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Di X, Li P, Xiahou Y, Wei H, Zhi S, Liu L. Recent Advances in Discovery, Structure, Bioactivity, and Biosynthesis of trans-AT Polyketides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:21318-21343. [PMID: 39302874 DOI: 10.1021/acs.jafc.4c03750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are among the most complex enzymes, which are responsible for generating a wide range of natural products, identified as trans-AT polyketides. These polyketides have received significant attention in drug development due to their structural diversity and potent bioactivities. With approximately 300 synthesized molecules discovered so far, trans-AT PKSs are found widespread in bacteria. Their biosynthesis pathways exhibit considerable genetic diversity, leading to the emergence of numerous enzymes with novel mechanisms, serving as a valuable resource for genetic engineering aimed at modifying small molecules' structures and creating new engineered enzymes. Despite the systematic discussions on trans-AT polyketides and their biosynthesis in earlier studies, the continuous advancements in tools, methods, compound identification, and biosynthetic pathways require a fresh update on accumulated knowledge. This review seeks to provide a comprehensive discussion for the 27 types of trans-AT polyketides discovered within the last seven years, detailing their sources, structures, biological activities, and biosynthetic pathways. By reviewing this new knowledge, a more profound understanding of the trans-AT polyketide family can be achieved.
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Affiliation(s)
- Xue Di
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
- College of Food Science and Engineering, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Peng Li
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
- College of Food Science and Engineering, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Yinuo Xiahou
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
- College of Food Science and Engineering, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Huamao Wei
- College of Food Science and Engineering, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Shuai Zhi
- School of Public Health, Ningbo University, Ningbo, Zhejiang 315000, China
| | - Liwei Liu
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
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2
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Scat S, Weissman KJ, Chagot B. Insights into docking in megasynthases from the investigation of the toblerol trans-AT polyketide synthase: many α-helical means to an end. RSC Chem Biol 2024; 5:669-683. [PMID: 38966669 PMCID: PMC11221535 DOI: 10.1039/d4cb00075g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/16/2024] [Indexed: 07/06/2024] Open
Abstract
The fidelity of biosynthesis by modular polyketide synthases (PKSs) depends on specific moderate affinity interactions between successive polypeptide subunits mediated by docking domains (DDs). These sequence elements are notably portable, allowing their transplantation into alternative biosynthetic and metabolic contexts. Herein, we use integrative structural biology to characterize a pair of DDs from the toblerol trans-AT PKS. Both are intrinsically disordered regions (IDRs) that fold into a 3 α-helix docking complex of unprecedented topology. The C-terminal docking domain (CDD) resembles the 4 α-helix type (4HB) CDDs, which shows that the same type of DD can be redeployed to form complexes of distinct geometry. By carefully re-examining known DD structures, we further extend this observation to type 2 docking domains, establishing previously unsuspected structural relations between DD types. Taken together, these data illustrate the plasticity of α-helical DDs, which allow the formation of a diverse topological spectrum of docked complexes. The newly identified DDs should also find utility in modular PKS genetic engineering.
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Affiliation(s)
- Serge Scat
- Université de Lorraine, CNRS, IMoPA F-54000 Nancy France
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3
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Little RF, Trottmann F, Hashizume H, Preissler M, Unger S, Sawa R, Kries H, Pidot S, Igarashi M, Hertweck C. Analysis of the Valgamicin Biosynthetic Pathway Reveals a General Mechanism for Cyclopropanol Formation across Diverse Natural Product Scaffolds. ACS Chem Biol 2024; 19:660-668. [PMID: 38358369 DOI: 10.1021/acschembio.3c00648] [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: 02/16/2024]
Abstract
Cyclopropanol rings are highly reactive and may function as molecular "warheads" that affect natural product bioactivity. Yet, knowledge on their biosynthesis is limited. Using gene cluster analyses, isotope labeling, and in vitro enzyme assays, we shed first light on the biosynthesis of the cyclopropanol-substituted amino acid cleonine, a residue in the antimicrobial depsipeptide valgamicin C and the cytotoxic glycopeptide cleomycin A2. We decipher the biosynthetic origin of valgamicin C and show that the cleonine cyclopropanol ring is derived from dimethylsulfoniopropionate (DMSP). Furthermore, we demonstrate that part of the biosynthesis is analogous to the formation of malleicyprol polyketides in pathogenic bacteria. By genome mining and metabolic profiling, we identify the potential to produce cyclopropanol rings in other bacterial species. Our results reveal a general mechanism for cyclopropyl alcohol biosynthesis across diverse natural products that may be harnessed for bioengineering and drug discovery.
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Affiliation(s)
- Rory F Little
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Hideki Hashizume
- Laboratory of Microbiology, Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Miriam Preissler
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Sandra Unger
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Ryuichi Sawa
- Laboratory of Molecular Structure Analysis, Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Hajo Kries
- Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Sacha Pidot
- Department of Microbiology and Immunology, Doherty Institute, 792 Elizabeth Street, Melbourne 3000, Australia
| | - Masayuki Igarashi
- Laboratory of Microbiology, Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
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4
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Mitronova GY, Quentin C, Belov VN, Wegener JW, Kiszka KA, Lehnart SE. 1,4-Benzothiazepines with Cyclopropanol Groups and Their Structural Analogues Exhibit Both RyR2-Stabilizing and SERCA2a-Stimulating Activities. J Med Chem 2023; 66:15761-15775. [PMID: 37991191 PMCID: PMC10726367 DOI: 10.1021/acs.jmedchem.3c01235] [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: 07/07/2023] [Revised: 10/24/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023]
Abstract
To discover new multifunctional agents for the treatment of cardiovascular diseases, we designed and synthesized a series of compounds with a cyclopropyl alcohol moiety and evaluated them in biochemical assays. Biological screening identified derivatives with dual activity: preventing Ca2+ leak through ryanodine receptor 2 (RyR2) and enhancing cardiac sarco-endoplasmic reticulum (SR) Ca2+ load by activation of Ca2+-dependent ATPase 2a (SERCA2a). The compounds that stabilize RyR2 at micro- and nanomolar concentrations are either structurally related to RyR-stabilizing drugs or Rycals or have structures similar to them. The novel compounds also demonstrate a good ability to increase ATP hydrolysis mediated by SERCA2a activity in cardiac microsomes, e.g., the half-maximal effective concentration (EC50) was as low as 383 nM for compound 12a, which is 1,4-benzothiazepine with two cyclopropanol groups. Our findings indicate that these derivatives can be considered as new lead compounds to improve cardiac function in heart failure.
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Affiliation(s)
- Gyuzel Y. Mitronova
- Department
of NanoBiophotonics, Max Planck Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
- German
Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen 37075, Germany
| | - Christine Quentin
- Department
of NanoBiophotonics, Max Planck Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Vladimir N. Belov
- Department
of NanoBiophotonics, Max Planck Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Jörg W. Wegener
- Department
of Cardiology & Pulmonology, Heart Research Center Göttingen, University Medical Center Göttingen, Robert-Koch-Strasse 42a, Göttingen 37075, Germany
- German
Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen 37075, Germany
| | - Kamila A. Kiszka
- Department
of NanoBiophotonics, Max Planck Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Stephan E. Lehnart
- Department
of Cardiology & Pulmonology, Heart Research Center Göttingen, University Medical Center Göttingen, Robert-Koch-Strasse 42a, Göttingen 37075, Germany
- German
Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen 37075, Germany
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5
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Gamit HA, Naik H, Chandarana KA, Chandwani S, Amaresan N. Secondary metabolites from methylotrophic bacteria: their role in improving plant growth under a stressed environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:28563-28574. [PMID: 36710311 DOI: 10.1007/s11356-023-25505-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Climate change is considered a natural disaster that causes the ecosystem to fluctuate and increase temperature, as well as the amount of UV radiation (UV-A and UV-B) on the Earth's surface. Consequently, greenhouse gases such as chlorofluorocarbons, methane, nitrogen oxide, and carbon dioxide have become obstacles to the development of sustainable agriculture. To overcome environmental stress such as phytopathogens, drought, salinity, heavy metals, and high-low temperatures, the utilization of microorganisms is a viable option. The synthesis of secondary metabolites by methylotrophic bacteria improves plant metabolism, enhances tolerance, and facilitates growth. The genus Methylobacterium is a pink-pigmented facultative methylotrophs which abundantly colonizes plants, especially young leaves, owing to the availability of methanol. Secondary metabolites such as amino acids, carotenoids, hormones, antimicrobial compounds, and other compounds produced by methylotrophic bacteria enhance plant metabolism under stress conditions. Therefore, in this review, we discuss the role of secondary metabolites produced by methylotrophic bacteria and their role in promoting plant growth under stress.
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Affiliation(s)
- Harshida A Gamit
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Surat, 394 350, Gujarat, India
| | - Hetvi Naik
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Surat, 394 350, Gujarat, India
| | - Komal A Chandarana
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Surat, 394 350, Gujarat, India
| | - Sapna Chandwani
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Surat, 394 350, Gujarat, India
| | - Natarajan Amaresan
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Surat, 394 350, Gujarat, India.
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6
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Hou A, Dickschat JS. Labelling studies in the biosynthesis of polyketides and non-ribosomal peptides. Nat Prod Rep 2023; 40:470-499. [PMID: 36484402 DOI: 10.1039/d2np00071g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: 2015 to 2022In this review, we discuss the recent advances in the use of isotopically labelled compounds to investigate the biosynthesis of polyketides, non-ribosomally synthesised peptides, and their hybrids. Also, we highlight the use of isotopes in the elucidation of their structures and investigation of enzyme mechanisms. The biosynthetic pathways of selected examples are presented in detail to reveal the principles of the discussed labelling experiments. The presented examples demonstrate that the application of isotopically labelled compounds is still the state of the art and can provide valuable information for the biosynthesis of natural products.
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Affiliation(s)
- Anwei Hou
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, West 7th Avenue No. 32, 300308 Tianjin, China.,Institute of Microbiology, Jiangxi Academy of Sciences, Changdong Road No. 7777, 330096 Nanchang, China
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.
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7
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Gao Q, Xu S. Site- and Stereoselective C(sp 3 )-H Borylation of Strained (Hetero)Cycloalkanols Enabled by Iridium Catalysis. Angew Chem Int Ed Engl 2023; 62:e202218025. [PMID: 36581587 DOI: 10.1002/anie.202218025] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022]
Abstract
Transition metal-catalyzed site- and stereoselective C-H activation of strained (hetero)cycloalkanes remains a formidable challenge. We herein report a carbamate-directed iridium-catalyzed asymmetric β-C(sp3 )-H borylation of cyclopropanol derivatives. A variety of densely functionalized cyclopropanols were obtained in good enantioselectivities via desymmetrization and kinetic resolution. In addition, site-selective C(sp3 )-H borylation of methine groups furnished α-borylated (hetero)cycloalkanols in moderate to good yields. The synthetic utility of the method was further shown in a gram-scale synthesis and diverse downstream transformations of borylated products.
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Affiliation(s)
- Qian Gao
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Senmiao Xu
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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8
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Ueoka R, Sondermann P, Leopold-Messer S, Liu Y, Suo R, Bhushan A, Vadakumchery L, Greczmiel U, Yashiroda Y, Kimura H, Nishimura S, Hoshikawa Y, Yoshida M, Oxenius A, Matsunaga S, Williamson RT, Carreira EM, Piel J. Genome-based discovery and total synthesis of janustatins, potent cytotoxins from a plant-associated bacterium. Nat Chem 2022; 14:1193-1201. [PMID: 36064972 PMCID: PMC7613652 DOI: 10.1038/s41557-022-01020-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 06/29/2022] [Indexed: 11/09/2022]
Abstract
Host-associated bacteria are increasingly being recognized as underexplored sources of bioactive natural products with unprecedented chemical scaffolds. A recently identified example is the plant-root-associated marine bacterium Gynuella sunshinyii of the chemically underexplored order Oceanospirillales. Its genome contains at least 22 biosynthetic gene clusters, suggesting a rich and mostly uncharacterized specialized metabolism. Here, in silico chemical prediction of a non-canonical polyketide synthase cluster has led to the discovery of janustatins, structurally unprecedented polyketide alkaloids with potent cytotoxicity that are produced in minute quantities. A combination of MS and two-dimensional NMR experiments, density functional theory calculations of 13C chemical shifts and semiquantitative interpretation of transverse rotating-frame Overhauser effect spectroscopy data were conducted to determine the relative configuration, which enabled the total synthesis of both enantiomers and assignment of the absolute configuration. Janustatins feature a previously unknown pyridodihydropyranone heterocycle and an unusual biological activity consisting of delayed, synchronized cell death at subnanomolar concentrations.
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Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Philipp Sondermann
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Stefan Leopold-Messer
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
| | - Yizhou Liu
- NMR Structure Elucidation, Process & Analytical Chemistry, Merck & Co. Inc., Rahway, NJ, USA
- Analytical Research & Development, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Rei Suo
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Agneya Bhushan
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
| | - Lida Vadakumchery
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
| | - Ute Greczmiel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
| | - Yoko Yashiroda
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Hiromi Kimura
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Shinichi Nishimura
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Yojiro Hoshikawa
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
| | - Minoru Yoshida
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Annette Oxenius
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - R Thomas Williamson
- NMR Structure Elucidation, Process & Analytical Chemistry, Merck & Co. Inc., Rahway, NJ, USA
- Department of Chemistry & Biochemistry, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Erick M Carreira
- Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland.
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland.
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9
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Pan-genome Analysis Reveals Comparative Genomic Features of Central Metabolic Pathways in Methylorubrum extorquens. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0154-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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10
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Trottmann F, Ishida K, Ishida-Ito M, Kries H, Groll M, Hertweck C. Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead. Nat Chem 2022; 14:884-890. [PMID: 35906404 PMCID: PMC9359912 DOI: 10.1038/s41557-022-01005-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 06/20/2022] [Indexed: 11/09/2022]
Abstract
Bacteria of the Burkholderia pseudomallei (BP) group pose a global health threat, causing the infectious diseases melioidosis, a common cause of pneumonia and sepsis, and glanders, a contagious zoonosis. A trait of BP bacteria is a conserved gene cluster coding for the biosynthesis of polyketides (malleicyprols) with a reactive cyclopropanol unit that is critical for virulence. Enzymes building this warhead represent ideal targets for antivirulence strategies but the biochemical basis of cyclopropanol formation is unknown. Here we describe the formation of the malleicyprol warhead. We show that BurG, an unusual NAD+-dependent member of the ketol-acid reductoisomerase family, constructs the strained cyclopropanol ring. Biochemical assays and a suite of eight crystal structures of native and mutated BurG with bound analogues and inhibitors provide snapshots of each step of the complex reaction mechanism, involving a concealed oxidoreduction and a C-S bond cleavage. Our findings illustrate a remarkable case of neofunctionalisation, where a biocatalyst from central metabolism has been evolutionarily repurposed for warhead production in pathogens.
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Affiliation(s)
- Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany
| | - Mie Ishida-Ito
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany
| | - Michael Groll
- Center for Protein Assemblies, Chemistry Department, Technical University Munich, Garching, Germany.
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (Leibniz-HKI), Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
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11
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Bajpai A, Mahawar H, Dubey G, Atoliya N, Parmar R, Devi MH, Kollah B, Mohanty SR. Prospect of pink pigmented facultative methylotrophs in mitigating abiotic stress and climate change. J Basic Microbiol 2022; 62:889-899. [DOI: 10.1002/jobm.202200087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/03/2022] [Accepted: 03/13/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Apekcha Bajpai
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
- Department of Microbiology Barkatullah University Bhopal India
| | - Himanshu Mahawar
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
- ICAR‐Directorate of Weed Research Jabalpur India
| | - Garima Dubey
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Nagvanti Atoliya
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Rakesh Parmar
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Mayanglambam H. Devi
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Bharati Kollah
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Santosh R. Mohanty
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
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12
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Good NM, Lee HD, Hawker ER, Su MZ, Gilad AA, Martinez-Gomez NC. Hyperaccumulation of Gadolinium by Methylorubrum extorquens AM1 Reveals Impacts of Lanthanides on Cellular Processes Beyond Methylotrophy. Front Microbiol 2022; 13:820327. [PMID: 35369483 PMCID: PMC8969499 DOI: 10.3389/fmicb.2022.820327] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/19/2022] [Indexed: 11/20/2022] Open
Abstract
Lanthanides (Ln) are a new group of life metals, and many questions remain regarding how they are acquired and used in biology. Methylotrophic bacteria can acquire, transport, biomineralize, and use Ln as part of a cofactor complex with pyrroloquinoline quinone (PQQ) in alcohol dehydrogenases. For most methylotrophic bacteria use is restricted to the light Ln, which range from lanthanum to samarium (atomic numbers 57–62). Understanding how the cell differentiates between light and heavy Ln, and the impacts of these metals on the metabolic network, will advance the field of Ln biochemistry and give insights into enzyme catalysis, stress homeostasis, and metal biomineralization and compartmentalization. We report robust methanol growth with the heavy Ln gadolinium by a genetic variant of the model methylotrophic bacterium Methylorubrum extorquens AM1, named evo-HLn, for “evolved for Heavy Lanthanides.” A non-synonymous single nucleotide polymorphism in a cytosolic hybrid histidine kinase/response regulator allowed for sweeping transcriptional alterations to heavy metal stress response, methanol oxidation, and central metabolism. Increased expression of genes for Ln acquisition and uptake, production of the Ln-chelating lanthanophore, PQQ biosynthesis, and phosphate transport and metabolism resulted in gadolinium hyperaccumulation of 36-fold with a trade-off for light Ln accumulation. Gadolinium was hyperaccumulated in an enlarged acidocalcisome-like compartment. This is the first evidence of a bacterial intracellular Ln-containing compartment that we name the “lanthasome.” Carotenoid and toblerol biosynthesis were also upregulated. Due to its unique capabilities, evo-HLn can be used to further magnetic resonance imaging (MRI) and bioremediation technologies. In this regard, we show that gadolinium hyperaccumulation was sufficient to produce MRI contrast in whole cells, and that evo-HLn was able to readily acquire the metal from the MRI contrast agent gadopentetic acid. Finally, hyperaccumulation of gadolinium, differential uptake of light and heavy Ln, increased PQQ levels, and phosphate transport provide new insights into strategies for Ln recovery.
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Affiliation(s)
- Nathan M. Good
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Harvey D. Lee
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States
- Division of Synthetic Biology, The Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, United States
| | - Emily R. Hawker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Morgan Z. Su
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Assaf A. Gilad
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States
- Division of Synthetic Biology, The Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, United States
- Department of Radiology, Michigan State University, East Lansing, MI, United States
| | - N. Cecilia Martinez-Gomez
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: N. Cecilia Martinez-Gomez,
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13
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Ma S, Mandalapu D, Wang S, Zhang Q. Biosynthesis of cyclopropane in natural products. Nat Prod Rep 2021; 39:926-945. [PMID: 34860231 DOI: 10.1039/d1np00065a] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: 2012 to 2021Cyclopropane attracts wide interests in the fields of synthetic and pharmaceutical chemistry, and chemical biology because of its unique structural and chemical properties. This structural motif is widespread in natural products, and is usually essential for biological activities. Nature has evolved diverse strategies to access this structural motif, and increasing knowledge of the enzymes forming cyclopropane (i.e., cyclopropanases) has been revealed over the last two decades. Here, the scientific literature from the last two decades relating to cyclopropane biosynthesis is summarized, and the enzymatic cyclopropanations, according to reaction mechanism, which can be grouped into two major pathways according to whether the reaction involves an exogenous C1 unit from S-adenosylmethionine (SAM) or not, is discussed. The reactions can further be classified based on the key intermediates required prior to cyclopropane formation, which can be carbocations, carbanions, or carbon radicals. Besides the general biosynthetic pathways of the cyclopropane-containing natural products, particular emphasis is placed on the mechanism and engineering of the enzymes required for forming this unique structure motif.
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Affiliation(s)
- Suze Ma
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | | | - Shu Wang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
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14
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Bauman KD, Butler KS, Moore BS, Chekan JR. Genome mining methods to discover bioactive natural products. Nat Prod Rep 2021; 38:2100-2129. [PMID: 34734626 PMCID: PMC8597713 DOI: 10.1039/d1np00032b] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Indexed: 12/22/2022]
Abstract
Covering: 2016 to 2021With genetic information available for hundreds of thousands of organisms in publicly accessible databases, scientists have an unprecedented opportunity to meticulously survey the diversity and inner workings of life. The natural product research community has harnessed this breadth of sequence information to mine microbes, plants, and animals for biosynthetic enzymes capable of producing bioactive compounds. Several orthogonal genome mining strategies have been developed in recent years to target specific chemical features or biological properties of bioactive molecules using biosynthetic, resistance, or transporter proteins. These "biosynthetic hooks" allow researchers to query for biosynthetic gene clusters with a high probability of encoding previously undiscovered, bioactive compounds. This review highlights recent case studies that feature orthogonal approaches that exploit genomic information to specifically discover bioactive natural products and their gene clusters.
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Affiliation(s)
- Katherine D Bauman
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Keelie S Butler
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, 27402, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, 27402, USA.
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15
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Scherlach K, Hertweck C. Mining and unearthing hidden biosynthetic potential. Nat Commun 2021; 12:3864. [PMID: 34162873 PMCID: PMC8222398 DOI: 10.1038/s41467-021-24133-5] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/04/2021] [Indexed: 12/11/2022] Open
Abstract
Genetically encoded small molecules (secondary metabolites) play eminent roles in ecological interactions, as pathogenicity factors and as drug leads. Yet, these chemical mediators often evade detection, and the discovery of novel entities is hampered by low production and high rediscovery rates. These limitations may be addressed by genome mining for biosynthetic gene clusters, thereby unveiling cryptic metabolic potential. The development of sophisticated data mining methods and genetic and analytical tools has enabled the discovery of an impressive array of previously overlooked natural products. This review shows the newest developments in the field, highlighting compound discovery from unconventional sources and microbiomes. Natural products are an important source of bioactive compounds and have versatile applications in different fields, but their discovery is challenging. Here, the authors review the recent developments in genome mining for discovery of natural products, focusing on compounds from unconventional microorganisms and microbiomes.
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Affiliation(s)
- Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
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16
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Guo X, Zhang J, Li X, Xiao E, Lange JD, Rienstra CM, Burke MD, Mitchell DA. Sterol Sponge Mechanism Is Conserved for Glycosylated Polyene Macrolides. ACS CENTRAL SCIENCE 2021; 7:781-791. [PMID: 34079896 PMCID: PMC8161476 DOI: 10.1021/acscentsci.1c00148] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 05/07/2023]
Abstract
Amphotericin-like glycosylated polyene macrolides (GPMs) are a clinically and industrially important family of natural products, but the mechanisms by which they exert their extraordinary biological activities have remained unclear for more than half a century. Amphotericin B exerts fungicidal action primarily via self-assembly into an extramembranous sponge that rapidly extracts ergosterol from fungal membranes, but it has remained unclear whether this mechanism is applicable to other GPMs. Using a highly conserved polyene-hemiketal region of GPMs that we hypothesized to represent a conserved ergosterol-binding domain, we bioinformatically mapped the entirety of the GPM sequence-function space and expanded the number of GPM biosynthetic gene clusters (BGCs) by 10-fold. We further leveraged bioinformatic predictions and tetrazine-based reactivity screening targeting the electron-rich polyene region of GPMs to discover a first-in-class methyltetraene- and diepoxide-containing GPM, kineosporicin, and to assign BGCs to many new producers of previously reported members. Leveraging a range of structurally diverse known and newly discovered GPMs, we found that the sterol sponge mechanism of fungicidal action is conserved.
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Affiliation(s)
- Xiaorui Guo
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jiabao Zhang
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Avenue, Urbana, Illinois 61801, United States
| | - Xinyi Li
- Department
of Biochemistry, Roger Adams Laboratory, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Emily Xiao
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Justin D. Lange
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Avenue, Urbana, Illinois 61801, United States
| | - Chad M. Rienstra
- Department
of Biochemistry and National Magnetic Resonance Facility at Madison, DeLuca Biochemistry Laboratories, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Martin D. Burke
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Avenue, Urbana, Illinois 61801, United States
- Department
of Biochemistry, Roger Adams Laboratory, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801 United States
| | - Douglas A. Mitchell
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Avenue, Urbana, Illinois 61801, United States
- Department
of Microbiology, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
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17
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Ueoka R, Meoded RA, Gran‐Scheuch A, Bhushan A, Fraaije MW, Piel J. Genome Mining of Oxidation Modules in
trans
‐Acyltransferase Polyketide Synthases Reveals a Culturable Source for Lobatamides. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Roy A. Meoded
- Institute of Microbiology ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Alejandro Gran‐Scheuch
- Molecular Enzymology Group University of Groningen Nijenborgh 4 9747AG Groningen The Netherlands
- Department of Chemical and Bioprocesses Engineering Pontificia Universidad Católica de Chile Avenida Vicuña Mackenna 4860 7820436 Santiago Chile
| | - Agneya Bhushan
- Institute of Microbiology ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Marco W. Fraaije
- Molecular Enzymology Group University of Groningen Nijenborgh 4 9747AG Groningen The Netherlands
| | - Jörn Piel
- Institute of Microbiology ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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18
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Ueoka R, Meoded RA, Gran‐Scheuch A, Bhushan A, Fraaije MW, Piel J. Genome Mining of Oxidation Modules in trans-Acyltransferase Polyketide Synthases Reveals a Culturable Source for Lobatamides. Angew Chem Int Ed Engl 2020; 59:7761-7765. [PMID: 32040255 PMCID: PMC7586987 DOI: 10.1002/anie.201916005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Indexed: 11/22/2022]
Abstract
Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are multimodular megaenzymes that biosynthesize many bioactive natural products. They contain a remarkable range of domains and module types that introduce different substituents into growing polyketide chains. As one such modification, we recently reported Baeyer-Villiger-type oxygen insertion into nascent polyketide backbones, thereby generating malonyl thioester intermediates. In this work, genome mining focusing on architecturally diverse oxidation modules in trans-AT PKSs led us to the culturable plant symbiont Gynuella sunshinyii, which harbors two distinct modules in one orphan PKS. The PKS product was revealed to be lobatamide A, a potent cytotoxin previously only known from a marine tunicate. Biochemical studies show that one module generates glycolyl thioester intermediates, while the other is proposed to be involved in oxime formation. The data suggest varied roles of oxygenation modules in the biosynthesis of polyketide scaffolds and support the importance of trans-AT PKSs in the specialized metabolism of symbiotic bacteria.
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Affiliation(s)
- Reiko Ueoka
- Institute of MicrobiologyETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Roy A. Meoded
- Institute of MicrobiologyETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Alejandro Gran‐Scheuch
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
- Department of Chemical and Bioprocesses EngineeringPontificia Universidad Católica de ChileAvenida Vicuña Mackenna 48607820436SantiagoChile
| | - Agneya Bhushan
- Institute of MicrobiologyETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Jörn Piel
- Institute of MicrobiologyETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
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19
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Mo XH, Zhang H, Wang TM, Zhang C, Zhang C, Xing XH, Yang S. Establishment of CRISPR interference in Methylorubrum extorquens and application of rapidly mining a new phytoene desaturase involved in carotenoid biosynthesis. Appl Microbiol Biotechnol 2020; 104:4515-4532. [PMID: 32215707 DOI: 10.1007/s00253-020-10543-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/02/2020] [Accepted: 03/11/2020] [Indexed: 02/04/2023]
Abstract
The methylotrophic bacterium Methylorubrum extorquens AM1 holds a great potential of a microbial cell factory in producing high value chemicals with methanol as the sole carbon and energy source. However, many gene functions remain unknown, hampering further rewiring of metabolic networks. Clustered regularly interspaced short palindromic repeat interference (CRISPRi) has been demonstrated to be a robust tool for gene knockdown in diverse organisms. In this study, we developed an efficient CRISPRi system through optimizing the promoter strength of Streptococcus pyogenes-derived deactivated cas9 (dcas9). When the dcas9 and sgRNA were respectively controlled by medium PR/tetO and strong PmxaF-g promoters, dynamic repression efficacy of cell growth through disturbing a central metabolism gene glyA was achieved from 41.9 to 96.6% dependent on the sgRNA targeting sites. Furthermore, the optimized CRISPRi system was shown to effectively decrease the abundance of exogenous fluorescent protein gene mCherry over 50% and to reduce the expression of phytoene desaturase gene crtI by 97.7%. We then used CRISPRi technology combined with 26 sgRNAs pool to rapidly discover a new phytoene desaturase gene META1_3670 from 2470 recombinant mutants. The gene function was further verified through gene deletion and complementation as well as phylogenetic tree analysis. In addition, we applied CRISPRi to repress the transcriptional level of squalene-hopene cyclase gene shc involved in hopanoid biosynthesis by 64.9%, which resulted in enhancing 1.9-fold higher of carotenoid production without defective cell growth. Thus, the CRISPRi system developed here provides a useful tool in mining functional gene of M. extorquens as well as in biotechnology for producing high-valued chemicals from methanol. KEY POINTS: Developing an efficient CRISPRi to knockdown gene expression in C1-utilizing bacteria CRISPRi combined with sgRNAs pool to rapidly discover a new phytoene desaturase gene Improvement of carotenoid production by repressing a competitive pathway.
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Affiliation(s)
- Xu-Hua Mo
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Hui Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Tian-Min Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Chong Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Cong Zhang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China
| | - Xin-Hui Xing
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, People's Republic of China.
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China.
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20
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Wu JS, Shi XH, Zhang YH, Yu JY, Fu XM, Li X, Chen KX, Guo YW, Shao CL, Wang CY. Co-cultivation With 5-Azacytidine Induced New Metabolites From the Zoanthid-Derived Fungus Cochliobolus lunatus. Front Chem 2019; 7:763. [PMID: 31781545 PMCID: PMC6857680 DOI: 10.3389/fchem.2019.00763] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/24/2019] [Indexed: 01/01/2023] Open
Abstract
The zoanthid-derived fungus Cochliobolus lunatus (TA26-46) has been proven to be a source of bioactive 14-membered resorcylic acid lactones (RALs). In the present study, chemical epigenetic manipulation was applied to this fungal strain with a DNA methyltransferase inhibitor resulting in the significant changes of the secondary metabolites. Cultivation of C. lunatus (TA26-46) with 10 μM 5-azacytidine in Czapek-Dox liquid medium led to the isolation of new types of metabolites, including two α-pyrones, cochliobopyrones A (1) and B (2), along with three isocoumarins (3–5) and one chromone (6). The planar structures of the new compounds (1–2) were elucidated by comprehensive analyses of NMR and HRESIMS data. Their challenging relative configurations were established by a combination of acetonide reaction, coupling constants and NOESY correlations analysis, and DP4+ probability calculation. Their absolute configurations were determined by comparing with the ECD calculation data of the fragment molecules, 6-(1,2-dihydroxypropyl)-4-methoxy-2H-pyran-2-ones. It is the first time to obtain α-pyrone compounds with the epoxy ring or bromine atom on the seven-numbered side chain. It could be concluded that chemical epigenetic agents could induce C. lunatus to produce new types of secondary metabolites differing from its original products (RALs).
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Affiliation(s)
- Jing-Shuai Wu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiao-Hui Shi
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ya-Hui Zhang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jia-Yin Yu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiu-Mei Fu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xin Li
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Kai-Xian Chen
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Yue-Wei Guo
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Chang-Lun Shao
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chang-Yun Wang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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21
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Trottmann F, Franke J, Richter I, Ishida K, Cyrulies M, Dahse H, Regestein L, Hertweck C. Cyclopropanol Warhead in Malleicyprol Confers Virulence of Human- and Animal-Pathogenic Burkholderia Species. Angew Chem Int Ed Engl 2019; 58:14129-14133. [PMID: 31353766 PMCID: PMC6790655 DOI: 10.1002/anie.201907324] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/20/2019] [Indexed: 12/16/2022]
Abstract
Burkholderia species such as B. mallei and B. pseudomallei are bacterial pathogens causing fatal infections in humans and animals (glanders and melioidosis), yet knowledge on their virulence factors is limited. While pathogenic effects have been linked to a highly conserved gene locus (bur/mal) in the B. mallei group, the metabolite associated to the encoded polyketide synthase, burkholderic acid (syn. malleilactone), could not explain the observed phenotypes. By metabolic profiling and molecular network analyses of the model organism B. thailandensis, the primary products of the cryptic pathway were identified as unusual cyclopropanol-substituted polyketides. First, sulfomalleicyprols were identified as inactive precursors of burkholderic acid. Furthermore, a highly reactive upstream metabolite, malleicyprol, was discovered and obtained in two stabilized forms. Cell-based assays and a nematode infection model showed that the rare natural product confers cytotoxicity and virulence.
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Affiliation(s)
- Felix Trottmann
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Jakob Franke
- Institute of Organic Chemistry, BMWZLeibniz University Hannover30167HannoverGermany
| | - Ingrid Richter
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Keishi Ishida
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Michael Cyrulies
- Department Bio Pilot PlantLeibniz Institute for Natural Product Research and Infection Biology (HKI)07745JenaGermany
| | - Hans‐Martin Dahse
- Department Infection BiologyLeibniz Institute for Natural Product Research and Infection Biology (HKI)07745JenaGermany
| | - Lars Regestein
- Department Bio Pilot PlantLeibniz Institute for Natural Product Research and Infection Biology (HKI)07745JenaGermany
| | - Christian Hertweck
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstr. 11a07745JenaGermany
- Natural Product ChemistryFaculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
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22
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Trottmann F, Franke J, Richter I, Ishida K, Cyrulies M, Dahse H, Regestein L, Hertweck C. Cyclopropanol Warhead in Malleicyprol Confers Virulence of Human‐ and Animal‐Pathogenic
Burkholderia
Species. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Felix Trottmann
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Jakob Franke
- Institute of Organic Chemistry, BMWZ Leibniz University Hannover 30167 Hannover Germany
| | - Ingrid Richter
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Michael Cyrulies
- Department Bio Pilot Plant Leibniz Institute for Natural Product Research and Infection Biology (HKI) 07745 Jena Germany
| | - Hans‐Martin Dahse
- Department Infection Biology Leibniz Institute for Natural Product Research and Infection Biology (HKI) 07745 Jena Germany
| | - Lars Regestein
- Department Bio Pilot Plant Leibniz Institute for Natural Product Research and Infection Biology (HKI) 07745 Jena Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
- Natural Product Chemistry Faculty of Biological Sciences Friedrich Schiller University Jena 07743 Jena Germany
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23
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Helfrich EJN, Ueoka R, Dolev A, Rust M, Meoded RA, Bhushan A, Califano G, Costa R, Gugger M, Steinbeck C, Moreno P, Piel J. Automated structure prediction of trans-acyltransferase polyketide synthase products. Nat Chem Biol 2019; 15:813-821. [PMID: 31308532 PMCID: PMC6642696 DOI: 10.1038/s41589-019-0313-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/23/2019] [Indexed: 12/01/2022]
Abstract
Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are among the most complex known enzymes from secondary metabolism and are responsible for the biosynthesis of highly diverse bioactive polyketides. However, most of these metabolites remain uncharacterized, since trans-AT PKSs frequently occur in poorly studied microbes and feature a remarkable array of non-canonical biosynthetic components with poorly understood functions. As a consequence, genome-guided natural product identification has been challenging. To enable de novo structural predictions for trans-AT PKS-derived polyketides, we developed the trans-AT PKS polyketide predictor (TransATor). TransATor is a versatile bio- and chemoinformatics web application that suggests informative chemical structures for even highly aberrant trans-AT PKS biosynthetic gene clusters, thus permitting hypothesis-based, targeted biotechnological discovery and biosynthetic studies. We demonstrate the applicative scope in several examples, including the characterization of new variants of bioactive natural products as well as structurally new polyketides from unusual bacterial sources.
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Affiliation(s)
- Eric J N Helfrich
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Reiko Ueoka
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Alon Dolev
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Michael Rust
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Roy A Meoded
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Agneya Bhushan
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Gianmaria Califano
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Rodrigo Costa
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, Paris, France
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität Jena, Jena, Germany
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK
| | - Pablo Moreno
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK.
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland.
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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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Meoded RA, Ueoka R, Helfrich EJN, Jensen K, Magnus N, Piechulla B, Piel J. A Polyketide Synthase Component for Oxygen Insertion into Polyketide Backbones. Angew Chem Int Ed Engl 2018; 57:11644-11648. [PMID: 29898240 PMCID: PMC6174933 DOI: 10.1002/anie.201805363] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/08/2018] [Indexed: 12/31/2022]
Abstract
Enzymatic core components from trans-acyltransferase polyketide synthases (trans-AT PKSs) catalyze exceptionally diverse biosynthetic transformations to generate structurally complex bioactive compounds. Here we focus on a group of oxygenases identified in various trans-AT PKS pathways, including those for pederin, oocydins, and toblerols. Using the oocydin pathway homologue (OocK) from Serratia plymuthica 4Rx13 and N-acetylcysteamine (SNAC) thioesters as test surrogates for acyl carrier protein (ACP)-tethered intermediates, we show that the enzyme inserts oxygen into β-ketoacyl moieties to yield malonyl ester SNAC products. Based on these data and the identification of a non-hydrolyzed oocydin congener with retained ester moiety, we propose a unified biosynthetic pathway of oocydins, haterumalides, and biselides. By providing access to internal ester, carboxylate pseudostarter, and terminal hydroxyl functions, oxygen insertion into polyketide backbones greatly expands the biosynthetic scope of PKSs.
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Affiliation(s)
- Roy A. Meoded
- Institute of MicrobiologyEigenössische Technische Hochschule (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Reiko Ueoka
- Institute of MicrobiologyEigenössische Technische Hochschule (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Eric J. N. Helfrich
- Institute of MicrobiologyEigenössische Technische Hochschule (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Katja Jensen
- Institute of MicrobiologyEigenössische Technische Hochschule (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Nancy Magnus
- Institute for Biological SciencesUniversity of RostockAlbert-Einstein-Straße 318059RostockGermany
| | - Birgit Piechulla
- Institute for Biological SciencesUniversity of RostockAlbert-Einstein-Straße 318059RostockGermany
| | - Jörn Piel
- Institute of MicrobiologyEigenössische Technische Hochschule (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
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26
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Meoded RA, Ueoka R, Helfrich EJN, Jensen K, Magnus N, Piechulla B, Piel J. A Polyketide Synthase Component for Oxygen Insertion into Polyketide Backbones. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805363] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Roy A. Meoded
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Reiko Ueoka
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Eric J. N. Helfrich
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Katja Jensen
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Nancy Magnus
- Institute for Biological Sciences; University of Rostock; Albert-Einstein-Straße 3 18059 Rostock Germany
| | - Birgit Piechulla
- Institute for Biological Sciences; University of Rostock; Albert-Einstein-Straße 3 18059 Rostock Germany
| | - Jörn Piel
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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27
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Hill RA, Sutherland A. Hot off the press. Nat Prod Rep 2018. [DOI: 10.1039/c8np90008f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as tundrenone from Methylobacter tundripaludum.
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