1
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Ray KA, Saif N, Keatinge-Clay AT. Modular polyketide synthase ketosynthases collaborate with upstream dehydratases to install double bonds. Chem Commun (Camb) 2024; 60:8712-8715. [PMID: 39056119 PMCID: PMC11321453 DOI: 10.1039/d4cc03034f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024]
Abstract
A VMYH motif was determined to help ketosynthases in polyketide assembly lines select α,β-unsaturated intermediates from an equilibrium mediated by an upstream dehydratase. Alterations of this motif decreased ketosynthase selectivity within a model tetraketide synthase, most significantly when replaced by the TNGQ motif of ketosynthases that accept D-β-hydroxy intermediates.
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Affiliation(s)
- Katherine A Ray
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th St., Austin, TX 78712, USA.
| | - Nisha Saif
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th St., Austin, TX 78712, USA.
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th St., Austin, TX 78712, USA.
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2
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Ray KA, Lutgens JD, Bista R, Zhang J, Desai RR, Hirsch M, Miyazawa T, Cordova A, Keatinge-Clay AT. Assessing and harnessing updated polyketide synthase modules through combinatorial engineering. Nat Commun 2024; 15:6485. [PMID: 39090122 PMCID: PMC11294587 DOI: 10.1038/s41467-024-50844-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
The modular nature of polyketide assembly lines and the significance of their products make them prime targets for combinatorial engineering. The recently updated module boundary has been successful for engineering short synthases, yet larger synthases constructed using the updated boundary have not been investigated. Here we describe our design and implementation of a BioBricks-like platform to rapidly construct 5 triketide, 25 tetraketide, and 125 pentaketide synthases to test every module combination of the pikromycin synthase. Anticipated products are detected from 60% of the triketide synthases, 32% of the tetraketide synthases, and 6.4% of the pentaketide synthases. We determine ketosynthase gatekeeping and module-skipping are the principal impediments to obtaining functional synthases. The platform is also employed to construct active hybrid synthases by incorporating modules from the erythromycin, spinosyn, and rapamycin assembly lines. The relaxed gatekeeping of a ketosynthase in the rapamycin synthase is especially encouraging in the quest to produce designer polyketides.
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Affiliation(s)
- Katherine A Ray
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Joshua D Lutgens
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ramesh Bista
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ronak R Desai
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Melissa Hirsch
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Takeshi Miyazawa
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Antonio Cordova
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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3
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Hirsch M, Desai RR, Annaswamy S, Keatinge-Clay AT. Mutagenesis Supports AlphaFold Prediction of How Modular Polyketide Synthase Acyl Carrier Proteins Dock With Downstream Ketosynthases. Proteins 2024. [PMID: 39078105 DOI: 10.1002/prot.26733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/07/2024] [Accepted: 07/05/2024] [Indexed: 07/31/2024]
Abstract
The docking of an acyl carrier protein (ACP) domain with a downstream ketosynthase (KS) domain in each module of a polyketide synthase (PKS) helps ensure accurate biosynthesis. If the polyketide chain bound to the ACP has been properly modified by upstream processing enzymes and is compatible with gatekeeping residues in the KS tunnel, a transacylation reaction can transfer it from the 18.1-Å phosphopantetheinyl arm of the ACP to the reactive cysteine of the KS. AlphaFold-Multimer predicts a general interface for these transacylation checkpoints. Half of the solutions obtained for 50 ACP/KS pairs show the KS motif TxLGDP forming the first turn of an α-helix, as in reported structures, while half show it forming a type I β-turn not previously observed. Solutions with the latter conformation may represent how these domains are relatively positioned during the transacylation reaction, as the entrance to the KS active site is relatively open and the phosphopantetheinylated ACP serine and the reactive KS cysteine are relatively closer-17.2 versus 20.9 Å, on average. To probe the predicted interface, 20 mutations were made to KS surface residues within the model triketide lactone synthase P1-P6-P7. The activities of these mutants are consistent with the proposed interface.
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Affiliation(s)
- Melissa Hirsch
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - Ronak R Desai
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Shreyas Annaswamy
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
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4
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Xiang C, Yao S, Wang R, Zhang L. Bioinformatic prediction of the stereoselectivity of modular polyketide synthase: an update of the sequence motifs in ketoreductase domain. Beilstein J Org Chem 2024; 20:1476-1485. [PMID: 38978744 PMCID: PMC11228615 DOI: 10.3762/bjoc.20.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/21/2024] [Indexed: 07/10/2024] Open
Abstract
Polyketides are a major class of natural products, including bioactive medicines such as erythromycin and rapamycin. They are often rich in stereocenters biosynthesized by the ketoreductase (KR) domain within the polyketide synthase (PKS) assembly line. Previous studies have identified conserved motifs in KR sequences that enable the bioinformatic prediction of product stereochemistry. However, the reliability and applicability of these prediction methods have not been thoroughly assessed. In this study, we conducted a comprehensive bioinformatic analysis of 1,762 KR sequences from cis-AT PKSs to reevaluate the residues involved in conferring stereoselectivity. Our findings indicate that the previously identified fingerprint motifs remain valid for KRs in β-modules from actinobacteria, but their reliability diminishes for KRs from other module types or taxonomic origins. Additionally, we have identified several new motifs that exhibit a strong correlation with the stereochemical outcomes of KRs. These updated fingerprint motifs for stereochemical prediction not only enhance our understanding of the enzymatic mechanisms governing stereocontrol but also facilitate accurate stereochemical prediction and genome mining of polyketides derived from modular cis-AT PKSs.
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Affiliation(s)
- Changjun Xiang
- Department of Chemistry, Fudan University, Shanghai 200433, China
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Shunyu Yao
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Ruoyu Wang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Lihan Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
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5
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Dell M, Tran MA, Capper MJ, Sundaram S, Fiedler J, Koehnke J, Hellmich UA, Hertweck C. Trapping of a Polyketide Synthase Module after C-C Bond Formation Reveals Transient Acyl Carrier Domain Interactions. Angew Chem Int Ed Engl 2024; 63:e202315850. [PMID: 38134222 DOI: 10.1002/anie.202315850] [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: 10/19/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 12/24/2023]
Abstract
Modular polyketide synthases (PKSs) are giant assembly lines that produce an impressive range of biologically active compounds. However, our understanding of the structural dynamics of these megasynthases, specifically the delivery of acyl carrier protein (ACP)-bound building blocks to the catalytic site of the ketosynthase (KS) domain, remains severely limited. Using a multipronged structural approach, we report details of the inter-domain interactions after C-C bond formation in a chain-branching module of the rhizoxin PKS. Mechanism-based crosslinking of an engineered module was achieved using a synthetic substrate surrogate that serves as a Michael acceptor. The crosslinked protein allowed us to identify an asymmetric state of the dimeric protein complex upon C-C bond formation by cryo-electron microscopy (cryo-EM). The possible existence of two ACP binding sites, one of them a potential "parking position" for substrate loading, was also indicated by AlphaFold2 predictions. NMR spectroscopy showed that a transient complex is formed in solution, independent of the linker domains, and photochemical crosslinking/mass spectrometry of the standalone domains allowed us to pinpoint the interdomain interaction sites. The structural insights into a branching PKS module arrested after C-C bond formation allows a better understanding of domain dynamics and provides valuable information for the rational design of modular assembly lines.
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Affiliation(s)
- Maria Dell
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), 07745, Jena, Germany
| | - Mai Anh Tran
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Michael J Capper
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Srividhya Sundaram
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), 07745, Jena, Germany
| | - Jonas Fiedler
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), 07745, Jena, Germany
| | - Jesko Koehnke
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
- Institute of Food Chemistry, Leibniz University Hannover, 30167, Hannover, Germany
| | - Ute A Hellmich
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, 60438, Frankfurt am Main, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), 07745, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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6
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Ray KA, Lutgens JD, Bista R, Zhang J, Desai RR, Hirsch M, Miyazawa T, Cordova A, Keatinge-Clay AT. Assessing and harnessing updated polyketide synthase modules through combinatorial engineering. RESEARCH SQUARE 2023:rs.3.rs-3157617. [PMID: 37546965 PMCID: PMC10402262 DOI: 10.21203/rs.3.rs-3157617/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The modular nature of polyketide assembly lines and the significance of their products make them prime targets for combinatorial engineering. While short synthases constructed using the recently updated module boundary have been shown to outperform those using the traditional boundary, larger synthases constructed using the updated boundary have not been investigated. Here we describe our design and implementation of a BioBricks-like platform to rapidly construct 5 triketide, 25 tetraketide, and 125 pentaketide synthases from the updated modules of the Pikromycin synthase. Every combinatorial possibility of modules 2-6 inserted between the first and last modules of the native synthase was constructed and assayed. Anticipated products were observed from 60% of the triketide synthases, 32% of the tetraketide synthases, and 6.4% of the pentaketide synthases. Ketosynthase gatekeeping and module-skipping were determined to be the principal impediments to obtaining functional synthases. The platform was also used to create functional hybrid synthases through the incorporation of modules from the Erythromycin, Spinosyn, and Rapamycin assembly lines. The relaxed gatekeeping observed from a ketosynthase in the Rapamycin synthase is especially encouraging in the quest to produce designer polyketides.
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Affiliation(s)
- Katherine A. Ray
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX
| | - Joshua D. Lutgens
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX
| | - Ramesh Bista
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX
| | - Jie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX
| | - Ronak R. Desai
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX
| | - Melissa Hirsch
- Department of Chemistry, The University of Texas at Austin, Austin, TX
| | - Takeshi Miyazawa
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX
| | - Antonio Cordova
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX
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7
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Zhang J, Bista R, Miyazawa T, Keatinge-Clay AT. Boosting titers of engineered triketide and tetraketide synthases to record levels through T7 promoter tuning. Metab Eng 2023; 78:93-98. [PMID: 37257684 PMCID: PMC11059570 DOI: 10.1016/j.ymben.2023.05.008] [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: 11/22/2022] [Revised: 05/24/2023] [Accepted: 05/28/2023] [Indexed: 06/02/2023]
Abstract
Modular polyketide synthases (PKS's) are promising platforms for the rational engineering of designer polyketides and commodity chemicals, yet their low productivities are a barrier to the practical biosynthesis of these compounds. Previously, we engineered triketide lactone synthases such as Pik167 using the recently updated module definition and showed they generate hundreds of milligrams of product per liter of Escherichia coli K207-3 shake flask culture. As the molar ratio between the 2 polypeptides of Pik167 is highly skewed, we sought to attenuate the strength of the T7 promoter controlling the production of the smaller, better-expressing polypeptide and thereby increase production of the first polypeptide under the control of an unoptimized T7 promoter. Through this strategy, a 1.8-fold boost in titer was obtained. After a further 1.5-fold boost obtained by increasing the propionate concentration in the media from 20 to 80 mM, a record titer of 791 mg L-1 (627 mg L-1 isolated) was achieved, a 2.6-fold increase overall. Spurred on by this result, the tetraketide synthase Pik1567 was engineered and the T7 promoter attenuation strategy was applied to its second and third genes. A 5-fold boost, from 20 mg L-1 to 100 mg L-1, in the titer of its tetraketide product was achieved.
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Affiliation(s)
- Jie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th St., Austin, TX, 78712, USA
| | - Ramesh Bista
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th St., Austin, TX, 78712, USA
| | - Takeshi Miyazawa
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th St., Austin, TX, 78712, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th St., Austin, TX, 78712, USA.
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8
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Zhan C, Lee N, Lan G, Dan Q, Cowan A, Wang Z, Baidoo EEK, Kakumanu R, Luckie B, Kuo RC, McCauley J, Liu Y, Valencia L, Haushalter RW, Keasling JD. Improved polyketide production in C. glutamicum by preventing propionate-induced growth inhibition. Nat Metab 2023; 5:1127-1140. [PMID: 37443355 DOI: 10.1038/s42255-023-00830-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/25/2023] [Indexed: 07/15/2023]
Abstract
Corynebacterium glutamicum is a promising host for production of valuable polyketides. Propionate addition, a strategy known to increase polyketide production by increasing intracellular methylmalonyl-CoA availability, causes growth inhibition in C. glutamicum. The mechanism of this inhibition was unclear before our work. Here we provide evidence that accumulation of propionyl-CoA and methylmalonyl-CoA induces growth inhibition in C. glutamicum. We then show that growth inhibition can be relieved by introducing methylmalonyl-CoA-dependent polyketide synthases. With germicidin as an example, we used adaptive laboratory evolution to leverage the fitness advantage of polyketide production in the presence of propionate to evolve improved germicidin production. Whole-genome sequencing revealed mutations in germicidin synthase, which improved germicidin titer, as well as mutations in citrate synthase, which effectively evolved the native glyoxylate pathway to a new methylcitrate pathway. Together, our results show that C. glutamicum is a capable host for polyketide production and we can take advantage of propionate growth inhibition to drive titers higher using laboratory evolution or to screen for production of polyketides.
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Affiliation(s)
- Chunjun Zhan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA
| | - Namil Lee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA
| | - Guangxu Lan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Qingyun Dan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Aidan Cowan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Zilong Wang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ramu Kakumanu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bridget Luckie
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Rita C Kuo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Joshua McCauley
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Luis Valencia
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Robert W Haushalter
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Departments of Chemical & Biomolecular Engineering and of Bioengineering, University of California, Berkeley, CA, USA.
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark.
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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9
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Chisuga T, Murakami S, Miyanaga A, Kudo F, Eguchi T. Structure-Based Analysis of Transient Interactions between Ketosynthase-like Decarboxylase and Acyl Carrier Protein in a Loading Module of Modular Polyketide Synthase. ACS Chem Biol 2023; 18:1398-1404. [PMID: 37216195 DOI: 10.1021/acschembio.3c00151] [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: 05/24/2023]
Abstract
Ketosynthase-like decarboxylase (KSQ) domains are widely distributed in the loading modules of modular type I polyketide synthases (PKSs) and catalyze the decarboxylation of the (alkyl-)malonyl unit bound to the acyl carrier protein (ACP) in the loading module for the construction of the PKS starter unit. Previously, we performed a structural and functional analysis of the GfsA KSQ domain involved in the biosynthesis of macrolide antibiotic FD-891. We furthermore revealed the recognition mechanism for the malonic acid thioester moiety of the malonyl-GfsA loading module ACP (ACPL) as a substrate. However, the exact recognition mechanism for the GfsA ACPL moiety remains unclear. Here, we present a structural basis for the interactions between the GfsA KSQ domain and GfsA ACPL. We determined the crystal structure of the GfsA KSQ-acyltransferase (AT) didomain in complex with ACPL (ACPL=KSQAT complex) by using a pantetheine crosslinking probe. We identified the key amino acid residues involved in the KSQ domain-ACPL interactions and confirmed the importance of these residues by mutational analysis. The binding mode of ACPL to the GfsA KSQ domain is similar to that of ACP to the ketosynthase domain in modular type I PKSs. Furthermore, comparing the ACPL=KSQAT complex structure with other full-length PKS module structures provides important insights into the overall architectures and conformational dynamics of the type I PKS modules.
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Affiliation(s)
- Taichi Chisuga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Tokyo 152-8551, Japan
| | - Satoshi Murakami
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Tokyo 152-8551, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-Okayama, Tokyo 152-8551, Japan
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10
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Wrobel CJJ, Schroeder FC. Repurposing degradation pathways for modular metabolite biosynthesis in nematodes. Nat Chem Biol 2023; 19:676-686. [PMID: 37024728 PMCID: PMC10559835 DOI: 10.1038/s41589-023-01301-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 02/24/2023] [Indexed: 04/08/2023]
Abstract
Recent studies have revealed that Caenorhabditis elegans and other nematodes repurpose products from biochemical degradation pathways for the combinatorial assembly of complex modular structures that serve diverse signaling functions. Building blocks from neurotransmitter, amino acid, nucleoside and fatty acid metabolism are attached to scaffolds based on the dideoxyhexose ascarylose or glucose, resulting in hundreds of modular ascarosides and glucosides. Genome-wide association studies have identified carboxylesterases as the key enzymes mediating modular assembly, enabling rapid compound discovery via untargeted metabolomics and suggesting that modular metabolite biosynthesis originates from the 'hijacking' of conserved detoxification mechanisms. Modular metabolites thus represent a distinct biosynthetic strategy for generating structural and functional diversity in nematodes, complementing the primarily polyketide synthase- and nonribosomal peptide synthetase-derived universe of microbial natural products. Although many aspects of modular metabolite biosynthesis and function remain to be elucidated, their identification demonstrates how phenotype-driven compound discovery, untargeted metabolomics and genomic approaches can synergize to facilitate the annotation of metabolic dark matter.
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Affiliation(s)
- Chester J J Wrobel
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
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11
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Liu L, Wang W, Chen M, Zhang Y, Mao H, Wang D, Chen Y, Li P. Characterization of three succinyl-CoA acyltransferases involved in polyketide chain assembly. Appl Microbiol Biotechnol 2023; 107:2403-2412. [PMID: 36929192 DOI: 10.1007/s00253-023-12481-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/18/2023]
Abstract
Polyketides are a class of natural products with astonishing structural diversities, fascinating biological activities, and a versatile of applications. In polyketides biosynthesis, acyltransferases (ATs) are the 'gatekeeping' enzymes selecting the specific CoA-activated acyl groups as building blocks and transferring them onto the phosphopantetheine arm of acyl carrier proteins (ACPs) to enable the following condensation reactions to assemble the polyketide chain. Herein, the Art2 protein from aurantinins, a group of the antibacterial polyketides, is characterized in vitro as an AT that can load a CoA-activated succinyl unit onto the first ACP domain of Art17 (ACPArt17-1). In addition, another two proteins, GbnB and EtnB, involved in the biosynthesis of gladiolin and etnangien respectively, were traced by literature mining, homologous searching, and product structure analysis and then identified as functional succinyl-CoA ATs by the ACPArt17-1 assays. Taken together, by the assay method employing ACPArt17-1 as an acyl acceptor, we identified three ATs that can introduce a succinyl unit into the polyketide assembly line, which enriches the toolbox of polyketide biosynthetic enzymes and sets a stage for incorporating a succinyl unit into polyketide backbones in synthetic biological manners. KEY POINTS: • Three acyltransferases that are able to load ACP with a succinyl unit were characterized in vitro. • ACPArt17-1 can be used as an acceptor to assay succinyl-CoA AT from different polyketides. • The succinyl unit can be incorporated into polyketides assembly process.
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Affiliation(s)
- Lilu Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenzhao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Meng Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuwei Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huijin Mao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dacheng Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengwei Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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12
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Keatinge-Clay AT, Miyazawa T, Zhang J, Ray KA, Lutgens JD, Bista R, Lin SN. Crystal structures reveal the framework of cis -acyltransferase modular polyketide synthases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.11.528132. [PMID: 36798387 PMCID: PMC9934609 DOI: 10.1101/2023.02.11.528132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Although the domains of cis -acyltransferase ( cis -AT) modular polyketide synthases (PKS's) have been understood at atomic resolution for over a decade, the domain-domain interactions responsible for the architectures and activities of these giant molecular assembly lines remain largely uncharacterized. The multimeric structure of the α 6 β 6 fungal fatty acid synthase (FAS) provides 6 equivalent reaction chambers for its acyl carrier protein (ACP) domains to shuttle carbon building blocks and the growing acyl chain between surrounding, oriented enzymatic domains. The presumed homodimeric oligomerization of cis -AT assembly lines is insufficient to provide similar reaction chambers; however, the crystal structure of a ketosynthase (KS)+AT didomain presented here and three already reported show an interaction between the AT domains appropriate for lateral multimerization. This interaction was used to construct a framework for the pikromycin PKS from its KS, AT, and docking domains that contains highly-ordered reaction chambers. Its AT domains also mediate vertical interactions, both with upstream KS domains and downstream docking domains.
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13
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Winter AJ, Rowe MT, Weir ANM, Akter N, Mbatha SZ, Walker PD, Williams C, Song Z, Race PR, Willis CL, Crump MP. Programmed Iteration Controls the Assembly of the Nonanoic Acid Side Chain of the Antibiotic Mupirocin. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202212393. [PMID: 38505625 PMCID: PMC10947060 DOI: 10.1002/ange.202212393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/11/2022]
Abstract
Mupirocin is a clinically important antibiotic produced by Pseudomonas fluorescens NCIMB 10586 that is assembled by a complex trans-AT polyketide synthase. The polyketide fragment, monic acid, is esterified by a 9-hydroxynonanoic acid (9HN) side chain which is essential for biological activity. The ester side chain assembly is initialised from a 3-hydroxypropionate (3HP) starter unit attached to the acyl carrier protein (ACP) MacpD, but the fate of this species is unknown. Herein we report the application of NMR spectroscopy, mass spectrometry, chemical probes and in vitro assays to establish the remaining steps of 9HN biosynthesis. These investigations reveal a complex interplay between a novel iterative or "stuttering" KS-AT didomain (MmpF), the multidomain module MmpB and multiple ACPs. This work has important implications for understanding the late-stage biosynthetic steps of mupirocin and will be important for future engineering of related trans-AT biosynthetic pathways (e.g. thiomarinol).
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Affiliation(s)
| | | | | | - Nahida Akter
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | | | - Paul D. Walker
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | | | - Zhongshu Song
- School of ChemistryUniversity of BristolBristolBS8 1TSUK
| | - Paul R. Race
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
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14
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Tao XB, LaFrance S, Xing Y, Nava AA, Martin H, Keasling J, Backman TH. ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design. Nucleic Acids Res 2022; 51:D532-D538. [PMID: 36416273 PMCID: PMC9825560 DOI: 10.1093/nar/gkac1075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/14/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
Megasynthase enzymes such as type I modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) play a central role in microbial chemical warfare because they can evolve rapidly by shuffling parts (catalytic domains) to produce novel chemicals. If we can understand the design rules to reshuffle these parts, PKSs and NRPSs will provide a systematic and modular way to synthesize millions of molecules including pharmaceuticals, biomaterials, and biofuels. However, PKS and NRPS engineering remains difficult due to a limited understanding of the determinants of PKS and NRPS fold and function. We developed ClusterCAD to streamline and simplify the process of designing and testing engineered PKS variants. Here, we present the highly improved ClusterCAD 2.0 release, available at https://clustercad.jbei.org. ClusterCAD 2.0 boasts support for PKS-NRPS hybrid and NRPS clusters in addition to PKS clusters; a vastly enlarged database of curated PKS, PKS-NRPS hybrid, and NRPS clusters; a diverse set of chemical 'starters' and loading modules; the new Domain Architecture Cluster Search Tool; and an offline Jupyter Notebook workspace, among other improvements. Together these features massively expand the chemical space that can be accessed by enzymes engineered with ClusterCAD.
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Affiliation(s)
- Xavier B Tao
- Department of Chemistry, University of California, Berkeley, CA 94720, USA,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sarah LaFrance
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Biofuels and Bioproducts Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA,QB3 Institute, University of California, Berkeley, CA 94720, USA
| | - Yifei Xing
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA
| | - Alberto A Nava
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Hector Garcia Martin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Biofuels and Bioproducts Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA,Department of Energy Agile BioFoundry, Emeryville, CA 94608, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Biofuels and Bioproducts Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA,Department of Bioengineering, University of California, Berkeley, CA 94720, USA,QB3 Institute, University of California, Berkeley, CA 94720, USA,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark 2800Copenhagen, Denmark,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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15
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Winter AJ, Rowe MT, Weir ANM, Akter N, Mbatha SZ, Walker PD, Williams C, Song Z, Race PR, Willis CL, Crump MP. Programmed Iteration Controls the Assembly of the Nonanoic Acid Side Chain of the Antibiotic Mupirocin. Angew Chem Int Ed Engl 2022; 61:e202212393. [PMID: 36227272 PMCID: PMC10098928 DOI: 10.1002/anie.202212393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/12/2022]
Abstract
Mupirocin is a clinically important antibiotic produced by Pseudomonas fluorescens NCIMB 10586 that is assembled by a complex trans-AT polyketide synthase. The polyketide fragment, monic acid, is esterified by a 9-hydroxynonanoic acid (9HN) side chain which is essential for biological activity. The ester side chain assembly is initialised from a 3-hydroxypropionate (3HP) starter unit attached to the acyl carrier protein (ACP) MacpD, but the fate of this species is unknown. Herein we report the application of NMR spectroscopy, mass spectrometry, chemical probes and in vitro assays to establish the remaining steps of 9HN biosynthesis. These investigations reveal a complex interplay between a novel iterative or "stuttering" KS-AT didomain (MmpF), the multidomain module MmpB and multiple ACPs. This work has important implications for understanding the late-stage biosynthetic steps of mupirocin and will be important for future engineering of related trans-AT biosynthetic pathways (e.g. thiomarinol).
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Affiliation(s)
| | - Matthew T. Rowe
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | | | - Nahida Akter
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | | | - Paul D. Walker
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | | | - Zhongshu Song
- School of Chemistry University of Bristol Bristol BS8 1TS UK
| | - Paul R. Race
- School of Biochemistry University of Bristol Bristol BS8 1TD UK
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16
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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: 10] [Impact Index Per Article: 5.0] [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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17
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Zhou W, Alharbi HA, Hummingbird E, Keatinge-Clay AT, Mahmud T. Functional Studies and Revision of the NFAT-133/TM-123 Biosynthetic Pathway in Streptomyces pactum. ACS Chem Biol 2022; 17:2039-2045. [PMID: 35904416 PMCID: PMC9391300 DOI: 10.1021/acschembio.2c00454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biosynthetic gene cluster of NFAT-133, an inhibitor of the nuclear factor of activated T cells, was recently identified in Streptomyces pactum ATCC 27456. This cluster is conspicuous by its highly disordered noncollinear type I modular polyketide synthase (PKS) genes that encode PKSs with one module more than those expected for the heptaketide NFAT-133 biosynthesis. Thus, the major metabolite NFAT-133 was proposed to derive from an octaketide analogue, TM-123. Here, we report that further bioinformatic analysis and gene inactivation studies suggest that NFAT-133 is not derived from TM-123 but rather a product of programmed KS7 extension skipping of a nascent heptaketide from the PKS assembly line that produces TM-123. Furthermore, identification of NFAT-133/TM-123 analogues from mutants of the ATCC 27456 strain suggests that NftN (a putative dehydrogenase), NftE (a cytochrome P450), and NftG (a putative hydrolase/decarboxylase) function "in trans" during the polyketide chain assembly processes.
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Affiliation(s)
- Wei Zhou
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Hattan A. Alharbi
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Eshe Hummingbird
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | | | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
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18
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D’Ambrosio HK, Ganley JG, Keeler AM, Derbyshire ER. A single amino acid residue controls acyltransferase activity in a polyketide synthase from Toxoplasma gondii. iScience 2022; 25:104443. [PMID: 35874921 PMCID: PMC9301873 DOI: 10.1016/j.isci.2022.104443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/12/2022] [Accepted: 05/16/2022] [Indexed: 11/17/2022] Open
Abstract
Type I polyketide synthases (PKSs) are multidomain, multimodule enzymes capable of producing complex polyketide metabolites. These modules contain an acyltransferase (AT) domain, which selects acyl-CoA substrates to be incorporated into the metabolite scaffold. Herein, we reveal the sequences of three AT domains from a polyketide synthase (TgPKS2) from the apicomplexan parasite Toxoplasma gondii. Phylogenic analysis indicates these ATs (AT1, AT2, and AT3) are distinct from domains in well-characterized microbial biosynthetic gene clusters. Biochemical investigations revealed that AT1 and AT2 hydrolyze malonyl-CoA but the terminal AT3 domain is non-functional. We further identify an "on-off switch" residue that controls activity such that a single amino acid change in AT3 confers hydrolysis activity while the analogous mutation in AT2 eliminates activity. This biochemical analysis of AT domains from an apicomplexan PKS lays the foundation for further molecular and structural studies on PKSs from T. gondii and other protists.
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Affiliation(s)
- Hannah K. D’Ambrosio
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Jack G. Ganley
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Aaron M. Keeler
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Emily R. Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
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19
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Schröder M, Roß T, Hemmerling F, Hahn F. Studying a Bottleneck of Multimodular Polyketide Synthase Processing: the Polyketide Structure-Dependent Performance of Ketoreductase Domains. ACS Chem Biol 2022; 17:1030-1037. [PMID: 35412301 DOI: 10.1021/acschembio.2c00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ketoreductases (KRs) are canonical domains of type I polyketide synthases (PKSs). They stereoselectively reduce ACP-bound β-ketothioester intermediates and are responsible for a large part of the stereocenters in reduced polyketides. Albeit essential for the understanding and engineering of PKS, the specific effects of altering the polyketide part of KR precursors on their performance has rarely been studied. We present investigations on the substrate-dependent performance of six isolated KR domains using a library of structurally diverse surrogates for PKS thioester intermediates. A pronounced correlation between the polyketide structure and the KR performance was observed with activity and stereoselectivity diminishing with growing deviation from the natural KR precursor structure. The extent of this decrease and the profile of arising side products was characteristic for the individual KRs. Our results reinforce the importance of structure-KR performance relationships and suggest extended studies with isolated domains and whole PKS modules.
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Affiliation(s)
- Marius Schröder
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
- Biomolekulares Wirkstoffzentrum, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - Theresa Roß
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Franziska Hemmerling
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
- Biomolekulares Wirkstoffzentrum, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie), Fakultät für Biologie, Chemie und Geowissenschaften, Department of Chemistry, Universität Bayreuth, 95447 Bayreuth, Germany
- Biomolekulares Wirkstoffzentrum, Leibniz Universität Hannover, 30167 Hannover, Germany
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20
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Engineering the stambomycin modular polyketide synthase yields 37-membered mini-stambomycins. Nat Commun 2022; 13:515. [PMID: 35082289 PMCID: PMC8792006 DOI: 10.1038/s41467-022-27955-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022] Open
Abstract
The modular organization of the type I polyketide synthases (PKSs) would seem propitious for rational engineering of desirable analogous. However, despite decades of efforts, such experiments remain largely inefficient. Here, we combine multiple, state-of-the-art approaches to reprogram the stambomycin PKS by deleting seven internal modules. One system produces the target 37-membered mini-stambomycin metabolites − a reduction in chain length of 14 carbons relative to the 51-membered parental compounds − but also substantial quantities of shunt metabolites. Our data also support an unprecedented off-loading mechanism of such stalled intermediates involving the C-terminal thioesterase domain of the PKS. The mini-stambomycin yields are reduced relative to wild type, likely reflecting the poor tolerance of the modules downstream of the modified interfaces to the non-native substrates. Overall, we identify factors contributing to the productivity of engineered whole assembly lines, but our findings also highlight the need for further research to increase production titers. Genetic engineering of the type I polyketide synthases (PKSs) to produce desirable analogous remains largely inefficient. Here, the authors leverage multiple approaches to delete seven internal modules from the stambomycin PKS and generate 37-membered mini-stambomycin macrolactones.
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21
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Chisuga T, Nagai A, Miyanaga A, Goto E, Kishikawa K, Kudo F, Eguchi T. Structural Insight into the Reaction Mechanism of Ketosynthase-Like Decarboxylase in a Loading Module of Modular Polyketide Synthases. ACS Chem Biol 2022; 17:198-206. [PMID: 34985877 DOI: 10.1021/acschembio.1c00856] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ketosynthase-like decarboxylase (KSQ) domains are widely distributed in the loading modules of modular polyketide synthases (PKSs) and are proposed to catalyze the decarboxylation of a malonyl or methylmalonyl unit for the construction of the PKS starter unit. KSQ domains have high sequence similarity to ketosynthase (KS) domains, which catalyze transacylation and decarboxylative condensation in polyketide and fatty acid biosynthesis, except that the catalytic Cys residue of KS domains is replaced by Gln in KSQ domains. Here, we present biochemical analyses of GfsA KSQ and CmiP4 KSQ, which are involved in the biosynthesis of FD-891 and cremimycin, respectively. In vitro analysis showed that these KSQ domains catalyze the decarboxylation of malonyl and methylmalonyl units. Furthermore, we determined the crystal structure of GfsA KSQ in complex with a malonyl thioester substrate analogue, which enabled identification of key amino acid residues involved in the decarboxylation reaction. The importance of these residues was confirmed by mutational analysis. On the basis of these findings, we propose a mechanism of the decarboxylation reaction catalyzed by GfsA KSQ. GfsA KSQ initiates decarboxylation by fixing the substrate in a suitable conformation for decarboxylation. The formation of enolate upon decarboxylation is assisted by two conserved threonine residues. Comparison of the structure of GfsA KSQ with those of KS domains suggests that the Gln residue in the active site of the KSQ domain mimics the acylated Cys residue in the active site of KS domains.
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Affiliation(s)
- Taichi Chisuga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Akira Nagai
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Ena Goto
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Kosuke Kishikawa
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O̅okayama, Meguro-ku, Tokyo 152-8851, Japan
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22
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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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23
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Cogan DP, Zhang K, Li X, Li S, Pintilie GD, Roh SH, Craik CS, Chiu W, Khosla C. Mapping the catalytic conformations of an assembly-line polyketide synthase module. Science 2021; 374:729-734. [PMID: 34735239 DOI: 10.1126/science.abi8358] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Dillon P Cogan
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Kaiming Zhang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,MOE Key Laboratory for Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xiuyuan Li
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Shanshan Li
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,MOE Key Laboratory for Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Grigore D Pintilie
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Soung-Hun Roh
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Department of Biological Sciences, Institute of Molecular Biology & Genetics, Seoul National University, Seoul 151-742, Korea
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA 94158, USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,Stanford ChEM-H, Stanford, CA 94305, USA
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24
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Heinrich S, Grote M, Sievers S, Kushnir S, Schulz F. Polyether Cyclization Cascade Alterations in Response to Monensin Polyketide Synthase Mutations. Chembiochem 2021; 23:e202100584. [PMID: 34729883 DOI: 10.1002/cbic.202100584] [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: 10/28/2021] [Indexed: 11/11/2022]
Abstract
The targeted manipulation of polyketide synthases has in recent years led to numerous new-to-nature polyketides. For type I polyketide synthases the response of post-polyketide synthases (PKS) processing enzymes onto the most frequently polyketide backbone manipulations is so far insufficiently studied. In particular, complex processes such as the polyether cyclisation in the biosynthesis of ionophores such as monensin pose interesting objects of research. We present here a study of the substrate promiscuity of the polyether cyclisation cascade enzymes in monensin biosynthesis in the conversion of redox derivatives of the nascent polyketide chain. LC-HRMS/MS2 -based studies revealed a remarkable flexibility of the post-PKS enzymes. They acted on derivatized polyketide backbones based on the three possible polyketide redox states within two different modules and gave rise to an altered polyether structure. One of these monensin derivatives was isolated and characterized by 2D-NMR spectroscopy, crystallography, and bioactivity studies.
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Affiliation(s)
- Sascha Heinrich
- Organic Chemistry I, Chemistry and Biochemistry of Natural Products, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Marius Grote
- Organic Chemistry I, Chemistry and Biochemistry of Natural Products, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Sonja Sievers
- Max PIanck Institute for molecular Physiology, COMAS - Compound Management and Screening Center, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Susanna Kushnir
- Organic Chemistry I, Chemistry and Biochemistry of Natural Products, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Frank Schulz
- Organic Chemistry I, Chemistry and Biochemistry of Natural Products, Ruhr-University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
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25
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Miyazawa T, Fitzgerald BJ, Keatinge-Clay AT. Preparative production of an enantiomeric pair by engineered polyketide synthases. Chem Commun (Camb) 2021; 57:8762-8765. [PMID: 34378565 DOI: 10.1039/d1cc03073f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Using the updated module boundary of polyketide assembly lines, modules from the pikromycin synthase were recombined into engineered synthases that furnish an enantiomeric pair of 2-stereocenter triketide lactones at >99% ee with yields up to 0.39 g per liter of E. coli K207-3 in shake flasks.
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Affiliation(s)
- Takeshi Miyazawa
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th St., Austin, TX 78712, USA.
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26
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Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
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Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
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27
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Li P, Chen M, Tang W, Guo Z, Zhang Y, Wang M, Horsman GP, Zhong J, Lu Z, Chen Y. Initiating polyketide biosynthesis by on-line methyl esterification. Nat Commun 2021; 12:4499. [PMID: 34301953 PMCID: PMC8302727 DOI: 10.1038/s41467-021-24846-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 07/09/2021] [Indexed: 12/04/2022] Open
Abstract
Aurantinins (ARTs) are antibacterial polyketides featuring a unique 6/7/8/5-fused tetracyclic ring system and a triene side chain with a carboxyl terminus. Here we identify the art gene cluster and dissect ART’s C-methyl incorporation patterns to study its biosynthesis. During this process, an apparently redundant methyltransferase Art28 was characterized as a malonyl-acyl carrier protein O-methyltransferase, which represents an unusual on-line methyl esterification initiation strategy for polyketide biosynthesis. The methyl ester bond introduced by Art28 is kept until the last step of ART biosynthesis, in which it is hydrolyzed by Art9 to convert inactive ART 9B to active ART B. The cryptic reactions catalyzed by Art28 and Art9 represent a protecting group biosynthetic logic to render the ART carboxyl terminus inert to unwanted side reactions and to protect producing organisms from toxic ART intermediates. Further analyses revealed a wide distribution of this initiation strategy for polyketide biosynthesis in various bacteria. Aurantinins are polyketides with unusual connectivities and broad antibacterial activity. Here the authors show the biosynthesis of aurantinins, which proceeds via an on-line methyl esterification at the terminus that enables the iterative chain elongations prior to condensation and cyclization.
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Affiliation(s)
- Pengwei Li
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Meng Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wei Tang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhengyan Guo
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuwei Zhang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Min Wang
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong, China
| | - Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Jin Zhong
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agriculture University, Nanjing, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources & CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
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28
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Wagner L, Roß T, Hollmann T, Hahn F. Cross-linking of a polyketide synthase domain leads to a recyclable biocatalyst for chiral oxygen heterocycle synthesis. RSC Adv 2021; 11:20248-20251. [PMID: 35479892 PMCID: PMC9033652 DOI: 10.1039/d1ra03692k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 05/26/2021] [Indexed: 12/17/2022] Open
Abstract
The potential of polyketide synthase (PKS) domains for chemoenzymatic synthesis can often not be tapped due to their low stability and activity in vitro. In this proof-of-principle study, the immobilisation of the heterocycle-forming PKS domain AmbDH3 as a cross-linked enzyme aggregate (CLEA) is described. The AmbDH3-CLEA showed good activity recovery, stability and recyclability. Repetitive reactions on the semi-preparative scale were performed with high conversion and isolated yield. Similar to that observed for the free enzyme, the aggregate retained substrate tolerance and the ability for kinetic resolution. This first example of a successful enzymatic PKS domain immobilisation demonstrates that cross-linking can in principle be applied to this type of enzyme to increase its applicability for chemoenzymatic synthesis. Cross-linking of the polyketide synthase domain AmbDH3 led to an active aggregate with improved properties for the chemoenzymatic synthesis of chiral oxygen heterocycles, such as recyclability and facile purification.![]()
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Affiliation(s)
- Lisa Wagner
- Department of Chemistry, Faculty of Biology, Chemistry and Earth Sciences, University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Theresa Roß
- Department of Chemistry, Faculty of Biology, Chemistry and Earth Sciences, University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Tim Hollmann
- Department of Chemistry, Faculty of Biology, Chemistry and Earth Sciences, University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
| | - Frank Hahn
- Department of Chemistry, Faculty of Biology, Chemistry and Earth Sciences, University of Bayreuth Universitätsstraße 30 95447 Bayreuth Germany
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29
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Hirsch M, Kumru K, Desai RR, Fitzgerald BJ, Miyazawa T, Ray KA, Saif N, Spears S, Keatinge-Clay AT. Insights into modular polyketide synthase loops aided by repetitive sequences. Proteins 2021; 89:1099-1110. [PMID: 33843112 DOI: 10.1002/prot.26083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/05/2021] [Accepted: 04/02/2021] [Indexed: 11/08/2022]
Abstract
The loops of modular polyketide synthases (PKSs) serve diverse functions but are largely uncharacterized. They frequently contain amino acid repeats resulting from genetic events such as slipped-strand mispairing. Determining the tolerance of loops to amino acid changes would aid in understanding and engineering these multidomain molecule factories. Here, tandem repeats in the DNA encoding 949 modules within 129 cis-acyltransferase PKSs were cataloged, and the locations of the corresponding amino acids within the module were identified. The most frequently inserted interdomain loop corresponds with the updated module boundary immediately downstream of the ketosynthase (KS), while the loops bordering the dehydratase are nearly intolerant to such insertions. From the 949 modules, no repetitive sequence loop insertions are located within ACP, and only 2 reside within KS, indicating the sensitivity of these domains to alteration.
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Affiliation(s)
- Melissa Hirsch
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - Kaan Kumru
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Ronak R Desai
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Brendan J Fitzgerald
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Takeshi Miyazawa
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Katherine A Ray
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Nisha Saif
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Samantha Spears
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
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30
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A [6+4]-cycloaddition adduct is the biosynthetic intermediate in streptoseomycin biosynthesis. Nat Commun 2021; 12:2092. [PMID: 33828077 PMCID: PMC8027225 DOI: 10.1038/s41467-021-22395-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/10/2021] [Indexed: 12/14/2022] Open
Abstract
Streptoseomycin (STM, 1) is a bacterial macrolactone that has a unique 5/14/10/6/6-pentacyclic ring with an ether bridge. We have previously identified the biosynthetic gene cluster for 1 and characterized StmD as [6 + 4]- and [4 + 2]-bispericyclase that catalyze a reaction leading to both 6/10/6- and 10/6/6-tricyclic adducts (6 and 7). The remaining steps, especially how to install and stabilize the required 10/6/6-tricyclic core for downstream modifications, remain unknown. In this work, we have identified three oxidoreductases that fix the required 10/6/6-tryciclic core. A pair of flavin-dependent oxidoreductases, StmO1 and StmO2, catalyze the direct hydroxylation at [6 + 4]-adduct (6). Subsequently, a spontaneous [3,3]-Cope rearrangement and an enol-ketone tautomerization result in the formation of 10/6/6-tricyclic intermediate 12b, which can be further converted to a stable 10/6/6-tricyclic alcohol 11 through a ketoreduction by StmK. Crystal structure of the heterodimeric complex NtfO1-NtfO2, homologues of StmO1-StmO2 with equivalent function, reveals protein-protein interactions. Our results demonstrate that the [6 + 4]-adduct instead of [4 + 2]-adduct is the bona fide biosynthetic intermediate.
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31
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Abt K, Castelo-Branco R, Leão PN. Biosynthesis of Chlorinated Lactylates in Sphaerospermopsis sp. LEGE 00249. JOURNAL OF NATURAL PRODUCTS 2021; 84:278-286. [PMID: 33444023 PMCID: PMC7923214 DOI: 10.1021/acs.jnatprod.0c00950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Indexed: 05/14/2023]
Abstract
Lactylates are an important group of molecules in the food and cosmetic industries. A series of natural halogenated 1-lactylates, chlorosphaerolactylates (1-4), were recently reported from Sphaerospermopsis sp. LEGE 00249. Here, we identify the cly biosynthetic gene cluster, containing all the necessary functionalities for the biosynthesis of the natural lactylates, based on in silico analyses. Using a combination of stable isotope incorporation experiments and bioinformatic analysis, we propose that dodecanoic acid and pyruvate are the key building blocks in the biosynthesis of 1-4. We additionally report minor analogues of these molecules with varying alkyl chains. This work paves the way to accessing industrially relevant lactylates through pathway engineering.
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Affiliation(s)
- Kathleen Abt
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
- Institute
of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Raquel Castelo-Branco
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
| | - Pedro N. Leão
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
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32
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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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33
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Grabowska AD, Brison Y, Maveyraud L, Gavalda S, Faille A, Nahoum V, Bon C, Guilhot C, Pedelacq JD, Chalut C, Mourey L. Molecular Basis for Extender Unit Specificity of Mycobacterial Polyketide Synthases. ACS Chem Biol 2020; 15:3206-3216. [PMID: 33237724 DOI: 10.1021/acschembio.0c00772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mycobacterium tuberculosis is the causative agent of the tuberculosis disease, which claims more human lives each year than any other bacterial pathogen. M. tuberculosis and other mycobacterial pathogens have developed a range of unique features that enhance their virulence and promote their survival in the human host. Among these features lies the particular cell envelope with high lipid content, which plays a substantial role in mycobacterial pathogenicity. Several envelope components of M. tuberculosis and other mycobacteria, e.g., mycolic acids, phthiocerol dimycocerosates, and phenolic glycolipids, belong to the "family" of polyketides, secondary metabolites synthesized by fascinating versatile enzymes-polyketide synthases. These megasynthases consist of multiple catalytic domains, among which the acyltransferase domain plays a key role in selecting and transferring the substrates required for polyketide extension. Here, we present three new crystal structures of acyltransferase domains of mycobacterial polyketide synthases and, for one of them, provide evidence for the identification of residues determining extender unit specificity. Unravelling the molecular basis for such specificity is of high importance considering the role played by extender units for the final structure of key mycobacterial components. This work provides major advances for the use of mycobacterial polyketide synthases as potential therapeutic targets and, more generally, contributes to the prediction and bioengineering of polyketide synthases with desired specificity.
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Affiliation(s)
- Anna D. Grabowska
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
| | - Yoann Brison
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
| | - Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
| | - Sabine Gavalda
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
| | - Alexandre Faille
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
| | - Virginie Nahoum
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
| | - Cécile Bon
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
| | - Christophe Guilhot
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
| | - Jean-Denis Pedelacq
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
| | - Christian Chalut
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France
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34
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Torres JP, Lin Z, Winter JM, Krug PJ, Schmidt EW. Animal biosynthesis of complex polyketides in a photosynthetic partnership. Nat Commun 2020; 11:2882. [PMID: 32513940 PMCID: PMC7280274 DOI: 10.1038/s41467-020-16376-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/29/2020] [Indexed: 11/09/2022] Open
Abstract
Complex polyketides are typically associated with microbial metabolism. Here, we report that animals also make complex, microbe-like polyketides. We show there is a widespread branch of fatty acid synthase- (FAS)-like polyketide synthase (PKS) proteins, which sacoglossan animals use to synthesize complex products. The purified sacogolassan protein EcPKS1 uses only methylmalonyl-CoA as a substrate, otherwise unknown in animal lipid metabolism. Sacoglossans are sea slugs, some of which eat algae, digesting the cells but maintaining functional chloroplasts. Here, we provide evidence that polyketides support this unusual photosynthetic partnership. The FAS-like PKS family represents an uncharacterized branch of polyketide and fatty acid metabolism, encoding a large diversity of biomedically relevant animal enzymes and chemicals awaiting discovery. The biochemical characterization of an intact animal polyketide biosynthetic enzyme opens the door to understanding the immense untapped metabolic potential of metazoans. Complex polyketides are usually produced by microbes, whereas the origin of polyketides found in animals remained unknown. This study shows that sacoglossan animals, such as sea slugs, employ fatty acid synthase-like proteins to produce microbe-like polyketides.
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Affiliation(s)
- Joshua P Torres
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Jaclyn M Winter
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Patrick J Krug
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA.
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35
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Hashimoto T, Kozone I, Hashimoto J, Suenaga H, Fujie M, Satoh N, Ikeda H, Shin-Ya K. Identification, cloning and heterologous expression of biosynthetic gene cluster for desertomycin. J Antibiot (Tokyo) 2020; 73:650-654. [PMID: 32457441 DOI: 10.1038/s41429-020-0319-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/22/2020] [Accepted: 05/01/2020] [Indexed: 01/23/2023]
Abstract
From our in-house microbial genome database of secondary metabolite producers, we identified a candidate biosynthetic gene cluster for desertomycin from Streptomyces nobilis JCM4274. We report herein the cloning of the 127-kb entire gene cluster for desertomycin biosynthesis using bacterial artificial chromosome vector. The entire biosynthetic gene cluster for desertomycin was introduced in the heterologous host, Streptomyces lividans TK23, with an average yield of more than 130 mg l-1.
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Affiliation(s)
- Takuya Hashimoto
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan. .,The Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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36
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Curran SC, Pereira JH, Baluyot MJ, Lake J, Puetz H, Rosenburg DJ, Adams P, Keasling JD. Structure and Function of BorB, the Type II Thioesterase from the Borrelidin Biosynthetic Gene Cluster. Biochemistry 2020; 59:1630-1639. [PMID: 32250597 DOI: 10.1021/acs.biochem.0c00126] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
α/β hydrolases make up a large and diverse protein superfamily. In natural product biosynthesis, cis-acting thioesterase α/β hydrolases can terminate biosynthetic assembly lines and release products by hydrolyzing or cyclizing the biosynthetic intermediate. Thioesterases can also act in trans, removing aberrant intermediates and restarting stalled biosynthesis. Knockout of this "editing" function leads to reduced product titers. The borrelidin biosynthetic gene cluster from Streptomyces parvulus Tü4055 contains a hitherto uncharacterized stand-alone thioesterase, borB. In this work, we demonstrate that purified BorB cleaves acyl substrates with a preference for propionate, which supports the hypothesis that it is also an editing thioesterase. The crystal structure of BorB shows a wedgelike hydrophobic substrate binding crevice that limits substrate length. To investigate the structure-function relationship, we made chimeric BorB variants using loop regions from characterized homologues with different specificities. BorB chimeras slightly reduced activity, arguing that the modified region is a not major determinant of substrate preference. The structure-function relationships described here contribute to the process of elimination for understanding thioesterase specificity and, ultimately, engineering and applying trans-acting thioesterases in biosynthetic assembly lines.
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Affiliation(s)
- Samuel C Curran
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Jose H Pereira
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Marian-Joy Baluyot
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Julie Lake
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Hendrik Puetz
- Department of Biochemistry, University of Cologne, 50923 Albertus-Magnus-Platz, Cologne 51149, Germany.,Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | | | - Paul Adams
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Jay D Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
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37
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An in vitro platform for engineering and harnessing modular polyketide synthases. Nat Commun 2020; 11:80. [PMID: 31900404 PMCID: PMC6941969 DOI: 10.1038/s41467-019-13811-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/21/2019] [Indexed: 11/15/2022] Open
Abstract
To harness the synthetic power of modular polyketide synthases (PKSs), many aspects of their biochemistry must be elucidated. A robust platform to study these megadalton assembly lines has not yet been described. Here, we in vitro reconstitute the venemycin PKS, a short assembly line that generates an aromatic product. Incubating its polypeptides, VemG and VemH, with 3,5-dihydroxybenzoic acid, ATP, malonate, coenzyme A, and the malonyl-CoA ligase MatB, venemycin production can be monitored by HPLC and NMR. Multi-milligram quantities of venemycin are isolable from dialysis-based reactors without chromatography, and the enzymes can be recycled. Assembly line engineering is performed using pikromycin modules, with synthases designed using the updated module boundaries outperforming those using the traditional module boundaries by over an order of magnitude. Using combinations of VemG, VemH, and their engineered derivatives, as well as the alternate starter unit 3-hydroxybenzoic acid, a combinatorial library of six polyketide products is readily accessed. A robust platform to study modular polyketide synthases (PKSs) in vitro is still unavailable. Here, the authors report the reconstitution of the venemycin PKS, engineer hybrid venemycin/pikromycin PKSs, and obtain much improved yields through employing the updated module boundaries.
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Nivina A, Yuet KP, Hsu J, Khosla C. Evolution and Diversity of Assembly-Line Polyketide Synthases. Chem Rev 2019; 119:12524-12547. [PMID: 31838842 PMCID: PMC6935866 DOI: 10.1021/acs.chemrev.9b00525] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Indexed: 12/11/2022]
Abstract
Assembly-line polyketide synthases (PKSs) are among the most complex protein machineries known in nature, responsible for the biosynthesis of numerous compounds used in the clinic. Their present-day diversity is the result of an evolutionary path that has involved the emergence of a multimodular architecture and further diversification of assembly-line PKSs. In this review, we provide an overview of previous studies that investigated PKS evolution and propose a model that challenges the currently prevailing view that gene duplication has played a major role in the emergence of multimodularity. We also analyze the ensemble of orphan PKS clusters sequenced so far to evaluate how large the entire diversity of assembly-line PKS clusters and their chemical products could be. Finally, we examine the existing techniques to access the natural PKS diversity in natural and heterologous hosts and describe approaches to further expand this diversity through engineering.
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Affiliation(s)
- Aleksandra Nivina
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
| | - Kai P. Yuet
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
| | - Jake Hsu
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
| | - Chaitan Khosla
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford
University, Stanford, California 94305, United States
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Zhang Z, Cepeda AJ, Robles ML, Hirsch M, Kumru K, Zhou JA, Keatinge-Clay AT. General chemoenzymatic route to two-stereocenter triketides employing assembly line ketoreductases. Chem Commun (Camb) 2019; 56:157-160. [PMID: 31799975 DOI: 10.1039/c9cc07966a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modular polyketide synthases (PKSs) are enzymatic assembly lines that fuse carbon fragments into complex chiral products. Here, their synthetic logic is employed to chemoenzymatically generate two-stereocenter triketides. Each of the four stereoisomers was constructed in a stereocontrolled manner using C-acylation and two PKS ketoreductases possessing opposite stereoselectivities.
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Affiliation(s)
- Zhicheng Zhang
- Department of Chemistry, The University of Texas at Austin, 100 E. 24th St., Austin, TX 78712, USA
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Peng H, Ishida K, Hertweck C. Loss of Single-Domain Function in a Modular Assembly Line Alters the Size and Shape of a Complex Polyketide. Angew Chem Int Ed Engl 2019; 58:18252-18256. [PMID: 31595618 PMCID: PMC6916388 DOI: 10.1002/anie.201911315] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Indexed: 12/14/2022]
Abstract
The structural wealth of complex polyketide metabolites produced by bacteria results from intricate, highly evolved biosynthetic programs of modular assembly lines, in which the number of modules defines the size of the backbone, and the domain composition controls the degree of functionalization. We report a remarkable case where polyketide chain length and scaffold depend on the function of a single β-keto processing domain: A ketoreductase domain represents a switch between diverging biosynthetic pathways leading either to the antifungal aureothin or to the nematicidal luteoreticulin. By a combination of heterologous expression, mutagenesis, metabolite analyses, and in vitro biotransformation we elucidate the factors governing non-colinear polyketide assembly involving module skipping and demonstrate that a simple point mutation in type I polyketide synthase (PKS) can have a dramatic effect on the metabolic profile. This finding sheds new light on possible evolutionary scenarios and may inspire future synthetic biology approaches.
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Affiliation(s)
- Huiyun Peng
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstrasse 11a07745JenaGermany
| | - Keishi Ishida
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstrasse 11a07745JenaGermany
| | - Christian Hertweck
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstrasse 11a07745JenaGermany
- Faculty of Biological SciencesChair for Natural Product ChemistryFriedrich Schiller University Jena07743JenaGermany
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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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Kawasaki D, Miyanaga A, Chisuga T, Kudo F, Eguchi T. Functional and Structural Analyses of the Split-Dehydratase Domain in the Biosynthesis of Macrolactam Polyketide Cremimycin. Biochemistry 2019; 58:4799-4803. [DOI: 10.1021/acs.biochem.9b00897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daisuke Kawasaki
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Taichi Chisuga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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Peng H, Ishida K, Hertweck C. Loss of Single‐Domain Function in a Modular Assembly Line Alters the Size and Shape of a Complex Polyketide. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Huiyun Peng
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Keishi Ishida
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Christian Hertweck
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
- Faculty of Biological SciencesChair for Natural Product ChemistryFriedrich Schiller University Jena 07743 Jena Germany
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Meinke JL, Simon AJ, Wagner DT, Morrow BR, You S, Ellington AD, Keatinge-Clay AT. Employing 25-Residue Docking Motifs from Modular Polyketide Synthases as Orthogonal Protein Connectors. ACS Synth Biol 2019; 8:2017-2024. [PMID: 31469555 DOI: 10.1021/acssynbio.9b00047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The proteins of trans-acyltransferase modular polyketide synthases (PKSs) self-organize into assembly lines, enabling the multienzyme biosynthesis of complex organic molecules. Docking domains comprised of ∼25 residues at the C- and N-termini of these polypeptides (CDDs and NDDs) help drive this association through the formation of four-helix bundles. Molecular connectors like these are desired in synthetic contexts, such as artificial biocatalytic systems and biomaterials, to orthogonally join proteins. Here, the ability of six CDD/NDD pairs to link non-PKS proteins is examined using green fluorescent protein (GFP) variants. As observed through size-exclusion chromatography and Förster resonance energy transfer (FRET), matched but not mismatched pairs of Venus+CDD and NDD+mTurquoise2 fusion proteins associate with low micromolar affinities.
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Liao J, Pang K, Sun G, Pai T, Hsu P, Lin J, Sun K, Hsieh C, Tang S. Chimeric 6-methylsalicylic acid synthase with domains of acyl carrier protein and methyltransferase from Pseudallescheria boydii shows novel biosynthetic activity. Microb Biotechnol 2019; 12:920-931. [PMID: 31199579 PMCID: PMC6681407 DOI: 10.1111/1751-7915.13445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/06/2019] [Accepted: 05/17/2019] [Indexed: 01/09/2023] Open
Abstract
Polyketides are important secondary metabolites, many of which exhibit potent pharmacological applications. Biosynthesis of polyketides is carried out by a single polyketide synthase (PKS) or multiple PKSs in successive elongations of enzyme-bound intermediates related to fatty acid biosynthesis. The polyketide gene PKS306 from Pseudallescheria boydii NTOU2362 containing domains of ketosynthase (KS), acyltransferase (AT), dehydratase (DH), acyl carrier protein (ACP) and methyltransferase (MT) was cloned in an attempt to produce novel chemical compounds, and this PKS harbouring green fluorescent protein (GFP) was expressed in Saccharomyces cerevisiae. Although fluorescence of GFP and fusion protein analysed by anti-GFP antibody were observed, no novel compound was detected. 6-methylsalicylic acid synthase (6MSAS) was then used as a template and engineered with PKS306 by combinatorial fusion. The chimeric PKS containing domains of KS, AT, DH and ketoreductase (KR) from 6MSAS with ACP and MT from PKS306 demonstrated biosynthesis of a novel compound. The compound was identified with a deduced chemical formula of C7 H10 O3 , and the chemical structure was named as 2-hydroxy-2-(propan-2-yl) cyclobutane-1,3-dione. The novel compound synthesized by the chimeric PKS in this study demonstrates the feasibility of combinatorial fusion of PKS genes to produce novel polyketides.
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Affiliation(s)
- Ji‐Long Liao
- Department of Bioscience and BiotechnologyCenter of Excellence for the OceansNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
| | - Ka‐Lai Pang
- Department of Marine BiologyCenter of Excellence for the OceansNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
| | - Guang‐Huan Sun
- Division of UrologyDepartment of SurgeryNational Defense Medical CenterTri‐Service General HospitalNo. 325, Sec. 2, Cheng‐gong Rd.TaipeiTaiwan
| | - Tun‐Wen Pai
- Department of Computer Science and EngineeringNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
| | - Pang‐Hung Hsu
- Department of Bioscience and BiotechnologyCenter of Excellence for the OceansNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
| | - Jyuan‐Siou Lin
- Department of Bioscience and BiotechnologyCenter of Excellence for the OceansNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
| | - Kuang‐Hui Sun
- Department of Biotechnology and Laboratory Science in MedicineNational Yang‐Ming UniversityNo. 155, Sec. 2, Linong StreetTaipeiTaiwan
- Department of Education and ResearchTaipei City HospitalTaipeiTaiwan
| | | | - Shye‐Jye Tang
- Department of Bioscience and BiotechnologyCenter of Excellence for the OceansNational Taiwan Ocean UniversityNo. 2 Pei‐Ning RoadKeelung20224Taiwan
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Kornfuehrer T, Eustáquio AS. Diversification of polyketide structures via synthase engineering. MEDCHEMCOMM 2019; 10:1256-1272. [PMID: 32180918 PMCID: PMC7053703 DOI: 10.1039/c9md00141g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/09/2019] [Indexed: 12/16/2022]
Abstract
Polyketide natural products possess diverse biological activities including antibiotic, anticancer, and immunosuppressive. Their equally varied and complex structures arise from head-to-tail condensation of simple carboxyacyl monomers. Since the seminal discovery that biosynthesis of polyketides such as the macrolide erythromycin is catalyzed by uncharacteristically large, multifunctional enzymes, termed modular type I polyketide synthases, chemists and biologists alike have been inspired to harness the apparent modularity of the synthases to further diversify polyketide structures. Yet, initial attempts to perform "combinatorial biosynthesis" failed due to challenges associated with maintaining the structural and catalytic integrity of large, chimeric synthases. Fast forward nearly 30 years, and advancements in our understanding of polyketide synthase structure and function have allowed the field to make significant progress toward effecting desired modifications to polyketide scaffolds in addition to engineering small, chiral fragments. This review highlights selected examples of polyketide diversification via control of monomer selection, oxidation state, stereochemistry, and cyclization. We conclude with a perspective on the present and future of polyketide structure diversification and hope that the examples presented here will encourage medicinal chemists to embrace polyketide synthetic biology as a means to revitalize polyketide drug discovery.
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Affiliation(s)
- Taylor Kornfuehrer
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences , College of Pharmacy , University of Illinois at Chicago , Chicago , Illinois 60607 , USA . ; Tel: +1 3124137082
| | - Alessandra S Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences , College of Pharmacy , University of Illinois at Chicago , Chicago , Illinois 60607 , USA . ; Tel: +1 3124137082
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Abstract
Stereospecific generation of α-amino ketones from common α-amino acids is difficult to achieve, often employing superstoichiometric alkylating reagents and requiring multiple protecting group manipulations. In contrast, the α-oxoamine synthase protein family performs this transformation stereospecifically in a single step without the need for protecting groups. Herein, we detail the characterization of the 8-amino-7-oxononanoate synthase (AONS) domain of the four-domain polyketide-like synthase SxtA, which natively mediates the formation of the ethyl ketone derivative of arginine. The function of each of the four domains is elucidated, leading to a revised proposal for the initiation of saxitoxin biosynthesis, a potent neurotoxin. We also demonstrate the synthetic potential of SxtA AONS, which is applied to the synthesis of a panel of novel α-amino ketones.
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Affiliation(s)
- Stephanie W Chun
- Department of Chemistry, University of Michigan, 930 North University Ave, Ann Arbor, MI 48109-1055, USA
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave, Ann Arbor, MI 48109-2216, USA
| | - Alison R H Narayan
- Department of Chemistry, University of Michigan, 930 North University Ave, Ann Arbor, MI 48109-1055, USA
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave, Ann Arbor, MI 48109-2216, USA
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Abstract
Bacterial natural products display astounding structural diversity, which, in turn, endows them with a remarkable range of biological activities that are of significant value to modern society. Such structural features are generated by biosynthetic enzymes that construct core scaffolds or perform peripheral modifications, and can thus define natural product families, introduce pharmacophores and permit metabolic diversification. Modern genomics approaches have greatly enhanced our ability to access and characterize natural product pathways via sequence-similarity-based bioinformatics discovery strategies. However, many biosynthetic enzymes catalyse exceptional, unprecedented transformations that continue to defy functional prediction and remain hidden from us in bacterial (meta)genomic sequence data. In this Review, we highlight exciting examples of unusual enzymology that have been uncovered recently in the context of natural product biosynthesis. These suggest that much of the natural product diversity, including entire substance classes, awaits discovery. New approaches to lift the veil on the cryptic chemistries of the natural product universe are also discussed.
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Tolmie C, Smit MS, Opperman DJ. Native roles of Baeyer–Villiger monooxygenases in the microbial metabolism of natural compounds. Nat Prod Rep 2019; 36:326-353. [DOI: 10.1039/c8np00054a] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Baeyer–Villiger monooxygenases function in the primary metabolism of atypical carbon sources, as well as the synthesis of complex microbial metabolites.
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Affiliation(s)
- Carmien Tolmie
- Department of Biotechnology
- University of the Free State
- Bloemfontein
- South Africa
| | - Martha S. Smit
- Department of Biotechnology
- University of the Free State
- Bloemfontein
- South Africa
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50
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Abstract
Enzymes that catalyze a Michael-type addition in polyketide biosynthesis are summarized and discussed.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
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