioesterases (TEs) are product offloading enzymes from FAS, PKS, and NRPS complexes. We review the diversity, structure, and mechanism of PKS and NRPS TEs and analyze TE loading and release steps as possible logic gates with a view to predicting TE function in new pathways.
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Affiliation(s)
- Mark E. Horsman
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
| | - Taylor P. A. Hari
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
| | - Christopher N. Boddy
- Department of chemistry
- Centre for Catalysis Research and Innovation
- University of Ottawa
- Canada
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14
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Ahmadi MK, Fawaz S, Fang L, Yu Z, Pfeifer BA. Molecular variation of the nonribosomal peptide-polyketide siderophore yersiniabactin through biosynthetic and metabolic engineering. Biotechnol Bioeng 2015; 113:1067-74. [DOI: 10.1002/bit.25872] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 10/29/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Mahmoud Kamal Ahmadi
- Department of Chemical and Biological Engineering; University at Buffalo; The State University of New York; Buffalo New York
| | - Samar Fawaz
- Department of Chemical and Biological Engineering; University at Buffalo; The State University of New York; Buffalo New York
| | - Lei Fang
- Department of Chemical and Biological Engineering; University at Buffalo; The State University of New York; Buffalo New York
| | - Zhipeng Yu
- Department of Chemistry; University at Buffalo; The State University of New York; Buffalo New York
| | - Blaine A Pfeifer
- Department of Chemical and Biological Engineering; University at Buffalo; The State University of New York; Buffalo New York
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15
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Zhang L, Mori T, Zheng Q, Awakawa T, Yan Y, Liu W, Abe I. Rational Control of Polyketide Extender Units by Structure‐Based Engineering of a Crotonyl‐CoA Carboxylase/Reductase in Antimycin Biosynthesis. Angew Chem Int Ed Engl 2015; 54:13462-5. [DOI: 10.1002/anie.201506899] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Lihan Zhang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Qingfei Zheng
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Yan Yan
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Wen Liu
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
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16
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Harnessing natural product assembly lines: structure, promiscuity, and engineering. J Ind Microbiol Biotechnol 2015; 43:371-87. [PMID: 26527577 DOI: 10.1007/s10295-015-1704-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/18/2015] [Indexed: 10/22/2022]
Abstract
Many therapeutically relevant natural products are biosynthesized by the action of giant mega-enzyme assembly lines. By leveraging the specificity, promiscuity, and modularity of assembly lines, a variety of strategies has been developed that enables the biosynthesis of modified natural products. This review briefly summarizes recent structural advances related to natural product assembly lines, discusses chemical approaches to probing assembly line structures in the absence of traditional biophysical data, and surveys efforts that harness the inherent or engineered promiscuity of assembly lines for the synthesis of non-natural polyketides and non-ribosomal peptide analogues.
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17
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Zhang L, Mori T, Zheng Q, Awakawa T, Yan Y, Liu W, Abe I. Rational Control of Polyketide Extender Units by Structure‐Based Engineering of a Crotonyl‐CoA Carboxylase/Reductase in Antimycin Biosynthesis. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506899] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lihan Zhang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Qingfei Zheng
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
| | - Yan Yan
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Wen Liu
- State Key Laboratory of Bio‐Organic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling road 345, Shanghai 200032 (China)
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7‐3‐1 Hongo, Bunkyo‐ku, Tokyo 113‐0033 (Japan)
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18
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19
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Giuliano MW, Miller SJ. Site-Selective Reactions with Peptide-Based Catalysts. SITE-SELECTIVE CATALYSIS 2015; 372:157-201. [DOI: 10.1007/128_2015_653] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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Jenner M, Afonso JP, Bailey HR, Frank S, Kampa A, Piel J, Oldham NJ. Acyl-Chain Elongation Drives Ketosynthase Substrate Selectivity intrans-Acyltransferase Polyketide Synthases. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Jenner M, Afonso JP, Bailey HR, Frank S, Kampa A, Piel J, Oldham NJ. Acyl-chain elongation drives ketosynthase substrate selectivity in trans-acyltransferase polyketide synthases. Angew Chem Int Ed Engl 2014; 54:1817-21. [PMID: 25529827 DOI: 10.1002/anie.201410219] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 11/10/2014] [Indexed: 11/09/2022]
Abstract
Type I modular polyketide synthases (PKSs), which are responsible for the biosynthesis of many biologically active agents, possess a ketosynthase (KS) domain within each module to catalyze chain elongation. Acylation of the KS active site Cys residue is followed by transfer to malonyl-ACP to yield an extended β-ketoacyl chain (ACP = acyl carrier protein). To date, the precise contribution of KS selectivity in controlling product fidelity has been unclear. Six KS domains from trans-acyltransferase (trans-AT) PKSs were subjected to a mass spectrometry based elongation assay, and higher substrate selectivity was identified for the elongating step than in preceding acylation. A close correspondence between the observed KS selectivity and that predicted by phylogenetic analysis was seen. These findings provide insights into the mechanism of KS selectivity in this important group of PKSs, can serve as guidance for engineering, and show that targeted mutagenesis can be used to expand the repertoire of acceptable substrates.
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Affiliation(s)
- Matthew Jenner
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD (UK)
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22
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Hari TPA, Labana P, Boileau M, Boddy CN. An evolutionary model encompassing substrate specificity and reactivity of type I polyketide synthase thioesterases. Chembiochem 2014; 15:2656-61. [PMID: 25354333 DOI: 10.1002/cbic.201402475] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Indexed: 11/10/2022]
Abstract
Bacterial polyketides are a rich source of chemical diversity and pharmaceutical agents. Understanding the biochemical basis for their biosynthesis and the evolutionary driving force leading to this diversity is essential to take advantage of the enzymes as biocatalysts and to access new chemical diversity for drug discovery. Biochemical characterization of the thioesterase (TE) responsible for 6-deoxyerythronolide macrocyclization shows that a small, evolutionarily accessible change to the substrate can increase the chemical diversity of products, including macrodiolide formation. We propose an evolutionary model in which TEs are by nature non-selective for the type of chemistry they catalyze, producing a range of metabolites. As one metabolite becomes essential for improving fitness in a particular environment, the TE evolves to enrich for that corresponding reactivity. This hypothesis is supported by our phylogenetic analysis, showing convergent evolution of macrodiolide-forming TEs.
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Affiliation(s)
- Taylor P A Hari
- Departments of Chemistry and Biology, Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON K1N 6N5 (Canada)
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23
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Abstract
Natural products are important sources of pharmaceuticals, in part owing to their diverse biological activities. Enzymes from natural product biosynthetic pathways have become attractive candidates as biocatalysts for modifying the structures and bioactivities of these complex compounds. Numerous enzymes have been harvested to generate innovative scaffolds, large-scale synthesis of chiral building blocks, and semisynthesis of medicinally relevant natural product derivatives. This review discusses recent examples from three areas: (a) polyketide catalytic domain engineering geared toward synthesis of new polyketides, (b) engineering of tailoring enzymes (other than oxidative enzymes) as biocatalysts, and (c) in vitro total synthesis of natural products using purified enzyme components. With the availability of exponentially increasing genomic information and new genome mining tools, many new and powerful biocatalysts tailored for pharmaceutical synthesis will likely emerge from secondary metabolism.
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25
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Precursor-Directed Biosynthesis of Curcumin Analogs inEscherichia coli. Biosci Biotechnol Biochem 2014; 74:641-5. [DOI: 10.1271/bbb.90866] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Cummings M, Breitling R, Takano E. Steps towards the synthetic biology of polyketide biosynthesis. FEMS Microbiol Lett 2014; 351:116-25. [PMID: 24372666 PMCID: PMC4237116 DOI: 10.1111/1574-6968.12365] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 11/29/2022] Open
Abstract
Nature is providing a bountiful pool of valuable secondary metabolites, many of which possess therapeutic properties. However, the discovery of new bioactive secondary metabolites is slowing down, at a time when the rise of multidrug-resistant pathogens and the realization of acute and long-term side effects of widely used drugs lead to an urgent need for new therapeutic agents. Approaches such as synthetic biology are promising to deliver a much-needed boost to secondary metabolite drug development through plug-and-play optimized hosts and refactoring novel or cryptic bacterial gene clusters. Here, we discuss this prospect focusing on one comprehensively studied class of clinically relevant bioactive molecules, the polyketides. Extensive efforts towards optimization and derivatization of compounds via combinatorial biosynthesis and classical engineering have elucidated the modularity, flexibility and promiscuity of polyketide biosynthetic enzymes. Hence, a synthetic biology approach can build upon a solid basis of guidelines and principles, while providing a new perspective towards the discovery and generation of novel and new-to-nature compounds. We discuss the lessons learned from the classical engineering of polyketide synthases and indicate their importance when attempting to engineer biosynthetic pathways using synthetic biology approaches for the introduction of novelty and overexpression of products in a controllable manner.
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Affiliation(s)
- Matthew Cummings
- Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
| | - Rainer Breitling
- Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
| | - Eriko Takano
- Faculty of Life Sciences, Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
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27
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Sandy M, Zhu X, Rui Z, Zhang W. Characterization of AntB, a Promiscuous Acyltransferase Involved in Antimycin Biosynthesis. Org Lett 2013; 15:3396-9. [DOI: 10.1021/ol4014365] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Moriah Sandy
- Department of Chemical and Biomolecular Engineering and Energy Biosciences Institute, University of California, Berkeley, California 94720, United States
| | - Xuejun Zhu
- Department of Chemical and Biomolecular Engineering and Energy Biosciences Institute, University of California, Berkeley, California 94720, United States
| | - Zhe Rui
- Department of Chemical and Biomolecular Engineering and Energy Biosciences Institute, University of California, Berkeley, California 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering and Energy Biosciences Institute, University of California, Berkeley, California 94720, United States
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28
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Pan E, Oswald NW, Legako AG, Life JM, Posner BA, MacMillan JB. Precursor-Directed Generation of Amidine Containing Ammosamide Analogs: Ammosamides E-P. Chem Sci 2013; 4:482-488. [PMID: 23209870 PMCID: PMC3510655 DOI: 10.1039/c2sc21442c] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Ammosamides E-F (1-2), are amidine analogs of the ammosamide family of alkaloids isolated from a marine-derived Streptomyces variabilis. Further studies with S. variabilis revealed a variety of aryl and alkyl amines added into the fermentation media could be efficiently incorporated into the ammosamide framework to generate a library of precursor-directed amidine analogs, ammosamides G-P (9 - 18). We demonstrate that the amines are introduced via non-enzymatic addition to the iminium ion of ammosamide C. Biological evaluation of the amidine analogs against quinone reductase 2 (QR2) showed low nM potency for a number of analogs. When tested for in vivo activity against a panel of non-small cell lung cancer (NSCLC) cell-lines there was a clear increase in potency by incorporation of lipophilic alkylamines, with the most potent compounds having sub μM IC(50) values (0.4 to 0.8 μM).
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Affiliation(s)
- Ende Pan
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, USA
| | - Nathaniel W. Oswald
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, USA
| | - Aaron G. Legako
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, USA
| | - Janie M. Life
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, USA
| | - Bruce A. Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, USA
| | - John B. MacMillan
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, USA
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29
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Cobb RE, Luo Y, Freestone T, Zhao H. Drug Discovery and Development via Synthetic Biology. Synth Biol (Oxf) 2013. [DOI: 10.1016/b978-0-12-394430-6.00010-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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30
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Yuzawa S, Kim W, Katz L, Keasling JD. Heterologous production of polyketides by modular type I polyketide synthases in Escherichia coli. Curr Opin Biotechnol 2012; 23:727-35. [DOI: 10.1016/j.copbio.2011.12.029] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 12/19/2011] [Accepted: 12/21/2011] [Indexed: 11/15/2022]
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31
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Abstract
Advanced biofuels produced by microorganisms have similar properties to petroleum-based fuels, and can 'drop in' to the existing transportation infrastructure. However, producing these biofuels in yields high enough to be useful requires the engineering of the microorganism's metabolism. Such engineering is not based on just one specific feedstock or host organism. Data-driven and synthetic-biology approaches can be used to optimize both the host and pathways to maximize fuel production. Despite some success, challenges still need to be met to move advanced biofuels towards commercialization, and to compete with more conventional fuels.
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32
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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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33
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Goss RJM, Shankar S, Fayad AA. The generation of "unnatural" products: synthetic biology meets synthetic chemistry. Nat Prod Rep 2012; 29:870-89. [PMID: 22744619 DOI: 10.1039/c2np00001f] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Natural product analogue generation is important, providing tools for chemical biology, enabling structure activity relationship determination and insight into the way in which natural products interact with their target biomolecules. The generation of analogues is also often necessary in order to improve bioavailability and to fine tune compounds' activity. This review provides an overview of the catalogue of approaches available for accessing series of analogues. Over the last few years there have been major advances in genome sequencing and the development of tools for biosynthetic pathway engineering; it is therefore becoming increasingly easy to combine molecular biology and synthetic organic chemistry in order to enable expeditious access to series of natural products. This review outlines the various ways of combining biology and chemistry that have been applied to analogue generation, drawing upon a series of examples to illustrate each approach.
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Affiliation(s)
- Rebecca J M Goss
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, UKNR4 7TJ
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34
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Pinto A, Wang M, Horsman M, Boddy CN. 6-Deoxyerythronolide B synthase thioesterase-catalyzed macrocyclization is highly stereoselective. Org Lett 2012; 14:2278-81. [PMID: 22519860 DOI: 10.1021/ol300707j] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Macrocyclic polyketide natural products are an indispensable source of therapeutic agents. The final stage of their biosynthesis, macrocyclization, is catalyzed regio- and stereoselectively by a thioesterase. A panel of substrates were synthesized to test their specificity for macrocyclization by the erythromycin polyketide synthase TE (DEBS TE) in vitro. It was shown that DEBS TE is highly stereospecific, successfully macrocyclizing a 14-member ring substrate with an R configured O-nucleophile, and highly regioselective, generating exclusively the 14-member lactone over the 12-member lactone.
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Affiliation(s)
- Atahualpa Pinto
- Department of Chemistry, Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON, Canada T1N 6N5
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35
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Wong FT, Khosla C. Combinatorial biosynthesis of polyketides--a perspective. Curr Opin Chem Biol 2012; 16:117-23. [PMID: 22342766 DOI: 10.1016/j.cbpa.2012.01.018] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 12/19/2011] [Accepted: 01/27/2012] [Indexed: 12/29/2022]
Abstract
Since their discovery, polyketide synthases have been attractive targets of biosynthetic engineering to make 'unnatural' natural products. Although combinatorial biosynthesis has made encouraging advances over the past two decades, the field remains in its infancy. In this enzyme-centric perspective, we discuss the scientific and technological challenges that could accelerate the adoption of combinatorial biosynthesis as a method of choice for the preparation of encoded libraries of bioactive small molecules. Borrowing a page from the protein structure prediction community, we propose a periodic challenge program to vet the most promising methods in the field, and to foster the collective development of useful tools and algorithms.
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Affiliation(s)
- Fong T Wong
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, United States
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36
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Prasad G, Amoroso JW, Borketey LS, Schnarr NA. N-activated β-lactams as versatile reagents for acyl carrier protein labeling. Org Biomol Chem 2012; 10:1992-2002. [PMID: 22293823 DOI: 10.1039/c2ob06846j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Acyl carrier proteins are critical components of fatty acid and polyketide biosynthesis. Their primary function is to shuttle intermediates between active sites via a covalently bound phosphopantetheine arm. Small molecules capable of acylating this prosthetic group will provide a simple and reversible means of introducing novel functionality onto carrier protein domains. A series of N-activated β-lactams are prepared to examine site-specific acylation of the phosphopantetheine-thiol. In general, β-lactams are found to be significantly more reactive than our previously studied β-lactones. Selectivity for the holo over apo-form of acyl carrier proteins is demonstrated indicating that only the phosphopantetheine-thiol is modified. Incorporation of an N-propargyloxycarbonyl group provides an alkyne handle for conjugation to fluorophores and affinity labels. The utility of these groups for mechanistic interrogation of a critical step in polyketide biosynthesis is examined through comparison to traditional probes. In all, we expect the probes described in this study to serve as valuable and versatile tools for mechanistic interrogation.
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Affiliation(s)
- Gitanjeli Prasad
- Department of Chemistry, University of Massachusetts, 710 N. Pleasant Street, Amherst, Massachusetts 01003, USA
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37
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Glenn WS, Nims E, O’Connor SE. Reengineering a Tryptophan Halogenase To Preferentially Chlorinate a Direct Alkaloid Precursor. J Am Chem Soc 2011; 133:19346-9. [DOI: 10.1021/ja2089348] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Weslee S. Glenn
- Department of Biological Chemistry, The John Innes Centre, Norwich NR4 7UH, U.K
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ezekiel Nims
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sarah E. O’Connor
- Department of Biological Chemistry, The John Innes Centre, Norwich NR4 7UH, U.K
- The University of East Anglia, Norwich NR4 7TJ, U.K
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39
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Zhang H, Boghigian BA, Armando J, Pfeifer BA. Methods and options for the heterologous production of complex natural products. Nat Prod Rep 2011; 28:125-51. [PMID: 21060956 PMCID: PMC9896020 DOI: 10.1039/c0np00037j] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This review will detail the motivations, experimental approaches, and growing list of successful cases associated with the heterologous production of complex natural products.
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Affiliation(s)
- Haoran Zhang
- Department of Chemical & Biological Engineering, Science & Technology Center, Tufts University, Medford, MA 02155, USA.
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40
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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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Zhang H, Wang Y, Wu J, Skalina K, Pfeifer BA. Complete Biosynthesis of Erythromycin A and Designed Analogs Using E. coli as a Heterologous Host. ACTA ACUST UNITED AC 2010; 17:1232-40. [DOI: 10.1016/j.chembiol.2010.09.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/05/2010] [Accepted: 09/14/2010] [Indexed: 10/18/2022]
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43
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Using chemobiosynthesis and synthetic mini-polyketide synthases to produce pharmaceutical intermediates in Escherichia coli. Appl Environ Microbiol 2010; 76:5221-7. [PMID: 20543042 DOI: 10.1128/aem.02961-09] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recombinant microbial whole-cell biocatalysis is a valuable approach for producing enantiomerically pure intermediates for the synthesis of complex molecules. Here, we describe a method to produce polyketide intermediates possessing multiple stereogenic centers by combining chemobiosynthesis and engineered mini-polyketide synthases (PKSs). Chemobiosynthesis allows the introduction of unnatural moieties, while a library of synthetic bimodular PKSs expressed from codon-optimized genes permits the introduction of a variety of ketide units. To validate the approach, intermediates for the synthesis of trans-9,10-dehydroepothilone D were generated. The designer molecules obtained have the potential to greatly reduce the manufacturing cost of epothilone analogues, thus facilitating their commercial development as therapeutic agents.
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Goranovic D, Kosec G, Mrak P, Fujs S, Horvat J, Kuscer E, Kopitar G, Petkovic H. Origin of the allyl group in FK506 biosynthesis. J Biol Chem 2010; 285:14292-300. [PMID: 20194504 DOI: 10.1074/jbc.m109.059600] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
FK506 (tacrolimus) is a secondary metabolite with a potent immunosuppressive activity, currently registered for use as immunosuppressant after organ transplantation. FK506 and FK520 are biogenetically related natural products that are synthesized by combined polyketide synthase/nonribosomal peptide synthetase systems. The entire gene cluster for biosynthesis of FK520 from Streptomyces hygroscopicus var. ascomyceticus has been cloned and sequenced. On the other hand, the FK506 gene cluster from Streptomyces sp. MA6548 (ATCC55098) was sequenced only partially, and it was reasonable to expect that additional genes would be required for the provision of substrate supply. Here we report the identification of a previously unknown region of the FK506 gene cluster from Streptomyces tsukubaensis NRRL 18488 containing genes encoding the provision of unusual building blocks for FK506 biosynthesis as well as a regulatory gene. Among others, we identified a group of genes encoding biosynthesis of the extender unit that forms the allyl group at carbon 21 of FK506. Interestingly, we have identified a small independent diketide synthase system involved in the biosynthesis of the allyl group. Inactivation of one of these genes, encoding an unusual ketosynthase domain, resulted in an FK506 nonproducing strain, and the production was restored when a synthetic analog of the allylmalonyl-CoA extender unit was added to the cultivation medium. Based on our results, we propose a biosynthetic pathway for the provision of an unusual five-carbon extender unit, which is carried out by a novel diketide synthase complex.
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Affiliation(s)
- Dusan Goranovic
- Acies Bio d.o.o., Tehnoloski Park 21, SI-1000 Ljubljana, Slovenia
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Mortison JD, Kittendorf JD, Sherman DH. Synthesis and biochemical analysis of complex chain-elongation intermediates for interrogation of molecular specificity in the erythromycin and pikromycin polyketide synthases. J Am Chem Soc 2009; 131:15784-93. [PMID: 19810731 PMCID: PMC2796446 DOI: 10.1021/ja9060596] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 6-deoxyerythronolide B synthase (DEBS) and pikromycin (Pik) polyketide synthase (PKS) are unique multifunctional enzyme systems that are responsible for the biosynthesis of the erythromycin and pikromycin 14-membered ring aglycones, respectively. Together, these natural product biosynthetic systems provide excellent platforms to examine the fundamental structural and catalytic elements that govern polyketide assembly, processing, and macrocyclization. In these studies, the native pentaketide intermediate for DEBS was synthesized and employed for in vitro chemoenzymatic synthesis of macrolactone products in engineered monomodules Ery5, Ery5-TE, and Ery6. A comparative analysis was performed with the corresponding Pik module 5 (PikAIII) and module 6 (PikAIV), dissecting key similarities and differences between these highly related PKSs. The data revealed that individual modules in the DEBS and Pik PKSs possess distinctive molecular selectivity profiles and suggest that substrate recognition has evolved unique characteristics in each system.
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Affiliation(s)
- Jonathan D Mortison
- Life Sciences Institute, Department of Chemistry, 210 Washtenaw Avenue, University of Michigan, Ann Arbor, Michigan 48109, USA
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Enhancement of Lovastatin Production by Supplementing Polyketide Antibiotics to the Submerged Culture of Aspergillus terreus. Appl Biochem Biotechnol 2009; 160:2014-25. [DOI: 10.1007/s12010-009-8762-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2009] [Accepted: 08/17/2009] [Indexed: 11/30/2022]
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Yan J, Gupta S, Sherman DH, Reynolds KA. Functional dissection of a multimodular polypeptide of the pikromycin polyketide synthase into monomodules by using a matched pair of heterologous docking domains. Chembiochem 2009; 10:1537-43. [PMID: 19437523 PMCID: PMC4652847 DOI: 10.1002/cbic.200900098] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Indexed: 11/08/2022]
Abstract
The pikromyin polyketide synthase (PKS) in Streptomyces venezulae is comprised of a loading module and six extension modules, which generate the corresponding 14-membered macrolactone product. PikAI is a multimodular component of this PKS and houses both the loading domain and the first two extension modules, joined by short intraprotein linkers. We have shown that PikAI can be separated into two proteins at either of these linkers, only when matched pairs of docking domains (DDs) from a heterologous modular phoslactomycin PKS are used in place of the intraprotein linker. In both cases the yields of pikromycin produced by the S. venezuelae mutant were 50% of that of a S. venezuelae strain expressing the native trimodular PikAI. This observation provides the first demonstration that such separations do not dramatically impact the efficiency of the entire in vivo biosynthetic process. Expression of module 2 as a monomodular protein fused to a heterologous N-terminal docking domain was also observed to give almost a tenfold improvement in the in vivo generation of pikromycin from a synthetic diketide intermediate. These results demonstrate the utility of DDs to manipulate biosynthetic processes catalyzed by modular PKSs and the quest to generate novel polyketide products.
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Affiliation(s)
- John Yan
- Department of Chemistry, Portland State University, 262 Science Building 2, 1719 SW 10th Avenue, Portland, OR 97201, FAX: 503- 725 9525
| | - Shuchi Gupta
- Department of Chemistry, Portland State University, 262 Science Building 2, 1719 SW 10th Avenue, Portland, OR 97201, FAX: 503- 725 9525
| | - David H. Sherman
- Life Sciences Institute and Department of Medicinal Chemistry, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, Fax: 734-615-3641
| | - Kevin A. Reynolds
- Department of Chemistry, Portland State University, 262 Science Building 2, 1719 SW 10th Avenue, Portland, OR 97201, FAX: 503- 725 9525
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Abstract
Acidic lipopeptide antibiotics are a new class of potent antibiotics, which includes daptomycin, A54145, calcium-dependent antibiotics (CDAs), friulimicins/amphomycins, laspartomycin/glycinocins and others. The importance of this novel class is exemplified by the success story of the clinically approved daptomycin, which is used for the treatment of skin infections and bacteremia caused by multidrug-resistant bacteria, including methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci. The potency of acidic lipopeptides is inherent in their chemical structure. The nonribosomally synthesized peptide cores consist of eleven to 13 amino acids, which are rigidified by the formation of a ten-membered ring. An N-terminal fatty acid, which facilitates insertion into the lipid bilayer of bacterial membranes, completes the structure. All these antibiotics contain multiple nonproteinogenic amino acids as well as different lipid tails; this yields remarkable structural diversity. This review summarizes the observed structural variety through a detailed description of the composition of the acidic lipopeptides. Furthermore, engineering approaches towards novel lipopeptides are presented. Recent discoveries in the field of tailoring enzymes, which enable structural plurality mainly by amino and fatty acid precursor biosynthesis, are highlighted.
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Affiliation(s)
- Matthias Strieker
- Chemistry and Biochemistry Department, Philipps-University Marburg, Hans-Meerwein-Strasse, Marburg, Germany
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Kusche BR, Phillips JB, Priestley ND. Nonactin biosynthesis: setting limits on what can be achieved with precursor-directed biosynthesis. Bioorg Med Chem Lett 2009; 19:1233-5. [PMID: 19167217 PMCID: PMC2854622 DOI: 10.1016/j.bmcl.2008.12.096] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 12/16/2008] [Accepted: 12/17/2008] [Indexed: 11/30/2022]
Abstract
Nonactin, produced by Streptomyces griseus ETH A7796, is a macrotetrolide assembled from nonactic acid. It is an effective inhibitor of drug efflux in multidrug resistant erythroleukemia K562 cells at sub-toxic concentrations and has been shown to possess both antibacterial and antitumor activity. As total synthesis is impractical for the generation of nonactin analogs we have studied precursor-directed biosynthesis as an alternative as it is known that nonactic acid can serve as a nonactin precursor in vivo. To determine the scope of the approach we prepared and evaluated a furan-based nonactic acid derivative, 11. Although no new nonactin analogs were detected when 11 was administered to S. griseus fermentative cultures, a significant inhibition of nonactin biosynthesis was noted (IC(50) approximately 100 microM). Cell mass, nonactic acid production and the generation of other secondary metabolites in the culture were unaffected by 11 demonstrating that 11 selectively inhibited the assembly of nonactin from nonactic acid. While we were unable to generate new nonactin analogs we have discovered, however, a useful inhibitor that we can use to probe the mechanism of nonactin assembly with the ultimate goal of developing more successful precursor-directed biosynthesis transformations.
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Affiliation(s)
- Brian R Kusche
- Department of Chemistry, The University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
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