1
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Schmalhofer M, Vagstad AL, Zhou Q, Bode HB, Groll M. Polyketide Trimming Shapes Dihydroxynaphthalene-Melanin and Anthraquinone Pigments. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400184. [PMID: 38491909 PMCID: PMC11165489 DOI: 10.1002/advs.202400184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/28/2024] [Indexed: 03/18/2024]
Abstract
Pigments such as anthraquinones (AQs) and melanins are antioxidants, protectants, or virulence factors. AQs from the entomopathogenic bacterium Photorhabdus laumondii are produced by a modular type II polyketide synthase system. A key enzyme involved in AQ biosynthesis is PlAntI, which catalyzes the hydrolysis of the bicyclic-intermediate-loaded acyl carrier protein, polyketide trimming, and assembly of the aromatic AQ scaffold. Here, multiple crystal structures of PlAntI in various conformations and with bound substrate surrogates or inhibitors are reported. Structure-based mutagenesis and activity assays provide experimental insights into the three sequential reaction steps to yield the natural product AQ-256. For comparison, a series of ligand-complex structures of two functionally related hydrolases involved in the biosynthesis of 1,8-dihydroxynaphthalene-melanin in pathogenic fungi is determined. These data provide fundamental insights into the mechanism of polyketide trimming that shapes pigments in pro- and eukaryotes.
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Affiliation(s)
- Maximilian Schmalhofer
- TUM School of Natural SciencesDepartment of BioscienceCentre for Protein AssembliesChair of BiochemistryTechnical University of Munich85748GarchingGermany
| | - Anna L. Vagstad
- Eidgenössische Technische Hochschule (ETH) ZürichInstitute of MicrobiologyZürich8093Switzerland
| | - Qiuqin Zhou
- Department of Natural Products in Organismic InteractionsMax Planck Institute for Terrestrial Microbiology35043MarburgGermany
- Present address:
Center for Mass Spectrometry and Optical Spectroscopy (CeMOS)Mannheim University of Applied Sciences68163MannheimGermany
| | - Helge B. Bode
- Department of Natural Products in Organismic InteractionsMax Planck Institute for Terrestrial Microbiology35043MarburgGermany
- Molecular BiotechnologyDepartment of BiosciencesGoethe University Frankfurt60438FrankfurtGermany
- Department of ChemistryPhillips Universität Marburg35043MarburgGermany
- Center for Synthetic Microbiology (SYNMIKRO)Phillips Universität Marburg35043MarburgGermany
- Senckenberg Gesellschaft für Naturforschung60325FrankfurtGermany
| | - Michael Groll
- TUM School of Natural SciencesDepartment of BioscienceCentre for Protein AssembliesChair of BiochemistryTechnical University of Munich85748GarchingGermany
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2
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Vijayanathan M, Vadakkepat AK, Mahendran KR, Sharaf A, Frandsen KEH, Bandyopadhyay D, Pillai MR, Soniya EV. Structural and mechanistic insights into Quinolone Synthase to address its functional promiscuity. Commun Biol 2024; 7:566. [PMID: 38745065 PMCID: PMC11093982 DOI: 10.1038/s42003-024-06152-2] [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: 12/29/2021] [Accepted: 04/07/2024] [Indexed: 05/16/2024] Open
Abstract
Quinolone synthase from Aegle marmelos (AmQNS) is a type III polyketide synthase that yields therapeutically effective quinolone and acridone compounds. Addressing the structural and molecular underpinnings of AmQNS and its substrate interaction in terms of its high selectivity and specificity can aid in the development of numerous novel compounds. This paper presents a high-resolution AmQNS crystal structure and explains its mechanistic role in synthetic selectivity. Additionally, we provide a model framework to comprehend structural constraints on ketide insertion and postulate that AmQNS's steric and electrostatic selectivity plays a role in its ability to bind to various core substrates, resulting in its synthetic diversity. AmQNS prefers quinolone synthesis and can accommodate large substrates because of its wide active site entrance. However, our research suggests that acridone is exclusively synthesized in the presence of high malonyl-CoA concentrations. Potential implications of functionally relevant residue mutations were also investigated, which will assist in harnessing the benefits of mutations for targeted polyketide production. The pharmaceutical industry stands to gain from these findings as they expand the pool of potential drug candidates, and these methodologies can also be applied to additional promising enzymes.
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Affiliation(s)
- Mallika Vijayanathan
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
- Department of Plant and Environment Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Abhinav Koyamangalath Vadakkepat
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE17HB, UK
| | - Kozhinjampara R Mahendran
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Abdoallah Sharaf
- SequAna Core Facility, Department of Biology, University of Konstanz, Konstanz, Germany
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt
| | - Kristian E H Frandsen
- Department of Plant and Environment Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Debashree Bandyopadhyay
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
| | - M Radhakrishna Pillai
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Eppurath Vasudevan Soniya
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India.
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3
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Zhang Y, Liu Z, Xiao G, Shi J, Liu B, Xiao N, Sun Z. Simultaneous DHA and organic selenium production by Schizochytrium sp.: a theoretical basis. Sci Rep 2023; 13:15607. [PMID: 37731016 PMCID: PMC10511486 DOI: 10.1038/s41598-023-42900-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023] Open
Abstract
Docosahexaenoic acid (DHA) and selenium (Se) are nutrients that confer several health benefits to both humans and animals. Widespread use of DHA in milk powder and health products requires large-scale mass production via Schizochytrium sp., while Se intended for human consumption is produced as organic Se via yeast. However, producing these nutrients on an industrial scale is constrained by various factors. We found that supplementing Schizochytrium sp. with Na2SeO3 (0.5 mg/L) improves its biomass and DHA production and also provides organic Se. De novo assembled transcriptome and biochemical indicators showed that Na2SeO3 promotes forming acetyl coenzyme A and L-cysteine via the glycerol kinase and cysteine synthase pathways, promoting DHA synthesis through the polyketide synthase pathway. However, high doses of Na2SeO3 (5 mg/L) limited the biomass of Schizochytrium sp. and DHA content. This study provided a theoretical basis for the simultaneous production of organic Se and DHA via Schizochytrium sp.
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Affiliation(s)
- Yunqiang Zhang
- Hunan Agricultural University Veterinary Faculty, No.1 Nongda Road, Furong District, Changsha City, 410000, Hunan, China
- Hunan Canzoho Biological Technology Co., Ltd., 321 Kangning Road, Changsha City, 410000, Hunan, China
| | - Zikui Liu
- Hunan Agricultural University Veterinary Faculty, No.1 Nongda Road, Furong District, Changsha City, 410000, Hunan, China
- Hunan Canzoho Biological Technology Co., Ltd., 321 Kangning Road, Changsha City, 410000, Hunan, China
| | - Gang Xiao
- Hunan Agricultural University Veterinary Faculty, No.1 Nongda Road, Furong District, Changsha City, 410000, Hunan, China
| | - Jiawei Shi
- Hunan Agricultural University Veterinary Faculty, No.1 Nongda Road, Furong District, Changsha City, 410000, Hunan, China
- Hunan Canzoho Biological Technology Co., Ltd., 321 Kangning Road, Changsha City, 410000, Hunan, China
| | - Baili Liu
- Hunan Canzoho Biological Technology Co., Ltd., 321 Kangning Road, Changsha City, 410000, Hunan, China
| | - Ning Xiao
- Hunan Agricultural University Veterinary Faculty, No.1 Nongda Road, Furong District, Changsha City, 410000, Hunan, China
| | - Zhiliang Sun
- Hunan Agricultural University Veterinary Faculty, No.1 Nongda Road, Furong District, Changsha City, 410000, Hunan, China.
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4
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Yang D, Eun H, Prabowo CPS. Metabolic Engineering and Synthetic Biology Approaches for the Heterologous Production of Aromatic Polyketides. Int J Mol Sci 2023; 24:ijms24108923. [PMID: 37240269 DOI: 10.3390/ijms24108923] [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: 04/18/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Polyketides are a diverse set of natural products with versatile applications as pharmaceuticals, nutraceuticals, and cosmetics, to name a few. Of several types of polyketides, aromatic polyketides comprising type II and III polyketides contain many chemicals important for human health such as antibiotics and anticancer agents. Most aromatic polyketides are produced from soil bacteria or plants, which are difficult to engineer and grow slowly in industrial settings. To this end, metabolic engineering and synthetic biology have been employed to efficiently engineer heterologous model microorganisms for enhanced production of important aromatic polyketides. In this review, we discuss the recent advancement in metabolic engineering and synthetic biology strategies for the production of type II and type III polyketides in model microorganisms. Future challenges and prospects of aromatic polyketide biosynthesis by synthetic biology and enzyme engineering approaches are also discussed.
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Affiliation(s)
- Dongsoo Yang
- Synthetic Biology and Enzyme Engineering Laboratory, Department of Chemical and Biological Engineering (BK21 Four), Korea University, Seoul 02481, Republic of Korea
| | - Hyunmin Eun
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Cindy Pricilia Surya Prabowo
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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5
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Feng Z. O-methyltransferases selectively modify anthraquinone natural products. Structure 2023; 31:507-508. [PMID: 37146572 DOI: 10.1016/j.str.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 05/07/2023]
Abstract
In this issue of Structure, Huber et al. identify five O-methyltransferases, and three of them catalyze the sequential methylation of the Gram-negative bacterium-derived aromatic polyketide anthraquinone AQ-256. They present co-crystal structures with bound AQ-256 and its methylated derivatives, which explains the specificities of these O-methyltransferases.
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Affiliation(s)
- Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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6
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Huber EM, Kreling L, Heinrich AK, Dünnebacke M, Pöthig A, Bode HB, Groll M. A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments. Structure 2023; 31:573-583.e5. [PMID: 36963398 DOI: 10.1016/j.str.2023.03.001] [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: 11/28/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/26/2023]
Abstract
Modification of the polyketide anthraquinone AQ-256 in the entomopathogenic Photorhabdus luminescens involves several O-methylations, but the biosynthetic gene cluster antA-I lacks corresponding tailoring enzymes. We here describe the identification of five putative, highly homologous O-methyltransferases encoded in the genome of P. luminescens. Activity assays in vitro and deletion experiments in vivo revealed that three of them account for anthraquinone tailoring by producing three monomethylated and two dimethylated species of AQ-256. X-ray structures of all five enzymes indicate high structural and mechanistic similarity. As confirmed by structure-based mutagenesis, a conserved histidine at the active site likely functions as a general base for substrate deprotonation and subsequent methyl transfer in all enzymes. Eight complex structures with AQ-256 as well as mono- and dimethylated derivatives confirm the substrate specificity patterns found in vitro and visualize how single amino acid differences in the active-site pockets impact substrate orientation and govern site-specific methylation.
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Affiliation(s)
- Eva M Huber
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany.
| | - Lukas Kreling
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Antje K Heinrich
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Maximilian Dünnebacke
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Alexander Pöthig
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Catalysis Research Center, Chair of Inorganic and Metal-Organic Chemistry, Ernst-Otto-Fischer-Str. 1, 85748 Garching, Germany
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Chemical Biology, Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, 35043 Marburg, Germany; Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany.
| | - Michael Groll
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany.
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7
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Enzymology of assembly line synthesis by modular polyketide synthases. Nat Chem Biol 2023; 19:401-415. [PMID: 36914860 DOI: 10.1038/s41589-023-01277-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/31/2023] [Indexed: 03/16/2023]
Abstract
Modular polyketide synthases (PKSs) run catalytic reactions over dozens of steps in a highly orchestrated manner. To accomplish this synthetic feat, they form megadalton multienzyme complexes that are among the most intricate proteins on earth. Polyketide products are of elaborate chemistry with molecular weights of usually several hundred daltons and include clinically important drugs such as erythromycin (antibiotic), rapamycin (immunosuppressant) and epothilone (anticancer drug). The term 'modular' refers to a hierarchical structuring of modules and domains within an overall assembly line arrangement, in which PKS organization is colinearly translated into the polyketide structure. New structural information obtained during the past few years provides substantial direct insight into the orchestration of catalytic events within a PKS module and leads to plausible models for synthetic progress along assembly lines. In light of these structural insights, the PKS engineering field is poised to enter a new era of engineering.
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8
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Wang J, Wang X, Li X, Kong L, Du Z, Li D, Gou L, Wu H, Cao W, Wang X, Lin S, Shi T, Deng Z, Wang Z, Liang J. C-N bond formation by a polyketide synthase. Nat Commun 2023; 14:1319. [PMID: 36899013 PMCID: PMC10006239 DOI: 10.1038/s41467-023-36989-w] [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: 06/15/2022] [Accepted: 02/28/2023] [Indexed: 03/12/2023] Open
Abstract
Assembly-line polyketide synthases (PKSs) are molecular factories that produce diverse metabolites with wide-ranging biological activities. PKSs usually work by constructing and modifying the polyketide backbone successively. Here, we present the cryo-EM structure of CalA3, a chain release PKS module without an ACP domain, and its structures with amidation or hydrolysis products. The domain organization reveals a unique "∞"-shaped dimeric architecture with five connected domains. The catalytic region tightly contacts the structural region, resulting in two stabilized chambers with nearly perfect symmetry while the N-terminal docking domain is flexible. The structures of the ketosynthase (KS) domain illustrate how the conserved key residues that canonically catalyze C-C bond formation can be tweaked to mediate C-N bond formation, revealing the engineering adaptability of assembly-line polyketide synthases for the production of novel pharmaceutical agents.
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Affiliation(s)
- Jialiang Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaojie Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Department of Molecular Biology, Shanghai Jikaixing Biotech Inc., Shanghai, 200131, China
| | - Xixi Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - LiangLiang Kong
- National Facility for Protein Science in Shanghai, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Zeqian Du
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dandan Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lixia Gou
- School of Life Science, North China University of Science and Technology, Tangshan, Hebei, China
| | - Hao Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Cao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Jingdan Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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9
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Dickinson MS, Miyazawa T, McCool RS, Keatinge-Clay AT. Priming enzymes from the pikromycin synthase reveal how assembly-line ketosynthases catalyze carbon-carbon chemistry. Structure 2022; 30:1331-1339.e3. [PMID: 35738283 PMCID: PMC9444953 DOI: 10.1016/j.str.2022.05.021] [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: 01/29/2022] [Revised: 04/28/2022] [Accepted: 05/27/2022] [Indexed: 10/17/2022]
Abstract
The first domain of modular polyketide synthases (PKSs) is most commonly a ketosynthase (KS)-like enzyme, KSQ, that primes polyketide synthesis. Unlike downstream KSs that fuse α-carboxyacyl groups to growing polyketide chains, it performs an extension-decoupled decarboxylation of these groups to generate primer units. When Pik127, a model triketide synthase constructed from modules of the pikromycin synthase, was studied by cryoelectron microscopy (cryo-EM), the dimeric didomain comprised of KSQ and the neighboring methylmalonyl-selective acyltransferase (AT) dominated the class averages and yielded structures at 2.5- and 2.8-Å resolution, respectively. Comparisons with ketosynthases complexed with their substrates revealed the conformation of the (2S)-methylmalonyl-S-phosphopantetheinyl portion of KSQ and KS substrates prior to decarboxylation. Point mutants of Pik127 probed the roles of residues in the KSQ active site, while an AT-swapped version of Pik127 demonstrated that KSQ can also decarboxylate malonyl groups. Mechanisms for how KSQ and KS domains catalyze carbon-carbon chemistry are proposed.
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Affiliation(s)
- Miles S Dickinson
- Sauer Structural Biology Lab, The University of Texas at Austin, 102 E. 24th Street, Austin, TX 78712, USA
| | - Takeshi Miyazawa
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th Street, Austin, TX 78712, USA
| | - Ryan S McCool
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th Street, Austin, TX 78712, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th Street, Austin, TX 78712, USA.
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10
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Löhr NA, Eisen F, Thiele W, Platz L, Motter J, Hüttel W, Gressler M, Müller M, Hoffmeister D. Unprecedented Mushroom Polyketide Synthases Produce the Universal Anthraquinone Precursor. Angew Chem Int Ed Engl 2022; 61:e202116142. [PMID: 35218274 PMCID: PMC9325552 DOI: 10.1002/anie.202116142] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Indexed: 11/11/2022]
Abstract
(Pre-)anthraquinones are widely distributed natural compounds and occur in plants, fungi, microorganisms, and animals, with atrochrysone (1) as the key biosynthetic precursor. Chemical analyses established mushrooms of the genus Cortinarius-the webcaps-as producers of atrochrysone-derived octaketide pigments. However, more recent genomic data did not provide any evidence for known atrochrysone carboxylic acid (4) synthases nor any other polyketide synthase (PKS) producing oligocyclic metabolites. Here, we describe an unprecedented class of non-reducing (NR-)PKS. In vitro assays with recombinant enzyme in combination with in vivo product formation in the heterologous host Aspergillus niger established CoPKS1 and CoPKS4 of C. odorifer as members of a new class of atrochrysone carboxylic acid synthases. CoPKS4 catalyzed both hepta- and octaketide synthesis and yielded 6-hydroxymusizin (6), along with 4. These first mushroom PKSs for oligocyclic products illustrate how the biosynthesis of bioactive natural metabolites evolved independently in various groups of life.
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Affiliation(s)
- Nikolai A Löhr
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Frederic Eisen
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Wiebke Thiele
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Lukas Platz
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Jonas Motter
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Wolfgang Hüttel
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Markus Gressler
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Dirk Hoffmeister
- Department Pharmaceutical Microbiology at the Hans-Knöll-Institute, Friedrich-Schiller-Universität, Beutenbergstrasse 11a, 07745, Jena, Germany
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11
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Shi J, Shi Y, Li JC, Wei W, Chen Y, Cheng P, Liu CL, Zhang H, Wu R, Zhang B, Jiao RH, Yu S, Liang Y, Tan RX, Ge HM. In Vitro Reconstitution of Cinnamoyl Moiety Reveals Two Distinct Cyclases for Benzene Ring Formation. J Am Chem Soc 2022; 144:7939-7948. [PMID: 35470672 DOI: 10.1021/jacs.2c02855] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cinnamoyl-containing natural products (CCNPs) are a small class of bacterial metabolites with notable bioactivities. The biosynthesis of cinnamoyl moiety has been proposed to be assembled by an unusual highly reducing (HR) type II polyketide synthases (PKS). However, the biosynthetic route, especially the cyclization step for the benzene ring formation, remains unclear. In this work, we successfully reconstituted the pathway of cinnamoyl moiety in kitacinnamycin biosynthesis through a step-wise approach in vitro and demonstrated that a three-protein complex, Kcn17-Kcn18-Kcn19, can catalyze 6π-electrocyclization followed by dehydrogenation to form the benzene ring. We found that the three-protein homologues were widely distributed among 207 HR type II PKS biosynthetic gene clusters including five known CCNPs. In contrast, in the biosynthesis of youssoufene, a cinnamoyl-containing polyene, we identified that the benzene ring formation was accomplished by a distinct orphan protein. Thus, our work resolved the long-standing mystery in cinnamoyl biosynthesis and revealed two distinct enzymes that can synthesize benzene rings via polyene precursors.
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Affiliation(s)
- Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yang Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jian Cheng Li
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wanqing Wei
- State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yu Chen
- State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ping Cheng
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Cheng Li Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Hao Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Rui Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Shouyun Yu
- State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yong Liang
- State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
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12
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Serapian S, Crosby J, Crump MP, van der Kamp MW. Path to Actinorhodin: Regio- and Stereoselective Ketone Reduction by a Type II Polyketide Ketoreductase Revealed in Atomistic Detail. JACS AU 2022; 2:972-984. [PMID: 35557750 PMCID: PMC9088766 DOI: 10.1021/jacsau.2c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 06/15/2023]
Abstract
In type II polyketide synthases (PKSs), which typically biosynthesize several antibiotic and antitumor compounds, the substrate is a growing polyketide chain, shuttled between individual PKS enzymes, while covalently tethered to an acyl carrier protein (ACP): this requires the ACP interacting with a series of different enzymes in succession. During biosynthesis of the antibiotic actinorhodin, produced by Streptomyces coelicolor, one such key binding event is between an ACP carrying a 16-carbon octaketide chain (actACP) and a ketoreductase (actKR). Once the octaketide is bound inside actKR, it is likely cyclized between C7 and C12 and regioselective reduction of the ketone at C9 occurs: how these elegant chemical and conformational changes are controlled is not yet known. Here, we perform protein-protein docking, protein NMR, and extensive molecular dynamics simulations to reveal a probable mode of association between actACP and actKR; we obtain and analyze a detailed model of the C7-C12-cyclized octaketide within the actKR active site; and we confirm this model through multiscale (QM/MM) reaction simulations of the key ketoreduction step. Molecular dynamics simulations show that the most thermodynamically stable cyclized octaketide isomer (7R,12R) also gives rise to the most reaction competent conformations for ketoreduction. Subsequent reaction simulations show that ketoreduction is stereoselective as well as regioselective, resulting in an S-alcohol. Our simulations further indicate several conserved residues that may be involved in selectivity of C7-12 cyclization and C9 ketoreduction. Detailed insights obtained on ACP-based substrate presentation in type II PKSs can help design ACP-ketoreductase systems with altered regio- or stereoselectivity.
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Affiliation(s)
- Stefano
A. Serapian
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - John Crosby
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Matthew P. Crump
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Marc W. van der Kamp
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
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13
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Chen A, Jiang Z, Burkart MD. Enzymology of standalone elongating ketosynthases. Chem Sci 2022; 13:4225-4238. [PMID: 35509474 PMCID: PMC9006962 DOI: 10.1039/d1sc07256k] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/09/2022] [Indexed: 12/16/2022] Open
Abstract
The β-ketoacyl-acyl carrier protein synthase, or ketosynthase (KS), catalyses carbon-carbon bond formation in fatty acid and polyketide biosynthesis via a decarboxylative Claisen-like condensation. In prokaryotes, standalone elongating KSs interact with the acyl carrier protein (ACP) which shuttles substrates to each partner enzyme in the elongation cycle for catalysis. Despite ongoing research for more than 50 years since KS was first identified in E. coli, the complex mechanism of KSs continues to be unravelled, including recent understanding of gating motifs, KS-ACP interactions, substrate recognition and delivery, and roles in unsaturated fatty acid biosynthesis. In this review, we summarize the latest studies, primarily conducted through structural biology and molecular probe design, that shed light on the emerging enzymology of standalone elongating KSs.
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Affiliation(s)
- Aochiu Chen
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Ziran Jiang
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
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14
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Löhr NA, Eisen F, Thiele W, Platz L, Motter J, Hüttel W, Gressler M, Müller M, Hoffmeister D. Unprecedented Mushroom Polyketide Synthases Produce the Universal Anthraquinone Precursor. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Nikolai A Löhr
- Friedrich-Schiller-Universitat Jena Pharmaceutical Microbiology GERMANY
| | - Frederic Eisen
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Wiebke Thiele
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Lukas Platz
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Jonas Motter
- Friedrich-Schiller-Universitat Jena Pharmaceutical Microbiology GERMANY
| | - Wolfgang Hüttel
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Markus Gressler
- Friedrich-Schiller-Universitat Jena Pharmaceutical Microbiology GERMANY
| | - Michael Müller
- Albert-Ludwigs-Universitat Freiburg Pharmaceutical and Medicinal Chemistry GERMANY
| | - Dirk Hoffmeister
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Pharmaceutical Microbiology at the Hans-Kn�ll-Institute Beutenbergstrasse 11a 07745 Jena GERMANY
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15
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Hulst MB, Grocholski T, Neefjes JJC, van Wezel GP, Metsä-Ketelä M. Anthracyclines: biosynthesis, engineering and clinical applications. Nat Prod Rep 2021; 39:814-841. [PMID: 34951423 DOI: 10.1039/d1np00059d] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: January 1995 to June 2021Anthracyclines are glycosylated microbial natural products that harbour potent antiproliferative activities. Doxorubicin has been widely used as an anticancer agent in the clinic for several decades, but its use is restricted due to severe side-effects such as cardiotoxicity. Recent studies into the mode-of-action of anthracyclines have revealed that effective cardiotoxicity-free anthracyclines can be generated by focusing on histone eviction activity, instead of canonical topoisomerase II poisoning leading to double strand breaks in DNA. These developments have coincided with an increased understanding of the biosynthesis of anthracyclines, which has allowed generation of novel compound libraries by metabolic engineering and combinatorial biosynthesis. Coupled to the continued discovery of new congeners from rare Actinobacteria, a better understanding of the biology of Streptomyces and improved production methodologies, the stage is set for the development of novel anthracyclines that can finally surpass doxorubicin at the forefront of cancer chemotherapy.
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Affiliation(s)
- Mandy B Hulst
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
| | - Thadee Grocholski
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Jacques J C Neefjes
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Centre, Leiden, The Netherlands
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
| | - Mikko Metsä-Ketelä
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
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16
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Hirsch M, Fitzgerald BJ, Keatinge-Clay AT. How cis-Acyltransferase Assembly-Line Ketosynthases Gatekeep for Processed Polyketide Intermediates. ACS Chem Biol 2021; 16:2515-2526. [PMID: 34590822 PMCID: PMC9879353 DOI: 10.1021/acschembio.1c00598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
With the redefinition of polyketide synthase (PKS) modules, a new appreciation of their most downstream domain, the ketosynthase (KS), is emerging. In addition to performing its well-established role of generating a carbon-carbon bond between an acyl-CoA building block and a growing polyketide, it may gatekeep against incompletely processed intermediates. Here, we investigate 739 KSs from 92 primarily actinomycete, cis-acyltransferase assembly lines. When KSs were separated into 16 families based on the chemistries at the α- and β-carbons of their polyketide substrates, a comparison of 32 substrate tunnel residues revealed unique sequence fingerprints. Surprisingly, additional fingerprints were detected when the chemistry at the γ-carbon was considered. Representative KSs were modeled bound to their natural polyketide substrates to better understand observed patterns, such as the substitution of a tryptophan by a smaller residue to accommodate an l-α-methyl group or the substitution of four smaller residues by larger ones to make better contact with a primer unit or diketide. Mutagenesis of a conserved glutamine in a KS within a model triketide synthase indicates that the substrate tunnel is sensitive to alteration and that engineering this KS to accept unnatural substrates may require several mutations.
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Affiliation(s)
- Melissa Hirsch
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Brendan J. Fitzgerald
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Adrian T. Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
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17
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Bagde SR, Mathews II, Fromme JC, Kim CY. Modular polyketide synthase contains two reaction chambers that operate asynchronously. Science 2021; 374:723-729. [PMID: 34735234 DOI: 10.1126/science.abi8532] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Saket R Bagde
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX 79968, USA.,Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Chu-Young Kim
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX 79968, USA.,Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, USA
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18
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19
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Lee WC, Choi S, Jang A, Yeon J, Hwang E, Kim Y. Structural basis of the complementary activity of two ketosynthases in aryl polyene biosynthesis. Sci Rep 2021; 11:16340. [PMID: 34381152 PMCID: PMC8358021 DOI: 10.1038/s41598-021-95890-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/02/2021] [Indexed: 12/26/2022] Open
Abstract
Aryl polyenes (APE) are one of the most widespread secondary metabolites among gram-negative bacteria. In Acinetobacter baumannii, strains belonging to the virulent global clone 2 (GC2) mostly contain APE biosynthesis genes; its relevance in elevated pathogenicity is of great interest. APE biosynthesis gene clusters harbor two ketosynthases (KSs): the heterodimeric KS-chain length factor complex, ApeO-ApeC, and the homodimeric ketoacyl-acyl carrier protein synthase I (FabB)-like KS, ApeR. The role of the two KSs in APE biosynthesis is unclear. We determined the crystal structures of the two KSs from a pathogenic A. baumannii strain. ApeO-ApeC and ApeR have similar cavity volumes; however, ApeR has a narrow cavity near the entrance. In vitro assay based on the absorption characteristics of polyene species indicated the generation of fully elongated polyene with only ApeO-ApeC, probably because of the funnel shaped active site cavity. However, adding ApeR to the reaction increases the throughput of APE biosynthesis. Mutagenesis at Tyr135 in the active site cavity of ApeR reduces the activity significantly, which suggests that the stacking of the aryl group between Tyr135 and Phe202 is important for substrate recognition. Therefore, the two KSs function complementarily in the generation of APE to enhance its production.
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Affiliation(s)
- Woo Cheol Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, South Korea
| | - Sungjae Choi
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, South Korea
| | - Ahjin Jang
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, South Korea
| | - Jiwon Yeon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, South Korea
| | - Eunha Hwang
- Bio-Chemical Analysis Team, Korea Basic Science Institute, Ochang, 28119, Chungcheongbuk-do, South Korea
| | - Yangmee Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, South Korea.
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20
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Hallin EI, Bramham CR, Kursula P. Structural properties and peptide ligand binding of the capsid homology domains of human Arc. Biochem Biophys Rep 2021; 26:100975. [PMID: 33732907 PMCID: PMC7941041 DOI: 10.1016/j.bbrep.2021.100975] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/14/2022] Open
Abstract
The activity-regulated cytoskeleton-associated protein (Arc) is important for synaptic plasticity and the normal function of the brain. Arc interacts with neuronal postsynaptic proteins, but the mechanistic details of its function have not been fully established. The C-terminal domain of Arc consists of tandem domains, termed the N- and C-lobe. The N-lobe harbours a peptide binding site, able to bind multiple targets. By measuring the affinity of human Arc towards various peptides from stargazin and guanylate kinase-associated protein (GKAP), we have refined its specificity determinants. We found two sites in the GKAP repeat region that bind to Arc and confirmed these interactions by X-ray crystallography. Phosphorylation of the stargazin peptide did not affect binding affinity but caused changes in thermodynamic parameters. Comparison of the crystal structures of three high-resolution human Arc-peptide complexes identifies three conserved C-H…π interactions at the binding cavity, explaining the sequence specificity of short linear motif binding by Arc. We further characterise central residues of the Arc lobe fold, show the effects of peptide binding on protein dynamics, and identify acyl carrier proteins as structures similar to the Arc lobes. We hypothesise that Arc may affect protein-protein interactions and phase separation at the postsynaptic density, affecting protein turnover and re-modelling of the synapse. The present data on Arc structure and ligand binding will help in further deciphering these processes.
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Affiliation(s)
| | | | - Petri Kursula
- Department of Biomedicine, University of Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Finland
- Biocenter Oulu, University of Oulu, Finland
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21
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Mindrebo JT, Chen A, Kim WE, Re RN, Davis TD, Noel JP, Burkart MD. Structure and Mechanistic Analyses of the Gating Mechanism of Elongating Ketosynthases. ACS Catal 2021; 11:6787-6799. [DOI: 10.1021/acscatal.1c00745] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jeffrey T. Mindrebo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Aochiu Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Woojoo E. Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Rebecca N. Re
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Tony D. Davis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Joseph P. Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, California 92037, United States
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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22
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Fauser J, Itzen A, Gulen B. Current Advances in Covalent Stabilization of Macromolecular Complexes for Structural Biology. Bioconjug Chem 2021; 32:879-890. [PMID: 33861574 DOI: 10.1021/acs.bioconjchem.1c00118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Structural characterization of macromolecular assemblies is often limited by the transient nature of the interactions. The development of specific chemical tools to covalently tether interacting proteins to each other has played a major role in various fundamental discoveries in recent years. To this end, protein engineering techniques such as mutagenesis, incorporation of unnatural amino acids, and methods using synthetic substrate/cosubstrate derivatives were employed. In this review, we give an overview of both commonly used and recently developed biochemical methodologies for covalent stabilization of macromolecular complexes enabling structural investigation via crystallography, nuclear magnetic resonance, and cryo-electron microscopy. We divided the strategies into nonenzymatic- and enzymatic-driven cross-linking and further categorized them in either naturally occurring or engineered covalent linkage. This review offers a compilation of recent advances in diverse scientific fields where the structural characterization of macromolecular complexes was achieved by the aid of intermolecular covalent linkage.
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Affiliation(s)
- Joel Fauser
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany.,Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany.,Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Burak Gulen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany.,Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
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23
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Yang D, Jang WD, Lee SY. Production of Carminic Acid by Metabolically Engineered Escherichia coli. J Am Chem Soc 2021; 143:5364-5377. [DOI: 10.1021/jacs.0c12406] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Dongsoo Yang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- BioProcess Engineering Research Center and BioInformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Woo Dae Jang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- BioProcess Engineering Research Center and BioInformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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24
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Sulpizio A, Crawford CEW, Koweek RS, Charkoudian LK. Probing the structure and function of acyl carrier proteins to unlock the strategic redesign of type II polyketide biosynthetic pathways. J Biol Chem 2021; 296:100328. [PMID: 33493513 PMCID: PMC7949117 DOI: 10.1016/j.jbc.2021.100328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 02/04/2023] Open
Abstract
Type II polyketide synthases (PKSs) are protein assemblies, encoded by biosynthetic gene clusters in microorganisms, that manufacture structurally complex and pharmacologically relevant molecules. Acyl carrier proteins (ACPs) play a central role in biosynthesis by shuttling malonyl-based building blocks and polyketide intermediates to catalytic partners for chemical transformations. Because ACPs serve as central hubs in type II PKSs, they can also represent roadblocks to successfully engineering synthases capable of manufacturing 'unnatural natural products.' Therefore, understanding ACP conformational dynamics and protein interactions is essential to enable the strategic redesign of type II PKSs. However, the inherent flexibility and transience of ACP interactions pose challenges to gaining insight into ACP structure and function. In this review, we summarize how the application of chemical probes and molecular dynamic simulations has increased our understanding of the structure and function of type II PKS ACPs. We also share how integrating these advances in type II PKS ACP research with newfound access to key enzyme partners, such as the ketosynthase-chain length factor, sets the stage to unlock new biosynthetic potential.
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Affiliation(s)
- Ariana Sulpizio
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, USA
| | | | - Rebecca S Koweek
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, USA
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25
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Klein JG, Wu Y, Kokona B, Charkoudian LK. Widening the bottleneck: Heterologous expression, purification, and characterization of the Ktedonobacter racemifer minimal type II polyketide synthase in Escherichia coli. Bioorg Med Chem 2020; 28:115686. [PMID: 33069071 DOI: 10.1016/j.bmc.2020.115686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/16/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
Abstract
Enzyme assemblies such as type II polyketide synthases (PKSs) produce a wide array of bioactive secondary metabolites. While the molecules produced by type II PKSs have found remarkable clinical success, the biosynthetic prowess of these enzymes has been stymied by 1) the inability to reconstitute the bioactivity of the minimal PKS enzymes in vitro and 2) limited exploration of type II PKSs from diverse phyla. To begin filling this unmet need, we expressed, purified, and characterized the ketosynthase chain length factor (KS-CLF) and acyl carrier protein (ACP) from Ktedonobacter racemifer (Kr). Using E. coli as a heterologous host, we obtained soluble proteins in titers signifying improvements over previous KS-CLF heterologous expression efforts. Characterization of these enzymes reveals that KrACP has self-malonylating activity. Sedimentation velocity analytical ultracentrifugation (SV-AUC) analysis of holo-KrACP and KrKS-CLF indicates that these enzymes do not interact in vitro, suggesting that the acylated state of these proteins might play an important role in facilitating biosynthetically relevant interactions. These results lay important groundwork for optimizing the interaction between KrKS-CLF and KrACP and exploring the biosynthetic potential of other non-actinomycete type II PKSs.
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Affiliation(s)
- Joshua G Klein
- Haverford College, Department of Chemistry, Haverford, PA 19041, United States
| | - Yang Wu
- Haverford College, Department of Chemistry, Haverford, PA 19041, United States
| | - Bashkim Kokona
- Haverford College, Department of Chemistry, Haverford, PA 19041, United States.
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26
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Mindrebo JT, Misson LE, Johnson C, Noel JP, Burkart MD. Activity Mapping the Acyl Carrier Protein: Elongating Ketosynthase Interaction in Fatty Acid Biosynthesis. Biochemistry 2020; 59:3626-3638. [PMID: 32857494 DOI: 10.1021/acs.biochem.0c00605] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Elongating ketosynthases (KSs) catalyze carbon-carbon bond-forming reactions during the committed step for each round of chain extension in both fatty acid synthases (FASs) and polyketide synthases (PKSs). A small α-helical acyl carrier protein (ACP) shuttles fatty acyl intermediates between enzyme active sites. To accomplish this task, the ACP relies on a series of dynamic interactions with multiple partner enzymes of FAS and associated FAS-dependent pathways. Recent structures of the Escherichia coli FAS ACP, AcpP, in covalent complexes with its two cognate elongating KSs, FabF and FabB, provide high-resolution details of these interfaces, but a systematic analysis of specific interfacial interactions responsible for stabilizing these complexes has not yet been undertaken. Here, we use site-directed mutagenesis with both in vitro and in vivo activity analyses to quantitatively evaluate these contacting surfaces between AcpP and FabF. We delineate the FabF interface into three interacting regions and demonstrate the effects of point mutants, double mutants, and region deletion variants. Results from these analyses reveal a robust and modular FabF interface capable of tolerating seemingly critical interface mutations with only the deletion of an entire region significantly compromising activity. Structure and sequence analyses of FabF orthologs from related type II FAS pathways indicate significant conservation of type II FAS KS interface residues and, overall, support its delineation into interaction regions. These findings strengthen our mechanistic understanding of molecular recognition events between ACPs and FAS enzymes and provide a blueprint for engineering ACP-dependent biosynthetic pathways.
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Affiliation(s)
- Jeffrey T Mindrebo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States.,Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Laetitia E Misson
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Caitlin Johnson
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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