1
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Zheng M, Zhang J, Zhang W, Yang L, Yan X, Tian W, Liu Z, Lin Z, Deng Z, Qu X. An Atypical Acyl‐CoA Synthetase Enables Efficient Biosynthesis of Extender Units for Engineering a Polyketide Carbon Scaffold. Angew Chem Int Ed Engl 2022; 61:e202208734. [DOI: 10.1002/anie.202208734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Jun Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Wan Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Lu Yang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Xiaoli Yan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Wenya Tian
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Zhihao Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Zhi Lin
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
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2
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Zheng M, Zhang J, Zhang W, Yang L, Yan X, Tian W, Liu Z, Lin Z, Deng Z, Qu X. An Atypical Acyl‐CoA Synthetase Enables Efficient Biosynthesis of Extender Units for Engineering a Polyketide Carbon Scaffold. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mengmeng Zheng
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Jun Zhang
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Wan Zhang
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Lu Yang
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Xiaoli Yan
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Wenya Tian
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Zhihao Liu
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Zhi Lin
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Zixin Deng
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Xudong Qu
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology 800 Dongchuan Rd. 200240 Shanghai CHINA
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3
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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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4
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Kufs JE, Hoefgen S, Rautschek J, Bissell AU, Graf C, Fiedler J, Braga D, Regestein L, Rosenbaum MA, Thiele J, Valiante V. Rational Design of Flavonoid Production Routes Using Combinatorial and Precursor-Directed Biosynthesis. ACS Synth Biol 2020; 9:1823-1832. [PMID: 32525654 DOI: 10.1021/acssynbio.0c00172] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Combinatorial biosynthesis has great potential for designing synthetic circuits and amplifying the production of new active compounds. Studies on multienzyme cascades are extremely useful for improving our knowledge on enzymatic catalysis. In particular, the elucidation of enzyme substrate promiscuity can be potentially used for bioretrosynthetic approaches, leading to the design of alternative and more convenient routes to produce relevant molecules. In this perspective, plant-derived polyketides are extremely adaptable to those synthetic biological applications. Here, we present a combination of an in vitro CoA ligase activity assay coupled with a bacterial multigene expression system that leads to precursor-directed biosynthesis of 21 flavonoid derivatives. When the vast knowledge from protein databases is exploited, the herein presented procedure can be easily repeated with additional plant-derived polyketides. Lastly, we report an efficient in vivo expression system that can be further exploited to heterologously express pathways not necessarily related to plant polyketide synthases.
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Affiliation(s)
- Johann E. Kufs
- Leibniz Research Cluster Group “Biobricks of Microbial Natural Product Syntheses”, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Jena 07745, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, Jena 07743, Germany
| | - Sandra Hoefgen
- Leibniz Research Cluster Group “Biobricks of Microbial Natural Product Syntheses”, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Jena 07745, Germany
| | - Julia Rautschek
- Leibniz Research Cluster Group “Biobricks of Microbial Natural Product Syntheses”, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Jena 07745, Germany
| | - Alexander U. Bissell
- Leibniz Research Cluster Group “Biobricks of Microbial Natural Product Syntheses”, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Jena 07745, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, Jena 07743, Germany
| | - Carola Graf
- Leibniz Research Cluster Group “Polymer Micro (bio)reactors”, Leibniz Institute of Polymer Research, Dresden 01069, Germany
| | - Jonas Fiedler
- Leibniz Research Cluster Group “Biobricks of Microbial Natural Product Syntheses”, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Jena 07745, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, Jena 07743, Germany
| | - Daniel Braga
- Synthetic Microbiology Group, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Jena 07745, Germany
| | - Lars Regestein
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Jena 07745, Germany
| | - Miriam A. Rosenbaum
- Faculty of Biological Sciences, Friedrich Schiller University, Jena 07743, Germany
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Jena 07745, Germany
| | - Julian Thiele
- Leibniz Research Cluster Group “Polymer Micro (bio)reactors”, Leibniz Institute of Polymer Research, Dresden 01069, Germany
| | - Vito Valiante
- Leibniz Research Cluster Group “Biobricks of Microbial Natural Product Syntheses”, Leibniz Institute for Natural Product Research and Infection Biology − Hans Knöll Institute, Jena 07745, Germany
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5
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Wang J, Ding N, Wu Y, Shi X, Qi B, Liu X, Wang X, Li J, Tu P, Shi S. Enzymatic synthesis of 2-hydroxy-4H-quinolizin-4-one scaffolds by integrating coenzyme a ligases and a type III PKS from Huperzia serrata. RSC Adv 2020; 10:23566-23572. [PMID: 35517366 PMCID: PMC9054772 DOI: 10.1039/d0ra04133e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/15/2020] [Indexed: 01/14/2023] Open
Abstract
2-Hydroxy-4H-quinolizin-4-one scaffolds were enzymatically synthesized by integrating three enzymes including phenylacetate-CoA ligase (PcPCL) from an endophytic fungus Penicillium chrysogenum MT-12, malonyl-CoA synthase (AtMatB) from Arabidopsis thaliana, and a type III polyketide synthase (HsPKS3) from Chinese club moss Huperzia serrata. The findings paved the way to produce these kinds of structurally interesting alkaloids by engineered microorganisms. One-pot enzymatic synthesis of 2-hydroxy-4H-quinolizin-4-one scaffolds was developed by integrating three enzymes PcPCL, AtMatB, and HsPKS3.![]()
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Affiliation(s)
- Juan Wang
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Ning Ding
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Yun Wu
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Xiaoping Shi
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Bowen Qi
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Xiao Liu
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Xiaohui Wang
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Jun Li
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Pengfei Tu
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Shepo Shi
- Modern Research Center for Traditional Chinese Medicine
- Beijing University of Chinese Medicine
- Beijing 100029
- China
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6
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Lim YP, Go MK, Raida M, Inoue T, Wenk MR, Keasling JD, Chang MW, Yew WS. Synthetic Enzymology and the Fountain of Youth: Repurposing Biology for Longevity. ACS OMEGA 2018; 3:11050-11061. [PMID: 30320257 PMCID: PMC6173508 DOI: 10.1021/acsomega.8b01620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Abstract
Caloric restriction (CR) is an intervention that can increase maximal lifespan in organisms, but its application to humans remains challenging. A more feasible approach to achieve lifespan extension is to develop CR mimetics that target biochemical pathways affected by CR. Recent studies in the engineering and structural characterization of polyketide synthases (PKSs) have facilitated their use as biocatalysts to produce novel polyketides. Here, we show that by establishing a combinatorial biosynthetic route in Escherichia coli and exploring the substrate promiscuity of a mutant PKS from alfalfa, 413 potential anti-ageing polyketides were biosynthesized. In this approach, novel acyl-coenzyme A (CoA) precursors generated by promiscuous acid-CoA ligases were utilized by PKS to generate polyketides which were then fed to Caenorhabditis elegans to study their potential efficacy in lifespan extension. It was found that CR mimetics like resveratrol can counter the age-associated decline in mitochondrial function and increase the lifespan of C. elegans. Using the mitochondrial respiration profile of C. elegans supplemented for 8 days with 50 μM resveratrol as a blueprint, we can screen our novel polyketides for potential CR mimetics with improved potency. This study highlights the utility of synthetic enzymology in the development of novel anti-ageing therapeutics.
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Affiliation(s)
- Yan Ping Lim
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Maybelle K. Go
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Manfred Raida
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Takao Inoue
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
| | - Markus R. Wenk
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Jay D. Keasling
- Department
of Chemical & Biomolecular Engineering, University of California at Berkeley, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Matthew W. Chang
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Wen Shan Yew
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
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7
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Callari R, Fischer D, Heider H, Weber N. Biosynthesis of angelyl-CoA in Saccharomyces cerevisiae. Microb Cell Fact 2018; 17:72. [PMID: 29753326 PMCID: PMC5948907 DOI: 10.1186/s12934-018-0925-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/07/2018] [Indexed: 11/24/2022] Open
Abstract
Background The angelic acid moiety represents an essential modification in many biologically active products. These products are commonly known as angelates and several studies have demonstrated their therapeutic benefits, including anti-inflammatory and anti-cancer effects. However, their availability for use in the development of therapeutics is limited due to poor extraction yields. Chemical synthesis has been achieved but its complexity prevents application, therefore microbial production may offer a promising alternative. Here, we engineered the budding yeast Saccharomyces cerevisiae to produce angelyl-CoA, the CoA-activated form of angelic acid. Results For yeast-based production of angelyl-CoA we first expressed genes recently identified in the biosynthetic cluster ssf of Streptomyces sp. SF2575 in S. cerevisiae. Exogenous feeding of propionate and heterologous expression of a propionyl-CoA synthase from Streptomyces sp. were initially employed to increase the intracellular propionyl-CoA level, resulting in production of angelyl-CoA in the order of 5 mg/L. Substituting the Streptomyces sp. propionyl-CoA carboxylase with a carboxylase derived from Streptomyces coelicolor resulted in angelyl-CoA levels up to 6.4 mg/L. In vivo analysis allowed identification of important intermediates in the pathway, including methyl-malonyl-CoA and 3-hydroxyl-2-methyl-butyryl-CoA. Furthermore, methyl-malonate supplementation and expression of matB CoA ligase from S. coelicolor allowed for methyl-malonyl-CoA synthesis and supported, together with parts of the ssf pathway, angelyl-CoA titres of approximately 1.5 mg/L. Finally, feeding of angelic acid to yeasts expressing acyl-CoA ligases from plant species led to angelyl-CoA production rates of approximately 40 mg/L. Conclusions Our results demonstrate the biosynthesis of angelyl-CoA in yeast from exogenously supplied carboxylic acid precursors. This is the first report on the activity of the ssf genes. We envision that our approach will provide a platform for a more sustainable production of the pharmaceutically important compound class of angelates. Electronic supplementary material The online version of this article (10.1186/s12934-018-0925-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roberta Callari
- Evolva SA, Duggingerstrasse 23, 4153, Reinach, Switzerland.,Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - David Fischer
- Evolva SA, Duggingerstrasse 23, 4153, Reinach, Switzerland
| | - Harald Heider
- Evolva SA, Duggingerstrasse 23, 4153, Reinach, Switzerland
| | - Nora Weber
- Evolva SA, Duggingerstrasse 23, 4153, Reinach, Switzerland.
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8
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Exploiting the Biosynthetic Potential of Type III Polyketide Synthases. Molecules 2016; 21:molecules21060806. [PMID: 27338328 PMCID: PMC6274091 DOI: 10.3390/molecules21060806] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/15/2016] [Accepted: 06/17/2016] [Indexed: 11/17/2022] Open
Abstract
Polyketides are structurally and functionally diverse secondary metabolites that are biosynthesized by polyketide synthases (PKSs) using acyl-CoA precursors. Recent studies in the engineering and structural characterization of PKSs have facilitated the use of target enzymes as biocatalysts to produce novel functionally optimized polyketides. These compounds may serve as potential drug leads. This review summarizes the insights gained from research on type III PKSs, from the discovery of chalcone synthase in plants to novel PKSs in bacteria and fungi. To date, at least 15 families of type III PKSs have been characterized, highlighting the utility of PKSs in the development of natural product libraries for therapeutic development.
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9
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Peter DM, Vögeli B, Cortina NS, Erb TJ. A Chemo-Enzymatic Road Map to the Synthesis of CoA Esters. Molecules 2016; 21:517. [PMID: 27104508 PMCID: PMC6273144 DOI: 10.3390/molecules21040517] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 04/11/2016] [Accepted: 04/15/2016] [Indexed: 11/24/2022] Open
Abstract
Coenzyme A (CoA) is a ubiquitous cofactor present in every known organism. The thioesters of CoA are core intermediates in many metabolic processes, such as the citric acid cycle, fatty acid biosynthesis and secondary metabolism, including polyketide biosynthesis. Synthesis of CoA-thioesters is vital for the study of CoA-dependent enzymes and pathways, but also as standards for metabolomics studies. In this work we systematically tested five chemo-enzymatic methods for the synthesis of the three most abundant acyl-CoA thioester classes in biology; saturated acyl-CoAs, α,β-unsaturated acyl-CoAs (i.e., enoyl-CoA derivatives), and α-carboxylated acyl-CoAs (i.e., malonyl-CoA derivatives). Additionally we report on the substrate promiscuity of three newly described acyl-CoA dehydrogenases that allow the simple conversion of acyl-CoAs into enoyl-CoAs. With these five methods, we synthesized 26 different CoA-thioesters with a yield of 40% or higher. The CoA esters produced range from short- to long-chain, include branched and α,β-unsaturated representatives as well as other functional groups. Based on our results we provide a general guideline to the optimal synthesis method of a given CoA-thioester in respect to its functional group(s) and the commercial availability of the precursor molecule. The proposed synthetic routes can be performed in small scale and do not require special chemical equipment, making them convenient also for biological laboratories.
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Affiliation(s)
- Dominik M Peter
- Institute for Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland.
- Biochemistry & Synthetic Biology of Microbial Metabolism Group, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043 Marburg, Germany.
| | - Bastian Vögeli
- Biochemistry & Synthetic Biology of Microbial Metabolism Group, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043 Marburg, Germany.
| | - Niña Socorro Cortina
- Biochemistry & Synthetic Biology of Microbial Metabolism Group, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043 Marburg, Germany.
| | - Tobias J Erb
- Biochemistry & Synthetic Biology of Microbial Metabolism Group, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043 Marburg, Germany.
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10
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Weissman KJ. Genetic engineering of modular PKSs: from combinatorial biosynthesis to synthetic biology. Nat Prod Rep 2016; 33:203-30. [DOI: 10.1039/c5np00109a] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This reviews covers on-going efforts at engineering the gigantic modular polyketide synthases (PKSs), highlighting both notable successes and failures.
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Affiliation(s)
- Kira J. Weissman
- UMR 7365
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA)
- CNRS-Université de Lorraine
- Biopôle de l'Université de Lorraine
- 54505 Vandœuvre-lès-Nancy Cedex
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11
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Go MK, Wongsantichon J, Cheung VWN, Chow JY, Robinson RC, Yew WS. Synthetic Polyketide Enzymology: Platform for Biosynthesis of Antimicrobial Polyketides. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00477] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maybelle Kho Go
- Department of Biochemistry,
Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597,
- NUS
Synthetic Biology for Clinical and Technological Innovation, Life
Sciences Institute, National University of Singapore, 28 Medical
Drive, Singapore 117456,
| | - Jantana Wongsantichon
- Institute
of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673
| | - Vivian Wing Ngar Cheung
- Department of Biochemistry,
Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597,
- NUS
Synthetic Biology for Clinical and Technological Innovation, Life
Sciences Institute, National University of Singapore, 28 Medical
Drive, Singapore 117456,
| | - Jeng Yeong Chow
- Department of Biochemistry,
Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597,
| | - Robert C. Robinson
- Department of Biochemistry,
Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597,
- Institute
of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673
| | - Wen Shan Yew
- Department of Biochemistry,
Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597,
- NUS
Synthetic Biology for Clinical and Technological Innovation, Life
Sciences Institute, National University of Singapore, 28 Medical
Drive, Singapore 117456,
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12
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Chang C, Huang R, Yan Y, Ma H, Dai Z, Zhang B, Deng Z, Liu W, Qu X. Uncovering the formation and selection of benzylmalonyl-CoA from the biosynthesis of splenocin and enterocin reveals a versatile way to introduce amino acids into polyketide carbon scaffolds. J Am Chem Soc 2015; 137:4183-90. [PMID: 25763681 DOI: 10.1021/jacs.5b00728] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Selective modification of carbon scaffolds via biosynthetic engineering is important for polyketide structural diversification. Yet, this scope is currently restricted to simple aliphatic groups due to (1) limited variety of CoA-linked extender units, which lack aromatic structures and chemical reactivity, and (2) narrow acyltransferase (AT) specificity, which is limited to aliphatic CoA-linked extender units. In this report, we uncovered and characterized the first aromatic CoA-linked extender unit benzylmalonyl-CoA from the biosynthetic pathways of splenocin and enterocin in Streptomyces sp. CNQ431. Its synthesis employs a deamination/reductive carboxylation strategy to convert phenylalanine into benzylmalonyl-CoA, providing a link between amino acid and CoA-linked extender unit synthesis. By characterization of its selection, we further validated that AT domains of splenocin, and antimycin polyketide synthases are able to select this extender unit to introduce the phenyl group into their dilactone scaffolds. The biosynthetic machinery involved in the formation of this extender unit is highly versatile and can be potentially tailored for tyrosine, histidine and aspartic acid. The disclosed aromatic extender unit, amino acid-oriented synthetic pathway, and aromatic-selective AT domains provides a systematic breakthrough toward current knowledge of polyketide extender unit formation and selection, and also opens a route for further engineering of polyketide carbon scaffolds using amino acids.
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Affiliation(s)
- Chenchen Chang
- †Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
| | - Rong Huang
- †Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
| | - Yan Yan
- ‡State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Hongmin Ma
- †Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
| | - Zheng Dai
- †Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
| | - Benying Zhang
- †Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
| | - Zixin Deng
- †Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
| | - Wen Liu
- ‡State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xudong Qu
- †Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
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13
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Finzel K, Lee DJ, Burkart MD. Using modern tools to probe the structure-function relationship of fatty acid synthases. Chembiochem 2015; 16:528-547. [PMID: 25676190 PMCID: PMC4545599 DOI: 10.1002/cbic.201402578] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 12/25/2022]
Abstract
Fatty acid biosynthesis is essential to life and represents one of the most conserved pathways in nature, preserving the same handful of chemical reactions across all species. Recent interest in the molecular details of the de novo fatty acid synthase (FAS) has been heightened by demand for renewable fuels and the emergence of multidrug-resistant bacterial strains. Central to FAS is the acyl carrier protein (ACP), a protein chaperone that shuttles the growing acyl chain between catalytic enzymes within the FAS. Human efforts to alter fatty acid biosynthesis for oil production, chemical feedstock, or antimicrobial purposes has been met with limited success, due in part to a lack of detailed molecular information behind the ACP-partner protein interactions inherent to the pathway. This review will focus on recently developed tools for the modification of ACP and analysis of protein-protein interactions, such as mechanism-based crosslinking, and the studies exploiting them. Discussion specific to each enzymatic domain will focus first on mechanism and known inhibitors, followed by available structures and known interactions with ACP. Although significant unknowns remain, new understandings of the intricacies of FAS point to future advances in manipulating this complex molecular factory.
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Affiliation(s)
- Kara Finzel
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358 (USA)
| | - D. John Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358 (USA)
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358 (USA)
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15
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Dubey NC, Tripathi BP, Müller M, Stamm M, Ionov L. Enhanced activity of acetyl CoA synthetase adsorbed on smart microgel: an implication for precursor biosynthesis. ACS APPLIED MATERIALS & INTERFACES 2015; 7:1500-1507. [PMID: 25561344 DOI: 10.1021/am5063376] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Acetyl coenzyme A (acetyl CoA) is an essential precursor molecule for synthesis of metabolites such as the polyketide-based drugs (tetracycline, mitharamycin, Zocor, etc.) fats, lipids, and cholesterol. Acetyl CoA synthetase (Acs) is one of the enzymes that catalyzes acetyl CoA synthesis, and this enzyme is essentially employed for continuous supply of the acetyl CoA for the production of these metabolites. To achieve reusable and a more robust entity of the enzyme, we carried out the immobilization of Acs on poly(N-isopropylacrylamide)-poly(ethylenimine) (PNIPAm-PEI) microgels via adsorption. Cationic PNIPAm-PEI microgel was synthesized by one-step graft copolymerization of NIPAm and N,N-methylene bis-acrylamide (MBA) from PEI. Adsorption studies of Acs on microgel indicated high binding of enzymes, with a maximum binding capacity of 286 μg/mg of microgel for Acs was achieved. The immobilized enzymes showed improved biocatalytic efficiency over free enzymes, beside this, the reaction parameters and circular dichroism (CD) spectroscopy studies indicated no significant changes in the enzyme structure after immobilization. This thoroughly characterized enzyme bioconjugate was further immobilized on an ultrathin membrane to assess the same reaction in flow through condition. Bioconjugate was covalently immobilized on a thin layer of preformed microgel support upon polyethylene terephthalate (PET) track etched membrane. The prepared membrane was used in a dead end filtration device to monitor the bioconversion efficiency and operational stability of cross-linked bioconjugate. The membrane reactor showed consistent operational stability and maintained >70% of initial activity after 7 consecutive operation cycles.
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Affiliation(s)
- Nidhi Chandrama Dubey
- Department of Nanostructured Materials, Leibniz-Institut für Polymerforschung Dresden e. V. , Hohe Str. 6, D-01069 Dresden, Germany
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Jacobson MP, Kalyanaraman C, Zhao S, Tian B. Leveraging structure for enzyme function prediction: methods, opportunities, and challenges. Trends Biochem Sci 2014; 39:363-71. [PMID: 24998033 DOI: 10.1016/j.tibs.2014.05.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/26/2014] [Accepted: 05/29/2014] [Indexed: 02/06/2023]
Abstract
The rapid growth of the number of protein sequences that can be inferred from sequenced genomes presents challenges for function assignment, because only a small fraction (currently <1%) has been experimentally characterized. Bioinformatics tools are commonly used to predict functions of uncharacterized proteins. Recently, there has been significant progress in using protein structures as an additional source of information to infer aspects of enzyme function, which is the focus of this review. Successful application of these approaches has led to the identification of novel metabolites, enzyme activities, and biochemical pathways. We discuss opportunities to elucidate systematically protein domains of unknown function, orphan enzyme activities, dead-end metabolites, and pathways in secondary metabolism.
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Affiliation(s)
- Matthew P Jacobson
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA.
| | - Chakrapani Kalyanaraman
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA
| | - Suwen Zhao
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA
| | - Boxue Tian
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA
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Dubey NC, Tripathi BP, Stamm M, Ionov L. Smart core-shell microgel support for acetyl coenzyme A synthetase: a step toward efficient synthesis of polyketide-based drugs. Biomacromolecules 2014; 15:2776-83. [PMID: 24938082 DOI: 10.1021/bm5006382] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The flexibility in tuning the structure and charge properties of PNIPAm microgels during their synthesis makes them a suitable choice for various biological applications. Two-step free radical polymerization, a common method employed for synthesis of core-shell microgel has been well adopted to obtain cationic poly(N-isopropylacrylamide-aminoethyl methacrylate) (PNIPAm-AEMA) shell and PNIPAm core. Scanning electron microscopy (SEM), dynamic light scattering (DLS), zeta potential, and ninhydrin assay suggests nearly monodispersed particles of cationic nature. Amino groups on the microgel provides suitable attachment point for covalent immobilization of acetyl coenzyme A synthetase (Acs) via 1-ethyl-3-(3-N,N- dimethylaminopropyl) carbodiimide (EDC) chemistry. On immobilization, 61.55% of initial activity of Acs has been retained, while Michaelis-Menten kinetics of the immobilized Acs indicates identical K(m) (Michaelis constant) but decrease in the V(max) (maximum substrate conversion rate) compared to free enzyme. Immobilized Acs shows an improvement in activity at wide temperature and pH range and also demonstrates good thermal, storage, and operational stability. The Acs-microgel bioconjugate has been successfully reused for four consecutive operation cycles with more than 50% initial activity.
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Affiliation(s)
- Nidhi C Dubey
- Department of Nanostructured Materials, Leibniz Institute of Polymer Research Dresden , Hohe Str. 6, D-01069 Dresden, Germany
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18
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Leitão AL, Enguita FJ. Fungal extrolites as a new source for therapeutic compounds and as building blocks for applications in synthetic biology. Microbiol Res 2014; 169:652-65. [PMID: 24636745 DOI: 10.1016/j.micres.2014.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 02/15/2014] [Accepted: 02/16/2014] [Indexed: 01/07/2023]
Abstract
Secondary metabolic pathways of fungal origin provide an almost unlimited resource of new compounds for medical applications, which can fulfill some of the, currently unmet, needs for therapeutic alternatives for the treatment of a number of diseases. Secondary metabolites secreted to the extracellular medium (extrolites) belong to diverse chemical and structural families, but the majority of them are synthesized by the condensation of a limited number of precursor building blocks including amino acids, sugars, lipids and low molecular weight compounds also employed in anabolic processes. In fungi, genes related to secondary metabolic pathways are frequently clustered together and show a modular organization within fungal genomes. The majority of fungal gene clusters responsible for the biosynthesis of secondary metabolites contain genes encoding a high molecular weight condensing enzyme which is responsible for the assembly of the precursor units of the metabolite. They also contain other auxiliary genes which encode enzymes involved in subsequent chemical modification of the metabolite core. Synthetic biology is a branch of molecular biology whose main objective is the manipulation of cellular components and processes in order to perform logically connected metabolic functions. In synthetic biology applications, biosynthetic modules from secondary metabolic processes can be rationally engineered and combined to produce either new compounds, or to improve the activities and/or the bioavailability of the already known ones. Recently, advanced genome editing techniques based on guided DNA endonucleases have shown potential for the manipulation of eukaryotic and bacterial genomes. This review discusses the potential application of genetic engineering and genome editing tools in the rational design of fungal secondary metabolite pathways by taking advantage of the increasing availability of genomic and biochemical data.
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Affiliation(s)
- Ana Lúcia Leitão
- Departamento de Ciências e Tecnologia da Biomassa, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, Caparica 2829-516, Portugal.
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa 1649-028, Portugal.
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Koryakina I, McArthur J, Randall S, Draelos MM, Musiol EM, Muddiman DC, Weber T, Williams GJ. Poly specific trans-acyltransferase machinery revealed via engineered acyl-CoA synthetases. ACS Chem Biol 2013; 8:200-8. [PMID: 23083014 DOI: 10.1021/cb3003489] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polyketide synthases construct polyketides with diverse structures and biological activities via the condensation of extender units and acyl thioesters. Although a growing body of evidence suggests that polyketide synthases might be tolerant to non-natural extender units, in vitro and in vivo studies aimed at probing and utilizing polyketide synthase specificity are severely limited to only a small number of extender units, owing to the lack of synthetic routes to a broad variety of acyl-CoA extender units. Here, we report the construction of promiscuous malonyl-CoA synthetase variants that can be used to synthesize a broad range of malonyl-CoA extender units substituted at the C2-position, several of which contain handles for chemoselective ligation and are not found in natural biosynthetic systems. We highlighted utility of these enzymes by probing the acyl-CoA specificity of several trans-acyltransferases, leading to the unprecedented discovery of poly specificity toward non-natural extender units, several of which are not found in naturally occurring biosynthetic pathways. These results reveal that polyketide biosynthetic machinery might be more tolerant to non-natural substrates than previously established, and that mutant synthetases are valuable tools for probing the specificity of biosynthetic machinery. Our data suggest new synthetic biology strategies for harnessing this promiscuity and enabling the regioselective modification of polyketides.
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Affiliation(s)
| | | | | | | | - Ewa M. Musiol
- Eberhard-Karls-Universität Tübingen, Interfakultäres Institut für
Mikrobiologie und Infektionsmedizin, Mikrobiologie/Biotechnologie,
Tübingen, Germany
| | | | - Tilmann Weber
- Eberhard-Karls-Universität Tübingen, Interfakultäres Institut für
Mikrobiologie und Infektionsmedizin, Mikrobiologie/Biotechnologie,
Tübingen, Germany
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