1
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Huang S, Ji H, Zheng J. Structural and computational insights into the substrate specificity of acyltransferase domains from modular polyketide synthases. FEBS J 2024; 291:3839-3855. [PMID: 38922792 DOI: 10.1111/febs.17206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/19/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Polyketides are natural products synthesized by polyketide synthases (PKSs), where acyltransferase (AT) domains play a crucial role in selection of extender units. Engineering of AT domains enables the site-specific incorporation of non-natural extender units, leading to generation of novel derivatives. Here, we determined the crystal structures of AT domains from the fifth module of tylosin PKS (TylAT5) derived from Streptomyces fradiae and the eighth module of spinosad PKS (SpnAT8) derived from Saccharopolyspora spinosa, and combined them with molecular dynamics simulations and enzyme kinetic studies to elucidate the molecular basis of substrate selection. The ethylmalonyl-CoA-specific conserved motif TAGH of TylAT5 and the MMCoA-specific conserved motif YASH of SpnAT8 were identified within the substrate-binding pocket, and several key residues close to the substrate acyl moiety were located. Through site-directed mutagenesis of four residues near the active site, we successfully reprogrammed the specificity of these two AT domains toward malonyl-CoA. Mutations in TylAT5 enhanced its catalytic activity 2.6-fold toward malonyl-CoA, and mutations in SpnAT8 eliminated the substrate promiscuity. These results extend our understanding of AT substrate specificity and would benefit the engineering of PKSs.
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Affiliation(s)
- Shuxin Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, China
| | - Huining Ji
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, China
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2
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Wang K, Liu N, Liu M, Zhao P, Zhong N, Challis GL, Huang Y. Discovery and Biosynthesis of Streptolateritic Acids A-D: Acyclic Pentacarboxylic Acids from Streptomyces sp. FXJ1.172 with Promising Activity against Potato Common Scab. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14760-14768. [PMID: 38899439 DOI: 10.1021/acs.jafc.4c02572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Potato common scab (PCS) is a widespread plant disease that lacks effective control measures. Using a small molecule elicitor, we activate the production of a novel class of polyketide antibiotics, streptolateritic acids A-D, in Streptomyces sp. FXJ1.172. These compounds show a promising control efficacy against PCS and an unusual acyclic pentacarboxylic acid structure. A gene cluster encoding a type I modular polyketide synthase is identified to be responsible for the biosynthesis of these metabolites. A cytochrome P450 (CYP) and an aldehyde dehydrogenase (ADH) encoded by two genes in the cluster are proposed to catalyze iterative oxidation of the starter-unit-derived methyl group and three of six branching methyl groups to carboxylic acids during chain assembly. Our findings highlight how activation of silent biosynthetic gene clusters can be employed to discover completely new natural product classes able to combat PCS and new types of modular polyketide synthase-based biosynthetic machinery.
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Affiliation(s)
- Kairui Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, PR China
| | - Ning Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Minghao Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Pan Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Naiqin Zhong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Gregory L Challis
- Department of Chemistry, 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 Peptide and Protein Science, Monash University, Clayton VIC 3800, Australia
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, PR China
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3
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Kissman EN, Sosa MB, Millar DC, Koleski EJ, Thevasundaram K, Chang MCY. Expanding chemistry through in vitro and in vivo biocatalysis. Nature 2024; 631:37-48. [PMID: 38961155 DOI: 10.1038/s41586-024-07506-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/01/2024] [Indexed: 07/05/2024]
Abstract
Living systems contain a vast network of metabolic reactions, providing a wealth of enzymes and cells as potential biocatalysts for chemical processes. The properties of protein and cell biocatalysts-high selectivity, the ability to control reaction sequence and operation in environmentally benign conditions-offer approaches to produce molecules at high efficiency while lowering the cost and environmental impact of industrial chemistry. Furthermore, biocatalysis offers the opportunity to generate chemical structures and functions that may be inaccessible to chemical synthesis. Here we consider developments in enzymes, biosynthetic pathways and cellular engineering that enable their use in catalysis for new chemistry and beyond.
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Affiliation(s)
- Elijah N Kissman
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Max B Sosa
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Douglas C Millar
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Edward J Koleski
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | | | - Michelle C Y Chang
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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4
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Chen L, Liu K, Hong J, Cui Z, He W, Wang Y, Deng Z, Tao M. The Discovery of Weddellamycin, a Tricyclic Polyene Macrolactam Antibiotic from an Antarctic Deep-Sea-Derived Streptomyces sp. DSS69, by Heterologous Expression. Mar Drugs 2024; 22:189. [PMID: 38667806 PMCID: PMC11051340 DOI: 10.3390/md22040189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/11/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Polyene macrolactams are a special group of natural products with great diversity, unique structural features, and a wide range of biological activities. Herein, a cryptic gene cluster for the biosynthesis of putative macrolactams was disclosed from a sponge-associated bacterium, Streptomyces sp. DSS69, by genome mining. Cloning and heterologous expression of the whole biosynthetic gene cluster led to the discovery of weddellamycin, a polyene macrolactam bearing a 23/5/6 ring skeleton. A negative regulator, WdlO, and two positive regulators, WdlA and WdlB, involved in the regulation of weddellamycin production were unraveled. The fermentation titer of weddellamycin was significantly improved by overexpression of wdlA and wdlB and deletion of wdlO. Notably, weddellamycin showed remarkable antibacterial activity against various Gram-positive bacteria including MRSA, with MIC values of 0.10-0.83 μg/mL, and antifungal activity against Candida albicans, with an MIC value of 3.33 μg/mL. Weddellamycin also displayed cytotoxicity against several cancer cell lines, with IC50 values ranging from 2.07 to 11.50 µM.
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Affiliation(s)
- Lu Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Kai Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Jiali Hong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Zhanzhao Cui
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Weijun He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Yemin Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Meifeng Tao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
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5
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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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6
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Heo KT, Lee B, Hwang GJ, Park B, Jang JP, Hwang BY, Jang JH, Hong YS. A unique dual acyltransferase system shared in the polyketide chain initiation of kidamycinone and rubiflavinone biosynthesis. Front Microbiol 2023; 14:1274358. [PMID: 38029143 PMCID: PMC10646177 DOI: 10.3389/fmicb.2023.1274358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023] Open
Abstract
The pluramycin family of natural products has diverse substituents at the C2 position, which are closely related to their biological activity. Therefore, it is important to understand the biosynthesis of C2 substituents. In this study, we describe the biosynthesis of C2 moieties in Streptomyces sp. W2061, which produces kidamycin and rubiflavinone C-1, containing anthrapyran aglycones. Sequence analysis of the loading module (Kid13) of the PKS responsible for the synthesis of these anthrapyran aglycones is useful for confirming the incorporation of atypical primer units into the corresponding products. Kid13 is a ketosynthase-like decarboxylase (KSQ)-type loading module with unusual dual acyltransferase (AT) domains (AT1-1 and AT1-2). The AT1-2 domain primarily loads ethylmalonyl-CoA and malonyl-CoA for rubiflavinone and kidamycinone and rubiflavinone, respectively; however, the AT1-1 domain contributed to the functioning of the AT1-2 domain to efficiently load ethylmalonyl-CoA for rubiflavinone. We found that the dual AT system was involved in the production of kidamycinone, an aglycone of kidamycin, and rubiflavinone C-1 by other shared biosynthetic genes in Streptomyces sp. W2061. This study broadens our understanding of the incorporation of atypical primer units into polyketide products.
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Affiliation(s)
- Kyung Taek Heo
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Byeongsan Lee
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
- College of Pharmacy, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Gwi Ja Hwang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Beomcheol Park
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
- College of Pharmacy, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Jun-Pil Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Bang Yeon Hwang
- College of Pharmacy, Chungbuk National University, Cheongju-si, Republic of Korea
| | - Jae-Hyuk Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
| | - Young-Soo Hong
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju-si, Republic of Korea
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7
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Yu Y, Rué Casamajo A, Finnigan W, Schnepel C, Barker R, Morrill C, Heath RS, De Maria L, Turner NJ, Scrutton NS. Structure-Based Design of Small Imine Reductase Panels for Target Substrates. ACS Catal 2023; 13:12310-12321. [PMID: 37736118 PMCID: PMC10510103 DOI: 10.1021/acscatal.3c02278] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/20/2023] [Indexed: 09/23/2023]
Abstract
Biocatalysis is important in the discovery, development, and manufacture of pharmaceuticals. However, the identification of enzymes for target transformations of interest requires major screening efforts. Here, we report a structure-based computational workflow to prioritize protein sequences by a score based on predicted activities on substrates, thereby reducing a resource-intensive laboratory-based biocatalyst screening. We selected imine reductases (IREDs) as a class of biocatalysts to illustrate the application of the computational workflow termed IREDFisher. Validation by using published data showed that IREDFisher can retrieve the best enzymes and increase the hit rate by identifying the top 20 ranked sequences. The power of IREDFisher is confirmed by computationally screening 1400 sequences for chosen reductive amination reactions with different levels of complexity. Highly active IREDs were identified by only testing 20 samples in vitro. Our speed test shows that it only takes 90 min to rank 85 sequences from user input and 30 min for the established IREDFisher database containing 591 IRED sequences. IREDFisher is available as a user-friendly web interface (https://enzymeevolver.com/IREDFisher). IREDFisher enables the rapid discovery of IREDs for applications in synthesis and directed evolution studies, with minimal time and resource expenditure. Future use of the workflow with other enzyme families could be implemented following the modification of the workflow scoring function.
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Affiliation(s)
- Yuqi Yu
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
- Augmented
Biologics Discovery & Design, Department of Biologics Engineering, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB21 6GH, U.K.
| | - Arnau Rué Casamajo
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - William Finnigan
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Christian Schnepel
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Rhys Barker
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Charlotte Morrill
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Rachel S. Heath
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Leonardo De Maria
- Medicinal
Chemistry, Research and Early Development, Respiratory and Immunology
(RI), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43150, Sweden
| | - Nicholas J. Turner
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Nigel S. Scrutton
- Department
of Chemistry, The University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, U.K.
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8
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Englund E, Schmidt M, Nava AA, Klass S, Keiser L, Dan Q, Katz L, Yuzawa S, Keasling JD. Biosensor Guided Polyketide Synthases Engineering for Optimization of Domain Exchange Boundaries. Nat Commun 2023; 14:4871. [PMID: 37573440 PMCID: PMC10423236 DOI: 10.1038/s41467-023-40464-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/28/2023] [Indexed: 08/14/2023] Open
Abstract
Type I modular polyketide synthases (PKSs) are multi-domain enzymes functioning like assembly lines. Many engineering attempts have been made for the last three decades to replace, delete and insert new functional domains into PKSs to produce novel molecules. However, inserting heterologous domains often destabilize PKSs, causing loss of activity and protein misfolding. To address this challenge, here we develop a fluorescence-based solubility biosensor that can quickly identify engineered PKSs variants with minimal structural disruptions. Using this biosensor, we screen a library of acyltransferase (AT)-exchanged PKS hybrids with randomly assigned domain boundaries, and we identify variants that maintain wild type production levels. We then probe each position in the AT linker region to determine how domain boundaries influence structural integrity and identify a set of optimized domain boundaries. Overall, we have successfully developed an experimentally validated, high-throughput method for making hybrid PKSs that produce novel molecules.
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Affiliation(s)
- Elias Englund
- Joint BioEnergy Institute, Emeryville, CA, USA
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Matthias Schmidt
- Joint BioEnergy Institute, Emeryville, CA, USA
- Institute of Applied Microbiology, Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
- Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA
| | - Alberto A Nava
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Sarah Klass
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Leah Keiser
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Qingyun Dan
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA
| | - Leonard Katz
- Joint BioEnergy Institute, Emeryville, CA, USA
- QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Satoshi Yuzawa
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Graduate school of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA.
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
- QB3, University of California, Berkeley, Berkeley, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark.
- Center for Synthetic biochemistry, Institute for Synthetic biology, Shenzhen Institute of Advanced Technology, Shenzhen, China.
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9
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Kim MC, Winter JM, Cullum R, Smith AJ, Fenical W. Expanding the Utility of Bioinformatic Data for the Full Stereostructural Assignments of Marinolides A and B, 24- and 26-Membered Macrolactones Produced by a Chemically Exceptional Marine-Derived Bacterium. Mar Drugs 2023; 21:367. [PMID: 37367692 DOI: 10.3390/md21060367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023] Open
Abstract
Marinolides A and B, two new 24- and 26-membered bacterial macrolactones, were isolated from the marine-derived actinobacterium AJS-327 and their stereostructures initially assigned by bioinformatic data analysis. Macrolactones typically possess complex stereochemistry, the assignments of which have been one of the most difficult undertakings in natural products chemistry, and in most cases, the use of X-ray diffraction methods and total synthesis have been the major methods of assigning their absolute configurations. More recently, however, it has become apparent that the integration of bioinformatic data is growing in utility to assign absolute configurations. Genome mining and bioinformatic analysis identified the 97 kb mld biosynthetic cluster harboring seven type I polyketide synthases. A detailed bioinformatic investigation of the ketoreductase and enoylreductase domains within the multimodular polyketide synthases, coupled with NMR and X-ray diffraction data, allowed for the absolute configurations of marinolides A and B to be determined. While using bioinformatics to assign the relative and absolute configurations of natural products has high potential, this method must be coupled with full NMR-based analysis to both confirm bioinformatic assignments as well as any additional modifications that occur during biosynthesis.
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Affiliation(s)
- Min Cheol Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
| | - Jaclyn M Winter
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA
| | - Reiko Cullum
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
| | - Alexander J Smith
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
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10
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Kudo F, Kishikawa K, Tsuboi K, Kido T, Usui T, Hashimoto J, Shin-Ya K, Miyanaga A, Eguchi T. Acyltransferase Domain Exchange between Two Independent Type I Polyketide Synthases in the Same Producer Strain of Macrolide Antibiotics. Chembiochem 2023; 24:e202200670. [PMID: 36602093 DOI: 10.1002/cbic.202200670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/06/2023]
Abstract
Streptomyces graminofaciens A-8890 produces two macrolide antibiotics, FD-891 and virustomycin A, both of which show significant biological activity. In this study, we identified the virustomycin A biosynthetic gene cluster, which encodes type I polyketide synthases (PKSs), ethylmalonyl-CoA biosynthetic enzymes, methoxymalony-acyl carrier protein biosynthetic enzymes, and post-PKS modification enzymes. Next, we demonstrated that the acyltransferase domain can be exchanged between the Vsm PKSs and the PKSs involved in FD-891 biosynthesis (Gfs PKSs), without any supply problems of the unique extender units. We exchanged the malonyltransferase domain in the loading module of Gfs PKS with the ethylmalonyltransferase domain and the methoxymalonyltransferase domain of Vsm PKSs. Consequently, the expected two-carbon-elongated analog 26-ethyl-FD-891 was successfully produced with a titer comparable to FD-891 production by the wild type; however, exchange with the methoxymalonyltransferase domain did not produce any FD-891 analogs. Furthermore, 26-ethyl-FD-891 showed potent cytotoxic activity against HeLa cells, like natural FD-891.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Kosuke Kishikawa
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Kazuma Tsuboi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Takafusa Kido
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Takeo Usui
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572, Ibaraki, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
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11
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Miyanaga A, Kawada K, Chisuga T, Kudo F, Eguchi T. Structural Basis of Transient Interactions of Acyltransferase VinK with the Loading Acyl Carrier Protein of the Vicenistatin Modular Polyketide Synthase. Biochemistry 2023; 62:17-21. [PMID: 36512613 DOI: 10.1021/acs.biochem.2c00645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Acyltransferase (AT) recognizes its cognate acyl carrier protein (ACP) for functional transfer of an acyl unit in polyketide biosynthesis. However, structural characterization of AT-ACP complexes is limited because of the weak and transient interactions between them. In the biosynthesis of macrolactam polyketide vicenistatin, the trans-acting loading AT VinK transfers a dipeptidyl unit from the stand-alone ACP VinL to the ACP domain (VinP1ACPL) of the loading module of modular polyketide synthase VinP1. Although the previously determined structure of the VinK-VinL complex clearly illustrates the VinL recognition mechanism of VinK, how VinK recognizes VinP1ACPL remains unclear. Here, the crystal structure of a covalent VinK-VinP1ACPL complex formed with a pantetheine-type cross-linking probe is reported at 3.0 Å resolution. The structure of the VinK-VinP1ACPL complex provides detailed insights into the transient interactions between VinK and VinP1ACPL. The importance of residues in the binding interface was confirmed by site-directed mutational analyses. The binding interface between VinK and VinP1ACPL is similar to that between VinK and VinL, although some of the interface residues are different. However, the ACP orientation and interaction mode observed in the VinK-VinP1ACPL complex are different from those observed in other AT-ACP complexes such as the disorazole trans-AT-ACP complex and cis-AT-ACP complexes of modular polyketide synthases. Thus, AT-ACP binding interface interactions are different in each type of AT-ACP pair.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Koichi Kawada
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Taichi Chisuga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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12
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Welch SD, Cossin J, Paulsel TQ, Williams GJ. Targeted Enzyme Modifications Enable Regioselective Biosynthesis of Fluorinated Polyketides. CHEM CATALYSIS 2022; 2:2440-2443. [PMID: 38213411 PMCID: PMC10783197 DOI: 10.1016/j.checat.2022.09.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
In attempts to enhance natural products as therapeutic agents, fluorination has emerged as a new tool for synthetic biologists and chemists. In recent articles published in Nature Chem. and Nature Chem. Bio., Grininger, Chang, and co-workers leveraged their expertise in engineering polyketide biosynthesis to incorporate fluorine into polyketide scaffolds.
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Affiliation(s)
- Sydney D. Welch
- Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Jared Cossin
- Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Thaddeus Q. Paulsel
- Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Gavin J. Williams
- Department of Chemistry, North Carolina State University, Raleigh, NC, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
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13
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Zheng M, Zhang J, Zhang W, Yang L, Yan X, Tian W, Liu Z, Lin Z, Deng Z, Qu X. An Atypical Acyl‐CoA Synthetase Enables Efficient Biosynthesis of Extender Units for Engineering a Polyketide Carbon Scaffold. Angew Chem Int Ed Engl 2022; 61:e202208734. [DOI: 10.1002/anie.202208734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Jun Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Wan Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Lu Yang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Xiaoli Yan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Wenya Tian
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Zhihao Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Zhi Lin
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
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14
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Zheng M, Zhang J, Zhang W, Yang L, Yan X, Tian W, Liu Z, Lin Z, Deng Z, Qu X. An Atypical Acyl‐CoA Synthetase Enables Efficient Biosynthesis of Extender Units for Engineering a Polyketide Carbon Scaffold. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mengmeng Zheng
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Jun Zhang
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Wan Zhang
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Lu Yang
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Xiaoli Yan
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Wenya Tian
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Zhihao Liu
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Zhi Lin
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Zixin Deng
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Xudong Qu
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology 800 Dongchuan Rd. 200240 Shanghai CHINA
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15
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Chisuga T, Nagai A, Miyanaga A, Goto E, Kishikawa K, Kudo F, Eguchi T. Structural Insight into the Reaction Mechanism of Ketosynthase-Like Decarboxylase in a Loading Module of Modular Polyketide Synthases. ACS Chem Biol 2022; 17:198-206. [PMID: 34985877 DOI: 10.1021/acschembio.1c00856] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ketosynthase-like decarboxylase (KSQ) domains are widely distributed in the loading modules of modular polyketide synthases (PKSs) and are proposed to catalyze the decarboxylation of a malonyl or methylmalonyl unit for the construction of the PKS starter unit. KSQ domains have high sequence similarity to ketosynthase (KS) domains, which catalyze transacylation and decarboxylative condensation in polyketide and fatty acid biosynthesis, except that the catalytic Cys residue of KS domains is replaced by Gln in KSQ domains. Here, we present biochemical analyses of GfsA KSQ and CmiP4 KSQ, which are involved in the biosynthesis of FD-891 and cremimycin, respectively. In vitro analysis showed that these KSQ domains catalyze the decarboxylation of malonyl and methylmalonyl units. Furthermore, we determined the crystal structure of GfsA KSQ in complex with a malonyl thioester substrate analogue, which enabled identification of key amino acid residues involved in the decarboxylation reaction. The importance of these residues was confirmed by mutational analysis. On the basis of these findings, we propose a mechanism of the decarboxylation reaction catalyzed by GfsA KSQ. GfsA KSQ initiates decarboxylation by fixing the substrate in a suitable conformation for decarboxylation. The formation of enolate upon decarboxylation is assisted by two conserved threonine residues. Comparison of the structure of GfsA KSQ with those of KS domains suggests that the Gln residue in the active site of the KSQ domain mimics the acylated Cys residue in the active site of KS domains.
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Affiliation(s)
- Taichi Chisuga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Akira Nagai
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Ena Goto
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Kosuke Kishikawa
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
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16
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17
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Miyanaga A, Ouchi R, Kudo F, Eguchi T. Complex structure of the acyltransferase VinK and the carrier protein VinL with a pantetheine cross-linking probe. Acta Crystallogr F Struct Biol Commun 2021; 77:294-302. [DOI: 10.1107/s2053230x21008761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/22/2021] [Indexed: 01/16/2023] Open
Abstract
Acyltransferases are responsible for the selection and loading of acyl units onto carrier proteins in polyketide and fatty-acid biosynthesis. Despite the importance of protein–protein interactions between the acyltransferase and the carrier protein, structural information on acyltransferase–carrier protein interactions is limited because of the transient interactions between them. In the biosynthesis of the polyketide vicenistatin, the acyltransferase VinK recognizes the carrier protein VinL for the transfer of a dipeptidyl unit. The crystal structure of a VinK–VinL covalent complex formed with a 1,2-bismaleimidoethane cross-linking reagent has been determined previously. Here, the crystal structure of a VinK–VinL covalent complex formed with a pantetheine cross-linking probe is reported at 1.95 Å resolution. In the structure of the VinK–VinL–probe complex, the pantetheine probe that is attached to VinL is covalently connected to the side chain of the mutated Cys106 of VinK. The interaction interface between VinK and VinL is essentially the same in the two VinK–VinL complex structures, although the position of the pantetheine linker slightly differs. This structural observation suggests that interface interactions are not affected by the cross-linking strategy used.
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18
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Yi D, Bayer T, Badenhorst CPS, Wu S, Doerr M, Höhne M, Bornscheuer UT. Recent trends in biocatalysis. Chem Soc Rev 2021; 50:8003-8049. [PMID: 34142684 PMCID: PMC8288269 DOI: 10.1039/d0cs01575j] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Indexed: 12/13/2022]
Abstract
Biocatalysis has undergone revolutionary progress in the past century. Benefited by the integration of multidisciplinary technologies, natural enzymatic reactions are constantly being explored. Protein engineering gives birth to robust biocatalysts that are widely used in industrial production. These research achievements have gradually constructed a network containing natural enzymatic synthesis pathways and artificially designed enzymatic cascades. Nowadays, the development of artificial intelligence, automation, and ultra-high-throughput technology provides infinite possibilities for the discovery of novel enzymes, enzymatic mechanisms and enzymatic cascades, and gradually complements the lack of remaining key steps in the pathway design of enzymatic total synthesis. Therefore, the research of biocatalysis is gradually moving towards the era of novel technology integration, intelligent manufacturing and enzymatic total synthesis.
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Affiliation(s)
- Dong Yi
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Thomas Bayer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Shuke Wu
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Mark Doerr
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Matthias Höhne
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
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19
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Stegemann F, Grininger M. Transacylation Kinetics in Fatty Acid and Polyketide Synthases and its Sensitivity to Point Mutations**. ChemCatChem 2021. [DOI: 10.1002/cctc.202002077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Franziska Stegemann
- Institute of Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences Goethe University Frankfurt Max-von-Laue-Str. 15 60438 Frankfurt am Main Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences Goethe University Frankfurt Max-von-Laue-Str. 15 60438 Frankfurt am Main Germany
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20
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Ji H, Shi T, Liu L, Zhang F, Tao W, Min Q, Deng Z, Bai L, Zhao Y, Zheng J. Computational studies on the substrate specificity of an acyltransferase domain from salinomycin polyketide synthase. Catal Sci Technol 2021. [DOI: 10.1039/d1cy00284h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The complex of SalAT14 and its cognate substrate EMCoA is apt to stay in a conformation suitable for the reaction. Computational investigations reveal the structural basis of AT specificity and could potentially help the engineering of modular PKSs.
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Affiliation(s)
- Huining Ji
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Liu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fa Zhang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wentao Tao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Min
- Pharmacy School, Hubei University of Science and Technology, Hubei, Xianning 437100, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yilei Zhao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
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21
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Kim MC, Winter JM, Cullum R, Li Z, Fenical W. Complementary Genomic, Bioinformatics, and Chemical Approaches Facilitate the Absolute Structure Assignment of Ionostatin, a Linear Polyketide from a Rare Marine-Derived Actinomycete. ACS Chem Biol 2020; 15:2507-2515. [PMID: 32852937 DOI: 10.1021/acschembio.0c00526] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new linear type-1 polyketide, ionostatin (1), has been fully defined using a combined genomic and bioinformatics approach coupled with confirmatory chemical analyses. The 41 carbon-containing polyether is the product of the 101 kbp ion biosynthetic cluster containing seven modular type-1 polyketide synthases. Ionostatin is composed of 15 chiral centers that were proposed using the stereospecificities installed by the different classes of ketoreductases and enoylreductases and confirmed by rigorous NMR analyses. Incorporated into the structure are two tetrahydrofuran rings that appear to be the product of stereospecific epoxidation, followed by stereospecific ring opening and cyclization. These transformations are proposed to be catalyzed by conserved enzymes analogous to those found in other bacterial-derived polyether biosynthetic clusters. Ionostatin shows moderate cancer cell cytotoxicity against U87 glioblastoma and SKOV3 ovarian carcinoma at 7.4 μg/mL.
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Affiliation(s)
- Min Cheol Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Jaclyn M. Winter
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Reiko Cullum
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Zhifei Li
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Moores Comprehensive Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
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22
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Interfacial plasticity facilitates high reaction rate of E. coli FAS malonyl-CoA:ACP transacylase, FabD. Proc Natl Acad Sci U S A 2020; 117:24224-24233. [PMID: 32929027 DOI: 10.1073/pnas.2009805117] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fatty acid synthases (FASs) and polyketide synthases (PKSs) iteratively elongate and often reduce two-carbon ketide units in de novo fatty acid and polyketide biosynthesis. Cycles of chain extensions in FAS and PKS are initiated by an acyltransferase (AT), which loads monomer units onto acyl carrier proteins (ACPs), small, flexible proteins that shuttle covalently linked intermediates between catalytic partners. Formation of productive ACP-AT interactions is required for catalysis and specificity within primary and secondary FAS and PKS pathways. Here, we use the Escherichia coli FAS AT, FabD, and its cognate ACP, AcpP, to interrogate type II FAS ACP-AT interactions. We utilize a covalent crosslinking probe to trap transient interactions between AcpP and FabD to elucidate the X-ray crystal structure of a type II ACP-AT complex. Our structural data are supported using a combination of mutational, crosslinking, and kinetic analyses, and long-timescale molecular dynamics (MD) simulations. Together, these complementary approaches reveal key catalytic features of FAS ACP-AT interactions. These mechanistic inferences suggest that AcpP adopts multiple, productive conformations at the AT binding interface, allowing the complex to sustain high transacylation rates. Furthermore, MD simulations support rigid body subdomain motions within the FabD structure that may play a key role in AT activity and substrate selectivity.
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23
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Production of Diverse Beauveriolide Analogs in Closely Related Fungi: a Rare Case of Fungal Chemodiversity. mSphere 2020; 5:5/5/e00667-20. [PMID: 32878933 PMCID: PMC7471007 DOI: 10.1128/msphere.00667-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Fungal chemodiversity is well known in part due to the production of diverse analogous compounds by a single biosynthetic gene cluster (BGC). Usually, similar or the same metabolites are produced by closely related fungal species under a given condition, the foundation of fungal chemotaxonomy. Here, we report a rare case of the production of the cyclodepsipeptide beauveriolides (BVDs) in three insect-pathogenic fungi. We found that the more closely related fungi Beauveria bassiana and Beauveria brongniartii produced structurally distinct analogs of BVDs, whereas the less-close relatives B. brongniartii and Cordyceps militaris biosynthesized structurally similar congeners under the same growth condition. It was verified that a conserved BGC containing four genes is responsible for BVD biosynthesis in three fungi, including a polyketide synthase (PKS) for the production of 3-hydroxy fatty acids (FAs) with chain length variations. In contrast to BVD production patterns, phylogenetic analysis of the BGC enzymes or enzyme domains largely resulted in the congruence relationship with fungal speciation. Feeding assays demonstrated that an FA with a chain length of eight carbon atoms was preferentially utilized, whereas an FA with a chain longer than 10 carbon atoms could not be used as a substrate for BVD biosynthesis. Insect survival assays suggested that the contribution of BVDs to fungal virulence might be associated with the susceptibility of insect species. The results of this study enrich the knowledge of fungal secondary metabolic diversity that can question the reliability of fungal chemotaxonomy.IMPORTANCE Fungal chemotaxonomy is an approach to classify fungi based on the fungal production profile of metabolites, especially the secondary metabolites. We found an atypical example that could question the reliability of fungal chemical classifications in this study, i.e., the more closely related entomopathogenic species Beauveria bassiana and Beauveria brongniartii produced structurally different congeners of the cyclodepsipeptide beauveriolides, whereas the rather divergent species B. brongniartii and Cordyceps militaris biosynthesized similar analogs under the same growth condition. The conserved biosynthetic gene cluster (BGC) containing four genes present in each species is responsible for beauveriolide production. In contrast to the compound formation profiles, the phylogenies of biosynthetic enzymes or enzymatic domains show associations with fungal speciation. Dependent on the insect species, production of beauveriolides may contribute to fungal virulence against the susceptible insect hosts. The findings in this study augment the diversity of fungal secondary metabolisms.
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24
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Drufva EE, Hix EG, Bailey CB. Site directed mutagenesis as a precision tool to enable synthetic biology with engineered modular polyketide synthases. Synth Syst Biotechnol 2020; 5:62-80. [PMID: 32637664 PMCID: PMC7327777 DOI: 10.1016/j.synbio.2020.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/04/2022] Open
Abstract
Modular polyketide synthases (PKSs) are a multidomain megasynthase class of biosynthetic enzymes that have great promise for the development of new compounds, from new pharmaceuticals to high value commodity and specialty chemicals. Their colinear biosynthetic logic has been viewed as a promising platform for synthetic biology for decades. Due to this colinearity, domain swapping has long been used as a strategy to introduce molecular diversity. However, domain swapping often fails because it perturbs critical protein-protein interactions within the PKS. With our increased level of structural elucidation of PKSs, using judicious targeted mutations of individual residues is a more precise way to introduce molecular diversity with less potential for global disruption of the protein architecture. Here we review examples of targeted point mutagenesis to one or a few residues harbored within the PKS that alter domain specificity or selectivity, affect protein stability and interdomain communication, and promote more complex catalytic reactivity.
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Key Words
- ACP, acyl carrier protein
- AT, acyltransferase
- DEBS, 6-deoxyerthronolide B synthase
- DH, dehydratase
- EI, enoylisomerase
- ER, enoylreductase
- KR, ketoreductase
- KS, ketosynthase
- LM, loading module
- MT, methyltransferase
- Mod, module
- PKS, polyketide synthase
- PS, pyran synthase
- Polyketide synthase
- Protein engineering
- Rational design
- SNAC, N-acetyl cysteamine
- Saturation mutagenesis
- Site directed mutagenesis
- Synthetic biology
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Affiliation(s)
- Erin E. Drufva
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| | - Elijah G. Hix
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| | - Constance B. Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
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Van Dolah FM, Morey JS, Milne S, Ung A, Anderson PE, Chinain M. Transcriptomic analysis of polyketide synthases in a highly ciguatoxic dinoflagellate, Gambierdiscus polynesiensis and low toxicity Gambierdiscus pacificus, from French Polynesia. PLoS One 2020; 15:e0231400. [PMID: 32294110 PMCID: PMC7159223 DOI: 10.1371/journal.pone.0231400] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/23/2020] [Indexed: 11/18/2022] Open
Abstract
Marine dinoflagellates produce a diversity of polyketide toxins that are accumulated in marine food webs and are responsible for a variety of seafood poisonings. Reef-associated dinoflagellates of the genus Gambierdiscus produce toxins responsible for ciguatera poisoning (CP), which causes over 50,000 cases of illness annually worldwide. The biosynthetic machinery for dinoflagellate polyketides remains poorly understood. Recent transcriptomic and genomic sequencing projects have revealed the presence of Type I modular polyketide synthases in dinoflagellates, as well as a plethora of single domain transcripts with Type I sequence homology. The current transcriptome analysis compares polyketide synthase (PKS) gene transcripts expressed in two species of Gambierdiscus from French Polynesia: a highly toxic ciguatoxin producer, G. polynesiensis, versus a non-ciguatoxic species G. pacificus, each assembled from approximately 180 million Illumina 125 nt reads using Trinity, and compares their PKS content with previously published data from other Gambierdiscus species and more distantly related dinoflagellates. Both modular and single-domain PKS transcripts were present. Single domain β-ketoacyl synthase (KS) transcripts were highly amplified in both species (98 in G. polynesiensis, 99 in G. pacificus), with smaller numbers of standalone acyl transferase (AT), ketoacyl reductase (KR), dehydratase (DH), enoyl reductase (ER), and thioesterase (TE) domains. G. polynesiensis expressed both a larger number of multidomain PKSs, and larger numbers of modules per transcript, than the non-ciguatoxic G. pacificus. The largest PKS transcript in G. polynesiensis encoded a 10,516 aa, 7 module protein, predicted to synthesize part of the polyether backbone. Transcripts and gene models representing portions of this PKS are present in other species, suggesting that its function may be performed in those species by multiple interacting proteins. This study contributes to the building consensus that dinoflagellates utilize a combination of Type I modular and single domain PKS proteins, in an as yet undefined manner, to synthesize polyketides.
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Affiliation(s)
- Frances M. Van Dolah
- Marine Genomics Core, Hollings Marine Laboratory, Charleston, SC, United States of America
- * E-mail:
| | - Jeanine S. Morey
- Marine Genomics Core, Hollings Marine Laboratory, Charleston, SC, United States of America
| | - Shard Milne
- Charleston Computational Genomics Group, Department of Computer Science, College of Charleston, Charleston, SC, United States of America
| | - André Ung
- Laboratoire des Biotoxines Marines, Institut Louis Malardé—UMR 241 EIO, Papeete, Tahiti, French Polynesia
| | - Paul E. Anderson
- Charleston Computational Genomics Group, Department of Computer Science, College of Charleston, Charleston, SC, United States of America
| | - Mireille Chinain
- Laboratoire des Biotoxines Marines, Institut Louis Malardé—UMR 241 EIO, Papeete, Tahiti, French Polynesia
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Zhang F, Ji H, Ali I, Deng Z, Bai L, Zheng J. Structural and Biochemical Insight into the Recruitment of Acyl Carrier Protein-Linked Extender Units in Ansamitocin Biosynthesis. Chembiochem 2020; 21:1309-1314. [PMID: 31777147 DOI: 10.1002/cbic.201900628] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Indexed: 01/17/2023]
Abstract
A few acyltransferase (AT) domains of modular polyketide synthases (PKSs) recruit acyl carrier protein (ACP)-linked extender units with unusual C2 substituents to confer functionalities that are not available in coenzyme A (CoA)-linked ones. In this study, an AT specific for methoxymalonyl (MOM)-ACP in the third module of the ansamitocin PKS was structurally and biochemically characterized. The AT uses a conserved tryptophan residue at the entrance of the substrate binding tunnel to discriminate between different carriers. A W275R mutation switches its carrier specificity from the ACP to the CoA molecule. The acyl-AT complex structures clearly show that the MOM-ACP accepted by the AT has the 2S instead of the opposite 2R stereochemistry that is predicted according to the biosynthetic derivation from a d-glycolytic intermediate. Together, these results reveal the structural basis of ATs recognizing ACP-linked extender units in polyketide biosynthesis.
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Affiliation(s)
- Fa Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Huining Ji
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Imtiaz Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
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Yu Z, Lv H, Wu Y, Wei T, Yang S, Ju D, Chen S. Enhancement of FK520 production in Streptomyces hygroscopicus by combining traditional mutagenesis with metabolic engineering. Appl Microbiol Biotechnol 2019; 103:9593-9606. [PMID: 31713669 DOI: 10.1007/s00253-019-10192-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/26/2019] [Accepted: 10/03/2019] [Indexed: 11/26/2022]
Abstract
FK520 (ascomycin), a 23-membered macrolide with immunosuppressive activity, is produced by Streptomyces hygroscopicus. The problem of low yield and high impurities (mainly FK523) limits the industrialized production of FK520. In this study, the FK520 yield was significantly improved by strain mutagenesis and genetic engineering. First, a FK520 high-producing strain SFK-6-33 (2432.2 mg/L) was obtained from SFK-36 (1588.4 mg/L) through ultraviolet radiation mutation coupled with streptomycin resistance screening. The endogenous crotonyl-CoA carboxylase/reductase (FkbS) was found to play an important role in FK520 biosynthesis, identified with CRISPR/dCas9 inhibition system. FkbS was overexpressed in SFK-6-33 to obtain the engineered strain SFK-OfkbS, which produced 2817.0 mg/L of FK520 resulting from an increase in intracellular ethylmalonyl-CoA levels. In addition, the FK520 levels could be further increased with supplementation of crotonic acid in SFK-OfkbS. Overexpression of acetyl-CoA carboxylase (ACCase), used for the synthesis of malonyl-CoA, was also investigated in SFK-6-33, which improved the FK520 yield to 3320.1 mg/L but showed no significant inhibition in FK523 production. To further enhance FK520 production, FkbS and ACCase combinatorial overexpression strain SFK-OASN was constructed; the FK520 production increased by 44.4% to 3511.4 mg/L, and the FK523/FK520 ratio was reduced from 9.6 to 5.6% compared with that in SFK-6-33. Finally, a fed-batch culture was carried out in a 5-L fermenter, and the FK520 yield reached 3913.9 mg/L at 168 h by feeding glycerol, representing the highest FK520 yield reported thus far. These results demonstrated that traditional mutagenesis combined with metabolic engineering was an effective strategy to improve FK520 production.
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Affiliation(s)
- Zhituo Yu
- Department of Biological Medicines, Fudan University School of Pharmacy, Shanghai, 201203, China
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, 201203, China
| | - Huihui Lv
- Department of Biological Medicines, Fudan University School of Pharmacy, Shanghai, 201203, China
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, 201203, China
| | - Yuanjie Wu
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, 201203, China
| | - Tengyun Wei
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, 201203, China
| | - Songbai Yang
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, 201203, China
| | - Dianwen Ju
- Department of Biological Medicines, Fudan University School of Pharmacy, Shanghai, 201203, China.
| | - Shaoxin Chen
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai, 201203, China.
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28
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Eng CH, Backman TWH, Bailey CB, Magnan C, García Martín H, Katz L, Baldi P, Keasling JD. ClusterCAD: a computational platform for type I modular polyketide synthase design. Nucleic Acids Res 2019; 46:D509-D515. [PMID: 29040649 PMCID: PMC5753242 DOI: 10.1093/nar/gkx893] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/24/2017] [Indexed: 01/10/2023] Open
Abstract
ClusterCAD is a web-based toolkit designed to leverage the collinear structure and deterministic logic of type I modular polyketide synthases (PKSs) for synthetic biology applications. The unique organization of these megasynthases, combined with the diversity of their catalytic domain building blocks, has fueled an interest in harnessing the biosynthetic potential of PKSs for the microbial production of both novel natural product analogs and industrially relevant small molecules. However, a limited theoretical understanding of the determinants of PKS fold and function poses a substantial barrier to the design of active variants, and identifying strategies to reliably construct functional PKS chimeras remains an active area of research. In this work, we formalize a paradigm for the design of PKS chimeras and introduce ClusterCAD as a computational platform to streamline and simplify the process of designing experiments to test strategies for engineering PKS variants. ClusterCAD provides chemical structures with stereochemistry for the intermediates generated by each PKS module, as well as sequence- and structure-based search tools that allow users to identify modules based either on amino acid sequence or on the chemical structure of the cognate polyketide intermediate. ClusterCAD can be accessed at https://clustercad.jbei.org and at http://clustercad.igb.uci.edu.
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Affiliation(s)
- Clara H Eng
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Tyler W H Backman
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Energy Agile BioFoundry, Emeryville, CA 94608, USA
| | - Constance B Bailey
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christophe Magnan
- Department of Computer Science, University of California, Irvine, CA 92697, USA.,Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA
| | - Héctor García Martín
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Energy Agile BioFoundry, Emeryville, CA 94608, USA
| | - Leonard Katz
- QB3 Institute, University of California, Berkeley, CA 94720, USA
| | - Pierre Baldi
- Department of Computer Science, University of California, Irvine, CA 92697, USA.,Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA
| | - Jay D Keasling
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.,Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Energy Agile BioFoundry, Emeryville, CA 94608, USA.,QB3 Institute, University of California, Berkeley, CA 94720, USA.,Department of Bioengineering, University of California, Berkeley, CA 94720, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2970 Horsholm, Denmark
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29
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Kornfuehrer T, Eustáquio AS. Diversification of polyketide structures via synthase engineering. MEDCHEMCOMM 2019; 10:1256-1272. [PMID: 32180918 PMCID: PMC7053703 DOI: 10.1039/c9md00141g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/09/2019] [Indexed: 12/16/2022]
Abstract
Polyketide natural products possess diverse biological activities including antibiotic, anticancer, and immunosuppressive. Their equally varied and complex structures arise from head-to-tail condensation of simple carboxyacyl monomers. Since the seminal discovery that biosynthesis of polyketides such as the macrolide erythromycin is catalyzed by uncharacteristically large, multifunctional enzymes, termed modular type I polyketide synthases, chemists and biologists alike have been inspired to harness the apparent modularity of the synthases to further diversify polyketide structures. Yet, initial attempts to perform "combinatorial biosynthesis" failed due to challenges associated with maintaining the structural and catalytic integrity of large, chimeric synthases. Fast forward nearly 30 years, and advancements in our understanding of polyketide synthase structure and function have allowed the field to make significant progress toward effecting desired modifications to polyketide scaffolds in addition to engineering small, chiral fragments. This review highlights selected examples of polyketide diversification via control of monomer selection, oxidation state, stereochemistry, and cyclization. We conclude with a perspective on the present and future of polyketide structure diversification and hope that the examples presented here will encourage medicinal chemists to embrace polyketide synthetic biology as a means to revitalize polyketide drug discovery.
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Affiliation(s)
- Taylor Kornfuehrer
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences , College of Pharmacy , University of Illinois at Chicago , Chicago , Illinois 60607 , USA . ; Tel: +1 3124137082
| | - Alessandra S Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences , College of Pharmacy , University of Illinois at Chicago , Chicago , Illinois 60607 , USA . ; Tel: +1 3124137082
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30
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Abstract
Reduced polyketides are a subclass of natural products that have a variety of medical, veterinary, and agricultural applications and are well known for their structural diversity. Although these compounds do not resemble each other, they are all made by a class of enzymes known as modular polyketide synthases (PKSs). The commonality of PKS domains/modules that compose PKSs and the understanding of the relationship between the sequence of the PKS and the structure of the compound it produces render modular PKSs as excellent targets for engineering to produce novel compounds with predicted structures. Here, we describe experimental protocols and considerations for modular PKS engineering and two case studies to produce commodity chemicals by engineered PKSs.
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31
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Zhang F, Shi T, Ji H, Ali I, Huang S, Deng Z, Min Q, Bai L, Zhao Y, Zheng J. Structural Insights into the Substrate Specificity of Acyltransferases from Salinomycin Polyketide Synthase. Biochemistry 2019; 58:2978-2986. [PMID: 31199122 DOI: 10.1021/acs.biochem.9b00305] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Salinomycin with antibacterial and anticoccidial activities is a commercial polyether polyketide widely used in animal husbandry as a food additive. Malonyl-CoA (MCoA), methylmalonyl-CoA (MMCoA), and ethylmalonyl-CoA (EMCoA) are used as extension units in its biosynthesis. To understand how the salinomycin modular polyketide synthase (PKS) strictly discriminates among these extension units, the acyltransferase (AT) domains selecting MCoA, MMCoA, and EMCoA were structurally characterized. Molecular dynamics simulations of the AT structures helped to reveal the key interactions involved in enzyme-substrate recognitions, which enabled the engineering of AT mutants with switched specificity. The catalytic efficiencies ( kcat/ Km) of these AT mutants are comparable with those of the wild-type AT domains. These results set the stage for engineering the AT substrate specificity of modular PKSs.
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Affiliation(s)
- Fa Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Huining Ji
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Imtiaz Ali
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Shuxin Huang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Qing Min
- Pharmacy School , Hubei University of Science and Technology , Hubei , Xianning 437100 , China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Yilei Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
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32
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Mo J, Wang S, Zhang W, Li C, Deng Z, Zhang L, Qu X. Efficient editing DNA regions with high sequence identity in actinomycetal genomes by a CRISPR-Cas9 system. Synth Syst Biotechnol 2019; 4:86-91. [PMID: 30891508 PMCID: PMC6403111 DOI: 10.1016/j.synbio.2019.02.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 11/28/2022] Open
Abstract
Actinobacteria able to produce varieties of bioactive natural products have been long appreciated by the field of drug discovery and development. Recently, a few of CRISPR/Cas9 systems bearing different types of replicons (pSG5 and pIJ101) were developed to efficiently edit their genomes. Despite wide application in gene editing, their utility in editing challenging DNA regions e.g. high sequence identity has not been compared. In this study, we confirmed that the widely used temperature-sensitive pSG5 replicon is indeed not suitable for editing modular polyketide synthase (PKS) genes due to causing unpredicted gene recombination. This problem can be addressed by replacing the pSG5 with the segregationally unstable pIJ101 replicon. By introducing a counter-selection marker CodA, convenient cloning sites in the single guide RNAs (sgRNAs) and homologous template scaffolds, we developed a new CRISPR-Cas9 system pMWCas9. This system was successfully used to delete/replace erythromycin PKS and other biosynthetic genes in Saccharopolyspora erythraea and Streptomyces sp. AL2110. By swapping the promoters of antB and antC with ermE and kasOp, we achieved a deacyl-antimycin hyper producer which produces a 9-fold higher yield than the original Streptomyces sp. AL2110 strain. Our results provide a robust and useful Cas9 tool for genetic studies in Actinobacteria.
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Affiliation(s)
- Jingjun Mo
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Shuwen Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Wan Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Chunyu Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
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33
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Connolly JA, Wilson A, Macioszek M, Song Z, Wang L, Mohammad HH, Yadav M, di Martino M, Miller CE, Hothersall J, Haines AS, Stephens ER, Crump MP, Willis CL, Simpson TJ, Winn PJ, Thomas CM. Defining the genes for the final steps in biosynthesis of the complex polyketide antibiotic mupirocin by Pseudomonas fluorescens NCIMB10586. Sci Rep 2019; 9:1542. [PMID: 30733464 PMCID: PMC6367315 DOI: 10.1038/s41598-018-38038-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 12/17/2018] [Indexed: 11/09/2022] Open
Abstract
The mupirocin trans-AT polyketide synthase pathway, provides a model system for manipulation of antibiotic biosynthesis. Its final phase involves removal of the tertiary hydroxyl group from pseudomonic acid B, PA-B, producing the fully active PA-A in a complex series of steps. To further clarify requirements for this conversion, we fed extracts containing PA-B to mutants of the producer strain singly deficient in each mup gene. This additionally identified mupM and mupN as required plus the sequence but not enzymic activity of mupL and ruled out need for other mup genes. A plasmid expressing mupLMNOPVCFU + macpE together with a derivative of the producer P. fluorescens strain NCIMB10586 lacking the mup cluster allowed conversion of PA-B to PA-A. MupN converts apo-mAcpE to holo-form while MupM is a mupirocin-resistant isoleucyl tRNA synthase, preventing self-poisoning. Surprisingly, the expression plasmid failed to allow the closely related P. fluorescens strain SBW25 to convert PA-B to PA-A.
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Affiliation(s)
- Jack A Connolly
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,School of Chemistry, University of St Andrews, BMS Building, North Haugh, St Andrews, KY16 9ST, UK
| | - Amber Wilson
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Malgorzata Macioszek
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Dr M. Macioszek, DOCS International Poland, ul. Grojecka 5, 02-019, Warszawa, Poland
| | - Zhongshu Song
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Luoyi Wang
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Hadi H Mohammad
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,College of Medicine, Kirkuk University, Kirkuk, Iraq
| | - Mukul Yadav
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Maura di Martino
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Ms M. di Martino, Dept Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Claire E Miller
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Dr C. E. Miller, The BioHub Birmingham, Birmingham Research Park, 97 Vincent Drive, Edgbaston, Birmingham, B15 2SQ, UK
| | - Joanne Hothersall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Anthony S Haines
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Elton R Stephens
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Christine L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Thomas J Simpson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Peter J Winn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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34
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Zhang W, Zhou L, Li C, Deng Z, Qu X. Rational engineering acyltransferase domain of modular polyketide synthase for expanding substrate specificity. Methods Enzymol 2019; 622:271-292. [DOI: 10.1016/bs.mie.2019.02.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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35
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Sabatini M, Comba S, Altabe S, Recio-Balsells AI, Labadie GR, Takano E, Gramajo H, Arabolaza A. Biochemical characterization of the minimal domains of an iterative eukaryotic polyketide synthase. FEBS J 2018; 285:4494-4511. [PMID: 30300504 PMCID: PMC6334511 DOI: 10.1111/febs.14675] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/03/2018] [Accepted: 09/25/2018] [Indexed: 01/19/2023]
Abstract
Iterative type I polyketide synthases (PKS) are megaenzymes essential to the biosynthesis of an enormously diverse array of bioactive natural products. Each PKS contains minimally three functional domains, β-ketosynthase (KS), acyltransferase (AT), and acyl carrier protein (ACP), and a subset of reducing domains such as ketoreductase (KR), dehydratase (DH), and enoylreductase (ER). The substrate selection, condensation reactions, and β-keto processing of the polyketide growing chain are highly controlled in a programmed manner. However, the structural features and mechanistic rules that orchestrate the iterative cycles, processing domains functionality, and chain termination in this kind of megaenzymes are often poorly understood. Here, we present a biochemical and functional characterization of the KS and the AT domains of a PKS from the mallard duck Anas platyrhynchos (ApPKS). ApPKS belongs to an animal PKS family phylogenetically more related to bacterial PKS than to metazoan fatty acid synthases. Through the dissection of the ApPKS enzyme into mono- to didomain fragments and its reconstitution in vitro, we determined its substrate specificity toward different starters and extender units. ApPKS AT domain can effectively transfer acetyl-CoA and malonyl-CoA to the ApPKS ACP stand-alone domain. Furthermore, the KS and KR domains, in the presence of Escherichia coli ACP, acetyl-CoA, and malonyl-CoA, showed the ability to catalyze the chain elongation and the β-keto reduction steps necessary to yield a 3-hydroxybutyryl-ACP derivate. These results provide new insights into the catalytic efficiency and specificity of this uncharacterized family of PKSs.
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Affiliation(s)
- Martin Sabatini
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Argentina
| | - Santiago Comba
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Argentina
| | - Silvia Altabe
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Argentina
| | - Alejandro I Recio-Balsells
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química de Rosario (IQUIR-CONICET), Universidad Nacional de Rosario, Argentina
| | - Guillermo R Labadie
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Química de Rosario (IQUIR-CONICET), Universidad Nacional de Rosario, Argentina
| | - Eriko Takano
- Manchester Centre of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology (MIB), University of Manchester, UK
| | - Hugo Gramajo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Argentina
| | - Ana Arabolaza
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Universidad Nacional de Rosario, Argentina
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36
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Peek J, Lilic M, Montiel D, Milshteyn A, Woodworth I, Biggins JB, Ternei MA, Calle PY, Danziger M, Warrier T, Saito K, Braffman N, Fay A, Glickman MS, Darst SA, Campbell EA, Brady SF. Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism. Nat Commun 2018; 9:4147. [PMID: 30297823 PMCID: PMC6175910 DOI: 10.1038/s41467-018-06587-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/29/2018] [Indexed: 11/25/2022] Open
Abstract
Rifamycin antibiotics (Rifs) target bacterial RNA polymerases (RNAPs) and are widely used to treat infections including tuberculosis. The utility of these compounds is threatened by the increasing incidence of resistance (RifR). As resistance mechanisms found in clinical settings may also occur in natural environments, here we postulated that bacteria could have evolved to produce rifamycin congeners active against clinically relevant resistance phenotypes. We survey soil metagenomes and identify a tailoring enzyme-rich family of gene clusters encoding biosynthesis of rifamycin congeners (kanglemycins, Kangs) with potent in vivo and in vitro activity against the most common clinically relevant RifR mutations. Our structural and mechanistic analyses reveal the basis for Kang inhibition of RifR RNAP. Unlike Rifs, Kangs function through a mechanism that includes interfering with 5'-initiating substrate binding. Our results suggest that examining soil microbiomes for new analogues of clinically used antibiotics may uncover metabolites capable of circumventing clinically important resistance mechanisms.
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Affiliation(s)
- James Peek
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Mirjana Lilic
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Daniel Montiel
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Aleksandr Milshteyn
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Ian Woodworth
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - John B Biggins
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Paula Y Calle
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Michael Danziger
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Thulasi Warrier
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kohta Saito
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Nathaniel Braffman
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Allison Fay
- Immunology Program, Sloan-Kettering Institute, New York, NY, 10065, USA
| | | | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
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37
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Lim YP, Go MK, Raida M, Inoue T, Wenk MR, Keasling JD, Chang MW, Yew WS. Synthetic Enzymology and the Fountain of Youth: Repurposing Biology for Longevity. ACS OMEGA 2018; 3:11050-11061. [PMID: 30320257 PMCID: PMC6173508 DOI: 10.1021/acsomega.8b01620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Abstract
Caloric restriction (CR) is an intervention that can increase maximal lifespan in organisms, but its application to humans remains challenging. A more feasible approach to achieve lifespan extension is to develop CR mimetics that target biochemical pathways affected by CR. Recent studies in the engineering and structural characterization of polyketide synthases (PKSs) have facilitated their use as biocatalysts to produce novel polyketides. Here, we show that by establishing a combinatorial biosynthetic route in Escherichia coli and exploring the substrate promiscuity of a mutant PKS from alfalfa, 413 potential anti-ageing polyketides were biosynthesized. In this approach, novel acyl-coenzyme A (CoA) precursors generated by promiscuous acid-CoA ligases were utilized by PKS to generate polyketides which were then fed to Caenorhabditis elegans to study their potential efficacy in lifespan extension. It was found that CR mimetics like resveratrol can counter the age-associated decline in mitochondrial function and increase the lifespan of C. elegans. Using the mitochondrial respiration profile of C. elegans supplemented for 8 days with 50 μM resveratrol as a blueprint, we can screen our novel polyketides for potential CR mimetics with improved potency. This study highlights the utility of synthetic enzymology in the development of novel anti-ageing therapeutics.
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Affiliation(s)
- Yan Ping Lim
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Maybelle K. Go
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Manfred Raida
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Takao Inoue
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
| | - Markus R. Wenk
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Jay D. Keasling
- Department
of Chemical & Biomolecular Engineering, University of California at Berkeley, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Matthew W. Chang
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Wen Shan Yew
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
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38
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Chevrette MG, Currie CR. Emerging evolutionary paradigms in antibiotic discovery. J Ind Microbiol Biotechnol 2018; 46:257-271. [PMID: 30269177 DOI: 10.1007/s10295-018-2085-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 09/25/2018] [Indexed: 12/11/2022]
Abstract
Antibiotics revolutionized medicine and remain its cornerstone. Despite their global importance and the continuous threat of resistant pathogens, few antibiotics have been discovered in recent years. Natural products, especially the secondary metabolites of Actinobacteria, have been the traditional discovery source of antibiotics. In nature, the chemistry of antibiotic natural products is shaped by the unique evolution and ecology of their producing organisms, yet these influences remain largely unknown. Here, we highlight the ecology of antibiotics employed by microbes in defensive symbioses and review the evolutionary processes underlying the chemical diversity and activity of microbe-derived antibiotics, including the dynamics of vertical and lateral transmission of biosynthetic pathways and the evolution of efficacy, targeting specificity, and toxicity. We argue that a deeper understanding of the ecology and evolution of microbial interactions and the metabolites that mediate them will allow for an alternative, rational approach to discover new antibiotics.
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Affiliation(s)
- Marc G Chevrette
- Department of Genetics, University of Wisconsin-Madison, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
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39
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Roulet J, Taton A, Golden JW, Arabolaza A, Burkart MD, Gramajo H. Development of a cyanobacterial heterologous polyketide production platform. Metab Eng 2018; 49:94-104. [PMID: 30036678 PMCID: PMC6279439 DOI: 10.1016/j.ymben.2018.07.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 11/21/2022]
Abstract
The development of new heterologous hosts for polyketides production represents an excellent opportunity to expand the genomic, physiological, and biochemical backgrounds that better fit the sustainable production of these valuable molecules. Cyanobacteria are particularly attractive for the production of natural compounds because they have minimal nutritional demands and several strains have well established genetic tools. Using the model strain Synechococcus elongatus, a generic platform was developed for the heterologous production of polyketide synthase (PKS)-derived compounds. The versatility of this system is based on interchangeable modules harboring promiscuous enzymes for PKS activation and the production of PKS extender units, as well as inducible circuits for a regulated expression of the PKS biosynthetic gene cluster. To assess the capability of this platform, we expressed the mycobacterial PKS-based mycocerosic biosynthetic pathway to produce multimethyl-branched esters (MBE). This work is a foundational step forward for the production of high value polyketides in a photosynthetic microorganism.
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Affiliation(s)
- Julia Roulet
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, 2000 Rosario, Argentina
| | - Arnaud Taton
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - James W Golden
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ana Arabolaza
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, 2000 Rosario, Argentina.
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Hugo Gramajo
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, 2000 Rosario, Argentina
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40
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Shen JJ, Chen F, Wang XX, Liu XF, Chen XA, Mao XM, Li YQ. Substrate Specificity of Acyltransferase Domains for Efficient Transfer of Acyl Groups. Front Microbiol 2018; 9:1840. [PMID: 30131798 PMCID: PMC6090053 DOI: 10.3389/fmicb.2018.01840] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/23/2018] [Indexed: 11/13/2022] Open
Abstract
Acyltransferase domains (ATs) of polyketide synthases (PKSs) are critical for loading of acyl groups on acyl carrier protein domains (A) via self- and trans-acylation reactions, to produce structurally diverse polyketides. However, the interaction specificity between ATs and unusual acyl units is rarely documented. In Streptomycestsukubaensis YN06, we found that AT4FkbB [an AT in the fourth module of tacrolimus (FK506) PKS] transferred both allylmalonyl (allmal) and emthylmalonyl (ethmal) units to ACPs, which was supposed responsible for the production of both FK506 and its analog FK520, respectively. Mutations of five residues in AT4FkbB (Q119A, L185I-V186D-V187T, and F203L) caused decreased efficiency of allmal transfer, but a higher ratio of ethmal transfer, supposedly due to less nucleophilic attacks between Ser599 in the active site of AT4FkbB and the carbonyl carbon in the allmal unit, as observed from molecular dynamics simulations. Furthermore, reverse mutations of these five residues in ethmal-specific ATs to the corresponding residues of AT4FkbB increased its binding affinity to allmal-CoA. Among these residues, Val187 of AT4FkbB mainly contributed to allmal recognition, and V187K mutant produced less FK520 than wild type. Our findings thus suggested that five critical residues within AT4FkbB were important for AT functionality in polyketide extension and potentially for targeting biosynthesis by generating desirable products and eliminating undesirable analogs.
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Affiliation(s)
- Jie-Jie Shen
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, China
| | - Fu Chen
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Xiao-Xuan Wang
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiao-Fang Liu
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, China
| | - Xin-Ai Chen
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, China
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, China
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, China
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41
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Musiol-Kroll EM, Wohlleben W. Acyltransferases as Tools for Polyketide Synthase Engineering. Antibiotics (Basel) 2018; 7:antibiotics7030062. [PMID: 30022008 PMCID: PMC6164871 DOI: 10.3390/antibiotics7030062] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/14/2018] [Accepted: 07/16/2018] [Indexed: 12/16/2022] Open
Abstract
Polyketides belong to the most valuable natural products, including diverse bioactive compounds, such as antibiotics, anticancer drugs, antifungal agents, immunosuppressants and others. Their structures are assembled by polyketide synthases (PKSs). Modular PKSs are composed of modules, which involve sets of domains catalysing the stepwise polyketide biosynthesis. The acyltransferase (AT) domains and their “partners”, the acyl carrier proteins (ACPs), thereby play an essential role. The AT loads the building blocks onto the “substrate acceptor”, the ACP. Thus, the AT dictates which building blocks are incorporated into the polyketide structure. The precursor- and occasionally the ACP-specificity of the ATs differ across the polyketide pathways and therefore, the ATs contribute to the structural diversity within this group of complex natural products. Those features make the AT enzymes one of the most promising tools for manipulation of polyketide assembly lines and generation of new polyketide compounds. However, the AT-based PKS engineering is still not straightforward and thus, rational design of functional PKSs requires detailed understanding of the complex machineries. This review summarizes the attempts of PKS engineering by exploiting the AT attributes for the modification of polyketide structures. The article includes 253 references and covers the most relevant literature published until May 2018.
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Affiliation(s)
- Ewa Maria Musiol-Kroll
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
| | - Wolfgang Wohlleben
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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42
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Zargar A, Barajas JF, Lal R, Keasling JD. Polyketide synthases as a platform for chemical product design. AIChE J 2018. [DOI: 10.1002/aic.16351] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Amin Zargar
- Lawrence Berkeley National LaboratoryJoint BioEnergy InstituteEmeryvilleCA94608
- Physical Biosciences Div.Lawrence Berkeley National LaboratoryBerkeleyCA94720
| | - Jesus F. Barajas
- Physical Biosciences Div.Lawrence Berkeley National LaboratoryBerkeleyCA94720
- Dept. of Energy Agile BioFoundryEmeryvilleCA94608
| | - Ravi Lal
- Lawrence Berkeley National LaboratoryJoint BioEnergy InstituteEmeryvilleCA94608
| | - Jay D. Keasling
- Lawrence Berkeley National LaboratoryJoint BioEnergy InstituteEmeryvilleCA94608
- Physical Biosciences Div.Lawrence Berkeley National LaboratoryBerkeleyCA94720
- QB3 Institute, University of California‐BerkeleyEmeryvilleCA94608
- Dept. of Chemical and Biomolecular EngineeringUniversity of CaliforniaBerkeleyCA94720
- Dept. of BioengineeringUniversity of CaliforniaBerkeleyCA94720
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43
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Khan RA. Natural products chemistry: The emerging trends and prospective goals. Saudi Pharm J 2018; 26:739-753. [PMID: 29991919 PMCID: PMC6036106 DOI: 10.1016/j.jsps.2018.02.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/05/2018] [Indexed: 01/01/2023] Open
Abstract
The role and contributions of natural products chemistry in advancements of the physical and biological sciences, its interdisciplinary domains, and emerging of new avenues by providing novel applications, constructive inputs, thrust, comprehensive understanding, broad perspective, and a new vision for future is outlined. The developmental prospects in bio-medical, health, nutrition, and other interrelated sciences along with some of the emerging trends in the subject area are also discussed as part of the current review of the basic and core developments, innovation in techniques, advances in methodology, and possible applications with their effects on the sciences in general and natural products chemistry in particular. The overview of the progress and ongoing developments in broader areas of the natural products chemistry discipline, its role and concurrent economic and scientific implications, contemporary objectives, future prospects as well as impending goals are also outlined. A look at the natural products chemistry in providing scientific progress in various disciplines is deliberated upon.
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Affiliation(s)
- Riaz A. Khan
- Department of Medicinal Chemistry, Qassim University, Qassim 51452, Saudi Arabia
- Manav Rachna International University, National Capital Region, Faridabad, HR 121 004, India
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44
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Santín O, Moncalián G. Loading of malonyl-CoA onto tandem acyl carrier protein domains of polyunsaturated fatty acid synthases. J Biol Chem 2018; 293:12491-12501. [PMID: 29921583 DOI: 10.1074/jbc.ra118.002443] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/04/2018] [Indexed: 12/13/2022] Open
Abstract
Omega-3 polyunsaturated fatty acids (PUFA) are produced in some unicellular organisms, such as marine gammaproteobacteria, myxobacteria, and thraustochytrids, by large enzyme complexes called PUFA synthases. These enzymatic complexes resemble bacterial antibiotic-producing proteins known as polyketide synthases (PKS). One of the PUFA synthase subunits is a conserved large protein (PfaA in marine proteobacteria) that contains three to nine tandem acyl carrier protein (ACP) domains as well as condensation and modification domains. In this work, a study of the PfaA architecture and its ability to initiate the synthesis by selecting malonyl units has been carried out. As a result, we have observed a self-acylation ability in tandem ACPs whose biochemical mechanism differ from the previously described for type II PKS. The acyltransferase domain of PfaA showed a high selectivity for malonyl-CoA that efficiently loads onto the ACPs domains. These results, together with the structural organization predicted for PfaA, suggest that this protein plays a key role at early stages of the anaerobic pathway of PUFA synthesis.
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Affiliation(s)
- Omar Santín
- From the Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011 Santander, Spain
| | - Gabriel Moncalián
- From the Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011 Santander, Spain
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45
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Miyanaga A, Ouchi R, Ishikawa F, Goto E, Tanabe G, Kudo F, Eguchi T. Structural Basis of Protein–Protein Interactions between a trans-Acting Acyltransferase and Acyl Carrier Protein in Polyketide Disorazole Biosynthesis. J Am Chem Soc 2018; 140:7970-7978. [DOI: 10.1021/jacs.8b04162] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Risako Ouchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Ena Goto
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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46
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Marcella AM, Barb AW. Acyl-coenzyme A:(holo-acyl carrier protein) transacylase enzymes as templates for engineering. Appl Microbiol Biotechnol 2018; 102:6333-6341. [PMID: 29858956 DOI: 10.1007/s00253-018-9114-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 01/18/2023]
Abstract
This review will cover the structure, enzymology, and related aspects that are important for structure-based engineering of the transacylase enzymes from fatty acid biosynthesis and polyketide synthesis. Furthermore, this review will focus on in vitro characteristics and not cover engineering of the upstream or downstream reactions or strategies to manipulate metabolic flux in vivo. The malonyl-coenzyme A(CoA)-holo-acyl-carrier protein (holo-ACP) transacylase (FabD) from Escherichia coli serves as a model for this enzyme with thorough descriptions of structure, enzyme mechanism, and effects of mutation on substrate binding presented in the literature. Here, we discuss multiple practical and theoretical considerations regarding engineering transacylase enzymes to accept non-cognate substrates and form novel acyl-ACPs for downstream reactions.
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Affiliation(s)
- Aaron M Marcella
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive, Molecular Biology Building, rm 4210, Ames, IA, 50011, USA
| | - Adam W Barb
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive, Molecular Biology Building, rm 4210, Ames, IA, 50011, USA.
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47
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Lim YH, Wong FT, Yeo WL, Ching KC, Lim YW, Heng E, Chen S, Tsai DJ, Lauderdale TL, Shia KS, Ho YS, Hoon S, Ang EL, Zhang MM, Zhao H. Auroramycin: A Potent Antibiotic from Streptomyces roseosporus by CRISPR-Cas9 Activation. Chembiochem 2018; 19:1716-1719. [PMID: 29799651 DOI: 10.1002/cbic.201800266] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Indexed: 11/09/2022]
Abstract
Silent biosynthetic gene clusters represent a potentially rich source of new bioactive compounds. We report the discovery, characterization, and biosynthesis of a novel doubly glycosylated 24-membered polyene macrolactam from a silent biosynthetic gene cluster in Streptomyces roseosporus by using the CRISPR-Cas9 gene cluster activation strategy. Structural characterization of this polyketide, named auroramycin, revealed a rare isobutyrylmalonyl extender unit and a unique pair of amino sugars. Relative and absolute stereochemistry were determined by using a combination of spectroscopic analyses, chemical derivatization, and computational analysis. The activated gene cluster for auroramycin production was also verified by transcriptional analyses and gene deletions. Finally, auroramycin exhibited potent anti-methicillin-resistant Staphylococcus aureus (anti-MRSA) activity towards clinical drug-resistant isolates.
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Affiliation(s)
- Yee Hwee Lim
- Organic Chemistry, Institute of Chemical and Engineering Sciences (ICES), A*STAR, 8 Biomedical Grove, Neuros #07-01/02/03, Singapore, 138665, Singapore
| | - Fong Tian Wong
- Molecular Engineering Lab (MEL), Biomedical Science Institutes, A*STAR, 61 Biopolis Drive, Proteos #13-02, Singapore, 138673, Singapore
| | - Wan Lin Yeo
- Metabolic Engineering Research Laboratory (MERL), Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore, 138669, Singapore
| | - Kuan Chieh Ching
- Organic Chemistry, Institute of Chemical and Engineering Sciences (ICES), A*STAR, 8 Biomedical Grove, Neuros #07-01/02/03, Singapore, 138665, Singapore
| | - Yi Wee Lim
- Organic Chemistry, Institute of Chemical and Engineering Sciences (ICES), A*STAR, 8 Biomedical Grove, Neuros #07-01/02/03, Singapore, 138665, Singapore
| | - Elena Heng
- Molecular Engineering Lab (MEL), Biomedical Science Institutes, A*STAR, 61 Biopolis Drive, Proteos #13-02, Singapore, 138673, Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute (BTI), A*STAR, 20 Biopolis Way, Centros #06-01, Singapore, 138668, Singapore
| | - De-Juin Tsai
- National Institute of Infectious Diseases and Vaccinology (DJT & TLL), and, Institute of Biotechnology and Pharmaceutical Research (KSS), National Health Research Institutes (NHRI), 35 Keyan Road, Zhunan Town, Miaoli County, 350, Taiwan, R.O.C
| | - Tsai-Ling Lauderdale
- National Institute of Infectious Diseases and Vaccinology (DJT & TLL), and, Institute of Biotechnology and Pharmaceutical Research (KSS), National Health Research Institutes (NHRI), 35 Keyan Road, Zhunan Town, Miaoli County, 350, Taiwan, R.O.C
| | - Kak-Shan Shia
- National Institute of Infectious Diseases and Vaccinology (DJT & TLL), and, Institute of Biotechnology and Pharmaceutical Research (KSS), National Health Research Institutes (NHRI), 35 Keyan Road, Zhunan Town, Miaoli County, 350, Taiwan, R.O.C
| | - Ying Swan Ho
- Bioprocessing Technology Institute (BTI), A*STAR, 20 Biopolis Way, Centros #06-01, Singapore, 138668, Singapore
| | - Shawn Hoon
- Molecular Engineering Lab (MEL), Biomedical Science Institutes, A*STAR, 61 Biopolis Drive, Proteos #13-02, Singapore, 138673, Singapore
| | - Ee Lui Ang
- Metabolic Engineering Research Laboratory (MERL), Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore, 138669, Singapore
| | - Mingzi M Zhang
- Metabolic Engineering Research Laboratory (MERL), Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore, 138669, Singapore
| | - Huimin Zhao
- Metabolic Engineering Research Laboratory (MERL), Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore, 138669, Singapore
- 215 Roger Adams Laboratory, Box C3, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
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48
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Li Y, Zhang W, Zhang H, Tian W, Wu L, Wang S, Zheng M, Zhang J, Sun C, Deng Z, Sun Y, Qu X, Zhou J. Structural Basis of a Broadly Selective Acyltransferase from the Polyketide Synthase of Splenocin. Angew Chem Int Ed Engl 2018. [PMID: 29536601 DOI: 10.1002/anie.201802805] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Polyketides are a large family of pharmaceutically important natural products, and the structural modification of their scaffolds is significant for drug development. Herein, we report high-resolution X-ray crystal structures of the broadly selective acyltransferase (AT) from the splenocin polyketide synthase (SpnD-AT) in the apo form and in complex with benzylmalonyl and pentynylmalonyl extender unit mimics. These structures revealed the molecular basis for the stereoselectivity and substrate specificity of SpnD-AT, and enabled the engineering of the industrially important Ery-AT6 to broaden its substrate scope to include three new types of extender units.
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Affiliation(s)
- Yuan Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Wan Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Hui Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Wenya Tian
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Lian Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Shuwen Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Jinru Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Chenghai Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Jiahai Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
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49
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Li Y, Zhang W, Zhang H, Tian W, Wu L, Wang S, Zheng M, Zhang J, Sun C, Deng Z, Sun Y, Qu X, Zhou J. Structural Basis of a Broadly Selective Acyltransferase from the Polyketide Synthase of Splenocin. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yuan Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Wan Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Hui Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Wenya Tian
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Lian Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology; College of Chemistry and Pharmacy; Northwest A&F University; 3 Taicheng Road, Yangling 712100 Shaanxi China
| | - Shuwen Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Jinru Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology; College of Chemistry and Pharmacy; Northwest A&F University; 3 Taicheng Road, Yangling 712100 Shaanxi China
| | - Chenghai Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Jiahai Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology; College of Chemistry and Pharmacy; Northwest A&F University; 3 Taicheng Road, Yangling 712100 Shaanxi China
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50
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Evolutionary stability of antibiotic protection in a defensive symbiosis. Proc Natl Acad Sci U S A 2018; 115:E2020-E2029. [PMID: 29444867 DOI: 10.1073/pnas.1719797115] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The increasing resistance of human pathogens severely limits the efficacy of antibiotics in medicine, yet many animals, including solitary beewolf wasps, successfully engage in defensive alliances with antibiotic-producing bacteria for millions of years. Here, we report on the in situ production of 49 derivatives belonging to three antibiotic compound classes (45 piericidin derivatives, 3 streptochlorin derivatives, and nigericin) by the symbionts of 25 beewolf host species and subspecies, spanning 68 million years of evolution. Despite a high degree of qualitative stability in the antibiotic mixture, we found consistent quantitative differences between species and across geographic localities, presumably reflecting adaptations to combat local pathogen communities. Antimicrobial bioassays with the three main components and in silico predictions based on the structure and specificity in polyketide synthase domains of the piericidin biosynthesis gene cluster yield insights into the mechanistic basis and ecoevolutionary implications of producing a complex mixture of antimicrobial compounds in a natural setting.
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