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Kries H, Trottmann F, Hertweck C. Novel Biocatalysts from Specialized Metabolism. Angew Chem Int Ed Engl 2024; 63:e202309284. [PMID: 37737720 DOI: 10.1002/anie.202309284] [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: 06/30/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/23/2023]
Abstract
Enzymes are increasingly recognized as valuable (bio)catalysts that complement existing synthetic methods. However, the range of biotransformations used in the laboratory is limited. Here we give an overview on the biosynthesis-inspired discovery of novel biocatalysts that address various synthetic challenges. Prominent examples from this dynamic field highlight remarkable enzymes for protecting-group-free amide formation and modification, control of pericyclic reactions, stereoselective hetero- and polycyclizations, atroposelective aryl couplings, site-selective C-H activations, introduction of ring strain, and N-N bond formation. We also explore unusual functions of cytochrome P450 monooxygenases, radical SAM-dependent enzymes, flavoproteins, and enzymes recruited from primary metabolism, which offer opportunities for synthetic biology, enzyme engineering, directed evolution, and catalyst design.
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Affiliation(s)
- Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Department of Chemistry, University of Bayreuth, Universitätsstr. 30, 95440, Bayreuth, Germany
| | - Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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2
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Dunbar KL, Dell M, Molloy EM, Kloss F, Hertweck C. Reconstitution of Iterative Thioamidation in Closthioamide Biosynthesis Reveals Tailoring Strategy for Nonribosomal Peptide Backbones. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kyle L. Dunbar
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Evelyn M. Molloy
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Florian Kloss
- Transfer Group Antiinfectives Leibniz Institute for Natural Product Research and Infection Biology HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
- Chair of Natural Product Chemistry Friedrich Schiller University Jena 07743 Jena Germany
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3
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Dunbar KL, Dell M, Molloy EM, Kloss F, Hertweck C. Reconstitution of Iterative Thioamidation in Closthioamide Biosynthesis Reveals Tailoring Strategy for Nonribosomal Peptide Backbones. Angew Chem Int Ed Engl 2019; 58:13014-13018. [PMID: 31276268 PMCID: PMC6772006 DOI: 10.1002/anie.201905992] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Indexed: 12/31/2022]
Abstract
Thioamide‐containing nonribosomal peptides (NRPs) are exceedingly rare. Recently the biosynthetic gene cluster for the thioamidated NRP antibiotic closthioamide (CTA) was reported, however, the enzyme responsible for and the timing of thioamide formation remained enigmatic. Here, genome editing, biochemical assays, and mutational studies are used to demonstrate that an Fe‐S cluster containing member of the adenine nucleotide α‐hydrolase protein superfamily (CtaC) is responsible for sulfur incorporation during CTA biosynthesis. However, unlike all previously characterized members, CtaC functions in a thiotemplated manner. In addition to prompting a revision of the CTA biosynthetic pathway, the reconstitution of CtaC provides the first example of a NRP thioamide synthetase. Finally, CtaC is used as a bioinformatic handle to demonstrate that thioamidated NRP biosynthetic gene clusters are more widespread than previously appreciated.
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Affiliation(s)
- Kyle L Dunbar
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Evelyn M Molloy
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Florian Kloss
- Transfer Group Antiinfectives, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Chair of Natural Product Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
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Dunbar KL, Büttner H, Molloy EM, Dell M, Kumpfmüller J, Hertweck C. Genome Editing Reveals Novel Thiotemplated Assembly of Polythioamide Antibiotics in Anaerobic Bacteria. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807970] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kyle L. Dunbar
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Hannah Büttner
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Evelyn M. Molloy
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry; Leibniz Institute for Natural Product Research and Infection Biology, HKI; Beutenbergstrasse 11a 07745 Jena Germany
- Natural Product Chemistry; Friedrich Schiller University; 07743 Jena Germany
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Dunbar KL, Büttner H, Molloy EM, Dell M, Kumpfmüller J, Hertweck C. Genome Editing Reveals Novel Thiotemplated Assembly of Polythioamide Antibiotics in Anaerobic Bacteria. Angew Chem Int Ed Engl 2018; 57:14080-14084. [PMID: 30193003 DOI: 10.1002/anie.201807970] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/23/2018] [Indexed: 12/18/2022]
Abstract
Closthioamide (CTA) is a unique symmetric nonribosomal peptide with six thioamide moieties that is produced by the Gram-positive obligate anaerobe Ruminiclostridium cellulolyticum. CTA displays potent inhibitory activity against important clinical pathogens, making it a promising drug candidate. Yet, the biosynthesis of this DNA gyrase-targeting antibiotic has remained enigmatic. Using a combination of genome mining, genome editing (targeted group II intron, CRISPR/Cas9), and heterologous expression, we show that CTA biosynthesis involves specialized enzymes for starter unit biosynthesis, amide bond formation, thionation, and dimerization. Surprisingly, CTA biosynthesis involves a novel thiotemplated peptide assembly line that markedly differs from known nonribosomal peptide synthetases. These findings provide the first insights into the biosynthesis of thioamide-containing nonribosomal peptides and offer a starting point for the discovery of related natural products.
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Affiliation(s)
- Kyle L Dunbar
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Hannah Büttner
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Evelyn M Molloy
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Natural Product Chemistry, Friedrich Schiller University, 07743, Jena, Germany
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Litomska A, Ishida K, Dunbar KL, Boettger M, Coyne S, Hertweck C. Enzymatic Thioamide Formation in a Bacterial Antimetabolite Pathway. Angew Chem Int Ed Engl 2018; 57:11574-11578. [DOI: 10.1002/anie.201804158] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 06/13/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Agnieszka Litomska
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Keishi Ishida
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Kyle L. Dunbar
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Marco Boettger
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Sébastien Coyne
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Christian Hertweck
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
- Faculty of Biological SciencesFriedrich Schiller University Jena 07743 Jena Germany
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Litomska A, Ishida K, Dunbar KL, Boettger M, Coyne S, Hertweck C. Enzymatic Thioamide Formation in a Bacterial Antimetabolite Pathway. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Agnieszka Litomska
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
| | - Kyle L. Dunbar
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
| | - Marco Boettger
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
| | - Sébastien Coyne
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
- Faculty of Biological Sciences; Friedrich Schiller University Jena; 07743 Jena Germany
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Wang Y, Wang J, Yu S, Wang F, Ma H, Yue C, Liu M, Deng Z, Huang Y, Qu X. Identifying the Minimal Enzymes for Unusual Carbon-Sulfur Bond Formation in Thienodolin Biosynthesis. Chembiochem 2016; 17:799-803. [PMID: 26854280 DOI: 10.1002/cbic.201500670] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 01/26/2023]
Affiliation(s)
- Yaya Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Jiali Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Shuqi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Fan Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Hongmin Ma
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Changwu Yue
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences, 1 Beichen West Road; Beijing 100101 China
- Guizhou Key Laboratory of Microbial Resources and Drug Development; Zunyi Medical College, 201 Dalian Road; Zunyi 563003 China
| | - Minghao Liu
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences, 1 Beichen West Road; Beijing 100101 China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Ying Huang
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences, 1 Beichen West Road; Beijing 100101 China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
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Baunach M, Ding L, Willing K, Hertweck C. Bacterial Synthesis of Unusual Sulfonamide and Sulfone Antibiotics by Flavoenzyme‐Mediated Sulfur Dioxide Capture. Angew Chem Int Ed Engl 2015; 54:13279-83. [DOI: 10.1002/anie.201506541] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/24/2015] [Indexed: 01/29/2023]
Affiliation(s)
- Martin Baunach
- Department of Biomolecular Chemistry, and Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena (Germany)
| | - Ling Ding
- Department of Biomolecular Chemistry, and Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena (Germany)
| | - Karsten Willing
- Department of Biomolecular Chemistry, and Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena (Germany)
| | - Christian Hertweck
- Department of Biomolecular Chemistry, and Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena (Germany)
- Chair for Natural Product Chemistry, Friedrich Schiller University, Jena (Germany)
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Baunach M, Ding L, Willing K, Hertweck C. Bacterial Synthesis of Unusual Sulfonamide and Sulfone Antibiotics by Flavoenzyme‐Mediated Sulfur Dioxide Capture. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506541] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Martin Baunach
- Department of Biomolecular Chemistry, and Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena (Germany)
| | - Ling Ding
- Department of Biomolecular Chemistry, and Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena (Germany)
| | - Karsten Willing
- Department of Biomolecular Chemistry, and Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena (Germany)
| | - Christian Hertweck
- Department of Biomolecular Chemistry, and Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena (Germany)
- Chair for Natural Product Chemistry, Friedrich Schiller University, Jena (Germany)
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Xie Y, Li Q, Song Y, Ma J, Ju J. Involvement of SgvP in Carbon-Sulfur Bond Formation during Griseoviridin Biosynthesis. Chembiochem 2014; 15:1183-9. [DOI: 10.1002/cbic.201400062] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Indexed: 01/26/2023]
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Coyne S, Litomska A, Chizzali C, Khalil MNA, Richter K, Beerhues L, Hertweck C. Control of Plant Defense Mechanisms and Fire Blight Pathogenesis through the Regulation of 6-Thioguanine Biosynthesis inErwinia amylovora. Chembiochem 2014; 15:373-6. [DOI: 10.1002/cbic.201300684] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Indexed: 01/20/2023]
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