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Ducrot L, López IL, Orrego AH, López-Gallego F. Coenzyme A Thioester Intermediates as Platform Molecules in Cell-Free Chemical Biomanufacturing. Chembiochem 2024; 25:e202300673. [PMID: 37994376 DOI: 10.1002/cbic.202300673] [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: 09/30/2023] [Revised: 11/06/2023] [Indexed: 11/24/2023]
Abstract
The in vitro synthesis of Coenzyme A (CoA)-thioester intermediates opens new avenues to transform simple molecules into more complex and multifunctional ones by assembling cell-free biosynthetic cascades. In this review, we have systematically cataloged known CoA-dependent enzyme reactions that have been successfully implemented in vitro. To faciliate their identification, we provide their UniProt ID when available. Based on this catalog, we have organized enzymes into three modules: activation, modification, and removal. i) The activation module includes enzymes capable of fusing CoA with organic molecules. ii) The modification module includes enzymes capable of catalyzing chemical modifications in the structure of acyl-CoA intermediates. And iii) the removal module includes enzymes able to remove the CoA and release an organic molecule different from the one activated in the upstream. Based on these reactions, we constructed a reaction network that summarizes the most relevant CoA-dependent biosynthetic pathways reported until today. From the information available in the articles, we have plotted the total turnover number of CoA as a function of the product titer, observing a positive correlation between both parameters. Therefore, the success of a CoA-dependent in vitro pathway depends on its ability to regenerate CoA, but also to regenerate other cofactors such as NAD(P)H and ATP.
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Affiliation(s)
- Laurine Ducrot
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Idania L López
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Alejandro H Orrego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Fernando López-Gallego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain
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2
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Trottmann F, Fiedler J, Ishida K, Ishida-Ito M, Little RF, Hertweck C. Bacterial Pathogen Channels Medium-Sized Fatty Acids into Malleicyprol Biosynthesis. ACS Chem Biol 2023; 18:1557-1563. [PMID: 37319349 DOI: 10.1021/acschembio.3c00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Bacterial pathogens of the Burkholderia pseudomallei (BP) group cause life-threatening infections in both humans and animals. Critical for the virulence of these often antibiotic-resistant pathogens is the polyketide hybrid metabolite malleicyprol, which features two chains, a short cyclopropanol-substituted chain and a long hydrophobic alkyl chain. The biosynthetic origin of the latter has remained unknown. Here, we report the discovery of novel overlooked malleicyprol congeners with varied chain lengths and identify medium-sized fatty acids as polyketide synthase (PKS) starter units that constitute the hydrophobic carbon tails. Mutational and biochemical analyses show that a designated coenzyme A-independent fatty acyl-adenylate ligase (FAAL, BurM) is essential for recruiting and activating fatty acids in malleicyprol biosynthesis. In vitro reconstitution of the BurM-catalyzed PKS priming reaction and analysis of ACP-bound building blocks reveal a key role of BurM in the toxin assembly. Insights into the function and role of BurM hold promise for the development of enzyme inhibitors as novel antivirulence therapeutics to combat infections with BP pathogens.
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Affiliation(s)
- Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Jonas Fiedler
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Mie Ishida-Ito
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Rory F Little
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
- Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
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3
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Takahashi S. Studies on Streptomyces sp. SN-593: reveromycin biosynthesis, β-carboline biomediator activating LuxR family regulator, and construction of terpenoid biosynthetic platform. J Antibiot (Tokyo) 2022; 75:432-444. [PMID: 35778609 DOI: 10.1038/s41429-022-00539-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/09/2022]
Abstract
Streptomyces represents an important reservoir for biologically active natural products. Understanding the biosynthetic mechanism and the mode of gene expression is important for enhanced metabolite production and evaluation of biological activities. This review provides an overview of biosynthetic studies investigating reveromycin and β-carboline biomediators that enhanced the production of reveromycin in Streptomyces sp. SN-593 through activation of the LuxR family regulator. Furthermore, based on the optimal expression of a pathway specific regulator controlling the mevalonate pathway gene cluster, Streptomyces sp. SN-593 was developed as a platform for terpenoid compounds mass production.
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Affiliation(s)
- Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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4
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Pang B, Li J, Eiben CB, Oksen E, Barcelos C, Chen R, Englund E, Sundstrom E, Keasling JD. Lepidopteran mevalonate pathway optimization in Escherichia coli efficiently produces isoprenol analogs for next-generation biofuels. Metab Eng 2021; 68:210-219. [PMID: 34673235 DOI: 10.1016/j.ymben.2021.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/12/2021] [Accepted: 10/16/2021] [Indexed: 12/31/2022]
Abstract
Terpenes constitute the largest class of natural products with over 55,000 compounds with versatile applications including drugs and biofuels. Introducing structural modifications to terpenes through metabolic engineering is an efficient and sustainable way to improve their properties. Here, we report the optimization of the lepidopteran mevalonate (LMVA) pathway towards the efficient production of isopentenyl pyrophosphate (IPP) analogs as terpene precursors. First, we linked the LMVA pathway to NudB, a promiscuous phosphatase, resulting in the production of the six-carbon analog of 3-methyl-3-buten-1-ol (isoprenol), 3-ethyl-3-buten-1-ol (C6-isoprenol). Using C6-isoprenol as the final product, we then engineered the LMVA pathway by redirecting its upstream portion from a thiolase-dependent pathway to a beta-oxidation pathway. The beta-oxidation LMVA pathway transforms valeric acid, a platform chemical that can be produced from biomass, into C6-isoprenol at a titer of 110.3 mg/L, improved from 5.5 mg/L by the thiolase LMVA pathway, which used propionic acid as a feedstock. Knockout of the E. coli endogenous thiolase genes further improved the C6-isoprenol titer to 390 mg/L, implying efficient production of homo isopentenyl pyrophosphate (HIPP). The beta-oxidation LMVA-NudB pathway also converts butanoic acid and hexanoic acid into isoprenol and isoprenol's seven-carbon analog, 3-propyl-3-buten-1-ol (C7-isoprenol), respectively, suggesting the beta-oxidation LMVA pathway produces IPP and C7-IPP from the corresponding fatty acids. Fuel property tests revealed the longer chain isoprenol analogs have lower water solubilities, similar or higher energy densities, and comparable research octane number (RON) boosting effects to isopentenols. This work not only optimizes the LMVA pathway, setting the basis for homoterpene biosynthesis to expand terpene chemical space, but provides an efficient pathway to produce isoprenol analogs as next-generation biofuels from sustainable feedstocks.
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Affiliation(s)
- Bo Pang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, United States
| | - Jia Li
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, PR China; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Christopher B Eiben
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Ethan Oksen
- Advanced Biofuels & Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Carolina Barcelos
- Advanced Biofuels & Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Rong Chen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; School of Public Health, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, PR China
| | - Elias Englund
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Eric Sundstrom
- Advanced Biofuels & Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, United States; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, United States; Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, DK 2970 Horsholm, Denmark; Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, Guangdong, 518055, PR China.
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5
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Panthee S, Kito N, Hayashi T, Shimizu T, Ishikawa J, Hamamoto H, Osada H, Takahashi S. β-carboline chemical signals induce reveromycin production through a LuxR family regulator in Streptomyces sp. SN-593. Sci Rep 2020; 10:10230. [PMID: 32576869 PMCID: PMC7311520 DOI: 10.1038/s41598-020-66974-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/27/2020] [Indexed: 12/21/2022] Open
Abstract
Actinomycetes bacteria produce diverse bioactive molecules that are useful as drug seeds. To improve their yield, researchers often optimize the fermentation medium. However, exactly how the extracellular chemicals present in the medium activate secondary metabolite gene clusters remains unresolved. BR-1, a β-carboline compound, was recently identified as a chemical signal that enhanced reveromycin A production in Streptomyces sp. SN-593. Here we show that BR-1 specifically bound to the transcriptional regulator protein RevU in the reveromycin A biosynthetic gene cluster, and enhanced RevU binding to its promoter. RevU belongs to the LuxR family regulator that is widely found in bacteria. Interestingly, BR-1 and its derivatives also enhanced the production of secondary metabolites in other Streptomyces species. Although LuxR-N-acyl homoserine lactone systems have been characterized in Gram-negative bacteria, we revealed LuxR-β-carboline system in Streptomyces sp. SN-593 for the production of secondary metabolites. This study might aid in understanding hidden chemical communication by β-carbolines.
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Affiliation(s)
- Suresh Panthee
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan.,Teikyo University Institute of Medical Mycology, Otsuka 359, Hachioji, Tokyo, Japan
| | - Naoko Kito
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan
| | - Teruo Hayashi
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan
| | - Takeshi Shimizu
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan
| | - Jun Ishikawa
- Department of Bioactive Molecules, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku, Tokyo, 162-8640, Japan
| | - Hiroshi Hamamoto
- Teikyo University Institute of Medical Mycology, Otsuka 359, Hachioji, Tokyo, Japan
| | - Hiroyuki Osada
- RIKEN Center for Sustainable Resource Science, Chemical Biology Research Group, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan.
| | - Shunji Takahashi
- RIKEN Center for Sustainable Resource Science, Natural Product Biosynthesis Research Unit, Wako, Hirosawa 2-1, 351-0198, Saitama, Japan.
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6
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Baran M, Grimes KD, Sibbald PA, Fu P, Boshoff HIM, Wilson DJ, Aldrich CC. Development of small-molecule inhibitors of fatty acyl-AMP and fatty acyl-CoA ligases in Mycobacterium tuberculosis. Eur J Med Chem 2020; 201:112408. [PMID: 32574901 DOI: 10.1016/j.ejmech.2020.112408] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/07/2020] [Accepted: 04/27/2020] [Indexed: 12/13/2022]
Abstract
Lipid metabolism in Mycobacterium tuberculosis (Mtb) relies on 34 fatty acid adenylating enzymes (FadDs) that can be grouped into two classes: fatty acyl-CoA ligases (FACLs) involved in lipid and cholesterol catabolism and long chain fatty acyl-AMP ligases (FAALs) involved in biosynthesis of the numerous essential and virulence-conferring lipids found in Mtb. The precise biochemical roles of many FACLs remain poorly characterized while the functionally non-redundant FAALs are much better understood. Here we describe the systematic investigation of 5'-O-[N-(alkanoyl)sulfamoyl]adenosine (alkanoyl adenosine monosulfamate, alkanoyl-AMS) analogs as potential multitarget FadD inhibitors for their antitubercular activity and biochemical selectivity towards representative FAAL and FACL enzymes. We identified several potent compounds including 12-azidododecanoyl-AMS 28, 11-phenoxyundecanoyl-AMS 32, and nonyloxyacetyl-AMS 36 with minimum inhibitory concentrations (MICs) against M. tuberculosis ranging from 0.098 to 3.13 μM. Compound 32 was notable for its impressive biochemical selectivity against FAAL28 (apparent Ki = 0.7 μM) versus FACL19 (Ki > 100 μM), and uniform activity against a panel of multidrug and extensively drug-resistant TB strains with MICs ranging from 3.13 to 12.5 μM in minimal (GAST) and rich (7H9) media. The SAR analysis provided valuable insights for further optimization of 32 and also identified limitations to overcome.
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Affiliation(s)
- Marzena Baran
- Department of Medicinal Chemistry, University of Minnesota, 8-101 WDH, 308 Harvard Street SE, Minneapolis, MN, 55455, United States
| | - Kimberly D Grimes
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Paul A Sibbald
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Peng Fu
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Helena I M Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, United States
| | - Daniel J Wilson
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 8-101 WDH, 308 Harvard Street SE, Minneapolis, MN, 55455, United States; Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States.
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7
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Demachi A, Uchida R, Arima S, Nagamitsu T, Hashimoto J, Komatsu M, Kozone I, Shin-Ya K, Tomoda H, Ikeda H. An Unusual Extender Unit Is Incorporated into the Modular Polyketide Synthase of Scopranones Biosynthesis. Biochemistry 2019; 58:5066-5073. [PMID: 31756295 DOI: 10.1021/acs.biochem.9b00908] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Scopranones, produced by Streptomyces sp. BYK-11038, are the novel bone morphogenetic protein inhibitors characterized by atypical two scoop-like moieties and a 3-furanone moiety. Two scoop-like moieties connected to a 3-furanone have not previously been reported in natural products, and their biosynthesis must occur via a unique pathway. Feeding experiments using 13C-labeled precursors indicated that scopranones were synthesized from three acetates and three butyrates in polyketide-type biosynthesis. Genome mining of Streptomyces sp. BYK-11038 revealed that the candidate biosynthetic gene cluster contains 21 open reading frames (ORFs), including three modular polyketide synthases (PKSs; SprA, SprB, and SprC), which were composed of 4 modules with one loading module and 18 additional ORFs (SprD to SprU) spanning a distance of 55 kbp. The characterization of in-frame deletion mutants and feeding experiments with the predicted extender units indicated that two genes, sprP and sprR, encoding discrete 3-oxoacyl-ACP synthases, and a gene, sprO, encoding crotonyl-CoA reductase, were involved in assembling an unusual C8 branched extender unit, 2-(2-ethylbutyl)malonyl-CoA. Additionally, three ORFs, sprM, sprN, and sprT, encoding cytochrome P450s and a monooxygenase, are important tailoring enzymes in post-PKS modification. SprT is an essential enzyme for decarboxylative ring contraction via oxidation, which converts the 2-pyranone to a 3-furanone.
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Affiliation(s)
- Ayumu Demachi
- Medicinal Research Laboratory, School of Pharmacy and Graduate School of Pharmaceutical Sciences , Kitasato University , 5-9-1 Shirokane , Minato-ku , Tokyo 108-8641 , Japan
| | - Ryuji Uchida
- Faculty of Pharmaceutical Sciences , Tohoku Medical and Pharmaceutical University , 4-4-1 Komatsushima, Aoba-ku , Sendai , Miyagi 981-8558 , Japan
| | - Shiho Arima
- Medicinal Research Laboratory, School of Pharmacy and Graduate School of Pharmaceutical Sciences , Kitasato University , 5-9-1 Shirokane , Minato-ku , Tokyo 108-8641 , Japan
| | - Tohru Nagamitsu
- Medicinal Research Laboratory, School of Pharmacy and Graduate School of Pharmaceutical Sciences , Kitasato University , 5-9-1 Shirokane , Minato-ku , Tokyo 108-8641 , Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium , 2-4-7 Aomi, Koto-ku , Tokyo 135-8073 , Japan
| | - Mamoru Komatsu
- Kitasato Institute for Life Sciences , Kitasato University , 1-15-1 Kitasato, Minami-ku , Sagamihara , Kanagawa 252-0373 , Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium , 2-4-7 Aomi, Koto-ku , Tokyo 135-8073 , Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology , 2-4-7 Aomi, Koto-ku , Tokyo 135-0064 , Japan
| | - Hiroshi Tomoda
- Medicinal Research Laboratory, School of Pharmacy and Graduate School of Pharmaceutical Sciences , Kitasato University , 5-9-1 Shirokane , Minato-ku , Tokyo 108-8641 , Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences , Kitasato University , 1-15-1 Kitasato, Minami-ku , Sagamihara , Kanagawa 252-0373 , Japan
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8
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Bilyk O, Samborskyy M, Leadlay PF. The biosynthetic pathway to ossamycin, a macrocyclic polyketide bearing a spiroacetal moiety. PLoS One 2019; 14:e0215958. [PMID: 31039188 PMCID: PMC6490886 DOI: 10.1371/journal.pone.0215958] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/11/2019] [Indexed: 01/08/2023] Open
Abstract
Ossamycin from Streptomyces hygroscopicus var. ossamyceticus is an antifungal and cytotoxic polyketide and a potent inhibitor of the mitochondrial ATPase. Analysis of a near-complete genome sequence of the ossamycin producer has allowed the identification of the 127-kbp ossamycin biosynthetic gene cluster. The presence in the cluster of a specific crotonyl-CoA carboxylase/reductase homologue suggests that the 5-methylhexanoate extension unit used in construction of the macrocyclic core is incorporated intact from the unusual precursor isobutyrylmalonyl-CoA. Surprisingly, the modular polyketide synthase uses only 14 extension modules to accomplish 15 cycles of polyketide chain extension, a rare example of programmed iteration on a modular polyketide synthase. Specific deletion of genes encoding cytochrome P450 enzymes has given insight into the late-stage tailoring of the ossamycin macrocycle required for the attachment of the unusual 2,3,4,6-deoxyaminohexose sugar l-ossamine to C-8 of the ossamycin macrocycle. The ossamycin cluster also encodes a putative spirocyclase enzyme, OssO, which may play a role in establishing the characteristic spiroketal moiety of the natural product.
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Affiliation(s)
- Oksana Bilyk
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Markiyan Samborskyy
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Peter F. Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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9
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Nofiani R, Philmus B, Nindita Y, Mahmud T. 3-Ketoacyl-ACP synthase (KAS) III homologues and their roles in natural product biosynthesis. MEDCHEMCOMM 2019; 10:1517-1530. [PMID: 31673313 DOI: 10.1039/c9md00162j] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/29/2019] [Indexed: 11/21/2022]
Abstract
The 3-ketoacyl-ACP synthase (KAS) III proteins are one of the most abundant enzymes in nature, as they are involved in the biosynthesis of fatty acids and natural products. KAS III enzymes catalyse a carbon-carbon bond formation reaction that involves the α-carbon of a thioester and the carbonyl carbon of another thioester. In addition to the typical KAS III enzymes involved in fatty acid and polyketide biosynthesis, there are proteins homologous to KAS III enzymes that catalyse reactions that are different from that of the traditional KAS III enzymes. Those include enzymes that are responsible for a head-to-head condensation reaction, the formation of acetoacetyl-CoA in mevalonate biosynthesis, tailoring processes via C-O bond formation or esterification, as well as amide formation. This review article highlights the diverse reactions catalysed by this class of enzymes and their role in natural product biosynthesis.
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Affiliation(s)
- Risa Nofiani
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA . .,Department of Chemistry , Universitas Tanjungpura , Pontianak , Indonesia
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Yosi Nindita
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
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10
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Zhang D, Wang J, Wang D, Kong Z, Zhou L, Zhang G, Gui Y, Li J, Huang J, Wang B, Liu C, Yin C, Li R, Li T, Wang J, Short DPG, Klosterman SJ, Bostock RM, Subbarao KV, Chen J, Dai X. Population genomics demystifies the defoliation phenotype in the plant pathogen Verticillium dahliae. THE NEW PHYTOLOGIST 2019; 222:1012-1029. [PMID: 30609067 PMCID: PMC6594092 DOI: 10.1111/nph.15672] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/18/2018] [Indexed: 05/19/2023]
Abstract
Verticillium dahliae is a broad host-range pathogen that causes vascular wilts in plants. Interactions between three hosts and specific V. dahliae genotypes result in severe defoliation. The underlying mechanisms of defoliation are unresolved. Genome resequencing, gene deletion and complementation, gene expression analysis, sequence divergence, defoliating phenotype identification, virulence analysis, and quantification of V. dahliae secondary metabolites were performed. Population genomics previously revealed that G-LSR2 was horizontally transferred from the fungus Fusarium oxysporum f. sp. vasinfectum to V. dahliae and is exclusively found in the genomes of defoliating (D) strains. Deletion of seven genes within G-LSR2, designated as VdDf genes, produced the nondefoliation phenotype on cotton, olive, and okra but complementation of two genes restored the defoliation phenotype. Genes VdDf5 and VdDf6 associated with defoliation shared homology with polyketide synthases involved in secondary metabolism, whereas VdDf7 shared homology with proteins involved in the biosynthesis of N-lauroylethanolamine (N-acylethanolamine (NAE) 12:0), a compound that induces defoliation. NAE overbiosynthesis by D strains also appears to disrupt NAE metabolism in cotton by inducing overexpression of fatty acid amide hydrolase. The VdDfs modulate the synthesis and overproduction of secondary metabolites, such as NAE 12:0, that cause defoliation either by altering abscisic acid sensitivity, hormone disruption, or sensitivity to the pathogen.
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Affiliation(s)
- Dan‐Dan Zhang
- Laboratory of Crop Verticillium WiltInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Jie Wang
- Laboratory of Crop Verticillium WiltInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Dan Wang
- Laboratory of Crop Verticillium WiltInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Zhi‐Qiang Kong
- Laboratory of Crop Verticillium WiltInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Lei Zhou
- Laboratory of Crop Verticillium WiltInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | | | - Yue‐Jing Gui
- Laboratory of Crop Verticillium WiltInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Jun‐Jiao Li
- Laboratory of Crop Verticillium WiltInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | | | - Bao‐Li Wang
- Laboratory of Crop Verticillium WiltInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Chun Liu
- GenomicsBGI‐ShenzhenShenzhen518083China
| | - Chun‐Mei Yin
- Laboratory of Crop Verticillium WiltInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Rui‐Xing Li
- Laboratory of Crop Verticillium WiltInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Ting‐Gang Li
- Laboratory of Crop Verticillium WiltInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Jin‐Long Wang
- Department of BiologyDuke UniversityDurhamNC27708USA
| | - Dylan P. G. Short
- Department of Plant PathologyUniversity of California, Davisc/o US Agricultural Research StationSalinasCA93905USA
| | - Steven J. Klosterman
- United States Department of AgricultureAgricultural Research ServiceCrop Improvement and Protection Research UnitSalinasCA93905USA
| | | | - Krishna V. Subbarao
- Department of Plant PathologyUniversity of California, Davisc/o US Agricultural Research StationSalinasCA93905USA
| | - Jie‐Yin Chen
- Laboratory of Crop Verticillium WiltInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Xiao‐Feng Dai
- Laboratory of Crop Verticillium WiltInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
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11
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Kinanthraquinone, a new anthraquinone carboxamide isolated from Streptomyces reveromyceticus SN-593-44. J Antibiot (Tokyo) 2018; 71:480-482. [DOI: 10.1038/s41429-017-0020-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 12/14/2017] [Accepted: 12/20/2017] [Indexed: 11/09/2022]
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12
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Ray L, Valentic TR, Miyazawa T, Withall DM, Song L, Milligan JC, Osada H, Takahashi S, Tsai SC, Challis GL. A crotonyl-CoA reductase-carboxylase independent pathway for assembly of unusual alkylmalonyl-CoA polyketide synthase extender units. Nat Commun 2016; 7:13609. [PMID: 28000660 PMCID: PMC5187497 DOI: 10.1038/ncomms13609] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 10/19/2016] [Indexed: 11/12/2022] Open
Abstract
Type I modular polyketide synthases assemble diverse bioactive natural products. Such multienzymes typically use malonyl and methylmalonyl-CoA building blocks for polyketide chain assembly. However, in several cases more exotic alkylmalonyl-CoA extender units are also known to be incorporated. In all examples studied to date, such unusual extender units are biosynthesized via reductive carboxylation of α, β-unsaturated thioesters catalysed by crotonyl-CoA reductase/carboxylase (CCRC) homologues. Here we show using a chemically-synthesized deuterium-labelled mechanistic probe, and heterologous gene expression experiments that the unusual alkylmalonyl-CoA extender units incorporated into the stambomycin family of polyketide antibiotics are assembled by direct carboxylation of medium chain acyl-CoA thioesters. X-ray crystal structures of the unusual β-subunit of the acyl-CoA carboxylase (YCC) responsible for this reaction, alone and in complex with hexanoyl-CoA, reveal the molecular basis for substrate recognition, inspiring the development of methodology for polyketide bio-orthogonal tagging via incorporation of 6-azidohexanoic acid and 8-nonynoic acid into novel stambomycin analogues.
Polyketides are typically assembled from a starter unit and malonyl- and/or methylmalonyl-CoA-derived extender units, but the macrolide antibiotics stambomycins incorporate non-standard alkylmalonyl-CoA extender units. Here, the authors describe the biosynthetic pathway responsible for this unusual synthesis.
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Affiliation(s)
- Lauren Ray
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Timothy R Valentic
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Takeshi Miyazawa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan.,Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - David M Withall
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Jacob C Milligan
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan.,Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Shunji Takahashi
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Saitama 351-0198, Japan
| | - Shiou-Chuan Tsai
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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13
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In silico identification of lysocin biosynthetic gene cluster from Lysobacter sp. RH2180-5. J Antibiot (Tokyo) 2016; 70:204-207. [DOI: 10.1038/ja.2016.102] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/09/2016] [Indexed: 11/08/2022]
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14
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Yushchuk O, Ostash B, Pham TH, Luzhetskyy A, Fedorenko V, Truman AW, Horbal L. Characterization of the Post-Assembly Line Tailoring Processes in Teicoplanin Biosynthesis. ACS Chem Biol 2016; 11:2254-64. [PMID: 27285718 DOI: 10.1021/acschembio.6b00018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Actinoplanes teichomyceticus produces teicoplanin (Tcp), a "last resort" lipoglycopeptide antibiotic used to treat severe multidrug resistant infections such as methicillin-resistant Staphylococcus aureus (MRSA). A number of studies have addressed various steps of Tcp biosynthesis using in vitro assays, although the exact sequence of Tcp peptide core tailoring reactions remained speculative. Here, we describe the generation and analysis of a set of A. teichomyceticus mutant strains that have been used to elucidate the sequence of reactions from the Tcp aglycone to mature Tcp. By combining these results with previously published data, we propose an updated order of post-assembly line tailoring processes in Tcp biosynthesis. We also demonstrate that the acyl-CoA-synthetase Tei13* and the type II thioesterase Tei30* are dispensable for Tcp production. Five Tcp derivatives featuring hitherto undescribed combinations of glycosylation and acylation patterns are described. The generation of strains that produce novel Tcp analogues now provides a platform for the production of additional Tcp-like molecules via combinatorial biosynthesis or chemical derivatization.
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Affiliation(s)
- Oleksandr Yushchuk
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Bohdan Ostash
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Thu H. Pham
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Andriy Luzhetskyy
- Department
of Pharmaceutical Biotechnology, Saarland University, Campus, Saarbrucken, Germany
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Center for Infectious Research (HZI), Saarbrucken, Germany
| | - Victor Fedorenko
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Andrew W. Truman
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, United Kingdom
| | - Liliya Horbal
- Department
of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
- Department
of Pharmaceutical Biotechnology, Saarland University, Campus, Saarbrucken, Germany
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