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Wang CY, Hu JQ, Wang DG, Li YZ, Wu C. Recent advances in discovery and biosynthesis of natural products from myxobacteria: an overview from 2017 to 2023. Nat Prod Rep 2024. [PMID: 38390645 DOI: 10.1039/d3np00062a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Covering: 2017.01 to 2023.11Natural products biosynthesized by myxobacteria are appealing due to their sophisticated chemical skeletons, remarkable biological activities, and intriguing biosynthetic enzymology. This review aims to systematically summarize the advances in the discovery methods, new structures, and bioactivities of myxobacterial NPs reported in the period of 2017-2023. In addition, the peculiar biosynthetic pathways of several structural families are also highlighted.
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Affiliation(s)
- Chao-Yi Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Jia-Qi Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - De-Gao Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
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Ahearne A, Phillips KE, Knehans T, Hoing M, Dowd SE, Stevens DC. Chromosomal organization of biosynthetic gene clusters, including those of nine novel species, suggests plasticity of myxobacterial specialized metabolism. Front Microbiol 2023; 14:1227206. [PMID: 37601375 PMCID: PMC10435759 DOI: 10.3389/fmicb.2023.1227206] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Natural products discovered from bacteria provide critically needed therapeutic leads for drug discovery, and myxobacteria are an established source for metabolites with unique chemical scaffolds and biological activities. Myxobacterial genomes accommodate an exceptional number and variety of biosynthetic gene clusters (BGCs) which encode for features involved in specialized metabolism. Methods In this study, we describe the collection, sequencing, and genome mining of 20 myxobacteria isolated from rhizospheric soil samples collected in North America. Results Nine isolates were determined to be novel species of myxobacteria including representatives from the genera Archangium, Myxococcus, Nannocystis, Polyangium, Pyxidicoccus, Sorangium, and Stigmatella. Growth profiles, biochemical assays, and descriptions were provided for all proposed novel species. We assess the BGC content of all isolates and observe differences between Myxococcia and Polyangiia clusters. Discussion Continued discovery and sequencing of novel myxobacteria from the environment provide BGCs for the genome mining pipeline. Utilizing complete or near-complete genome sequences, we compare the chromosomal organization of BGCs of related myxobacteria from various genera and suggest that the spatial proximity of hybrid, modular clusters contributes to the metabolic adaptability of myxobacteria.
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Affiliation(s)
- Andrew Ahearne
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Kayleigh E. Phillips
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Thomas Knehans
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Miranda Hoing
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Scot E. Dowd
- Molecular Research LP (MR DNA), Shallowater, TX, United States
| | - David Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
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3
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Ahearne A, Phillips K, Knehans T, Hoing M, Dowd SE, Stevens DC. Chromosomal organization of biosynthetic gene clusters suggests plasticity of myxobacterial specialized metabolism including descriptions for nine novel species: Archangium lansinium sp. nov., Myxococcus landrumus sp. nov., Nannocystis bainbridgea sp. nov., Nannocystis poenicansa sp. nov., Nannocystis radixulma sp. nov., Polyangium mundeleinium sp. nov., Pyxidicoccus parkwaysis sp. nov., Sorangium aterium sp. nov., Stigmatella ashevillena sp. nov. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531766. [PMID: 36945379 PMCID: PMC10028903 DOI: 10.1101/2023.03.08.531766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Natural products discovered from bacteria provide critically needed therapeutic leads for drug discovery, and myxobacteria are an established source for metabolites with unique chemical scaffolds and biological activities. Myxobacterial genomes accommodate an exceptional number and variety of biosynthetic gene clusters (BGCs) which encode for features involved in specialized metabolism. Continued discovery and sequencing of novel myxobacteria from the environment provides BGCs for the genome mining pipeline. Herein, we describe the collection, sequencing, and genome mining of 20 myxobacteria isolated from rhizospheric soil samples collected in North America. Nine isolates where determined to be novel species of myxobacteria including representatives from the genera Archangium, Myxococcus, Nannocystis, Polyangium, Pyxidicoccus, Sorangium, and Stigmatella. Growth profiles, biochemical assays, and descriptions are provided for all proposed novel species. We assess the BGC content of all isolates and observe differences between Myxococcia and Polyangiia clusters. Utilizing complete or near complete genome sequences we compare the chromosomal organization of BGCs of related myxobacteria from various genera and suggest spatial proximity of hybrid, modular clusters contributes to the metabolic adaptability of myxobacteria.
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Affiliation(s)
- Andrew Ahearne
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Kayleigh Phillips
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Thomas Knehans
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Miranda Hoing
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Scot E. Dowd
- MR DNA, Molecular Research LP, Shallowater, TX 79363, USA
| | - D. Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
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Winand L, Lernoud L, Meyners SA, Kuhr K, Hiller W, Nett M. Myxococcus xanthus as Host for the Production of Benzoxazoles. Chembiochem 2023; 24:e202200635. [PMID: 36484355 DOI: 10.1002/cbic.202200635] [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: 11/04/2022] [Revised: 12/09/2022] [Accepted: 12/09/2022] [Indexed: 12/13/2022]
Abstract
Benzoxazoles are important structural motifs in pharmaceutical drugs. Here, we present the heterologous production of 3-hydroxyanthranilate-derived benzoxazoles in the host bacterium Myxococcus xanthus following the expression of two genes from the nataxazole biosynthetic gene cluster of Streptomyces sp. Tü 6176. The M. xanthus expression strain achieved a benzoxazole titer of 114.6±7.4 mg L-1 upon precursor supplementation, which is superior to other bacterial production systems. Crosstalk between the heterologously expressed benzoxazole pathway and the endogenous myxochelin pathway led to the combinatorial biosynthesis of benzoxazoles featuring a 2,3-dihydroxybenzoic acid (2,3-DHBA) building block. Subsequent in vitro studies confirmed that this crosstalk is not only due to the availability of 2,3-DHBA in M. xanthus, rather, it is promoted by the adenylating enzyme MxcE from the myxochelin pathway, which contributes to the activation of aryl carboxylic acids and delivers them to benzoxazole biosynthesis.
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Affiliation(s)
- Lea Winand
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Str. 66, 44227, Dortmund, Germany
| | - Lucia Lernoud
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Str. 66, 44227, Dortmund, Germany
| | - Saskia Anna Meyners
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Str. 66, 44227, Dortmund, Germany
| | - Katharina Kuhr
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Str. 66, 44227, Dortmund, Germany
| | - Wolf Hiller
- Department of Chemistry and Chemical Biology, NMR Laboratory, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Str. 66, 44227, Dortmund, Germany
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Narh Mensah DL, Wingfield BD, Coetzee MPA. Nonribosomal peptide synthetase gene clusters and characteristics of predicted NRPS-dependent siderophore synthetases in Armillaria and other species in the Physalacriaceae. Curr Genet 2023; 69:7-24. [PMID: 36369495 DOI: 10.1007/s00294-022-01256-w] [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: 08/26/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/13/2022]
Abstract
Fungal secondary metabolites are often pathogenicity or virulence factors synthesized by genes contained in secondary metabolite gene clusters (SMGCs). Nonribosomal polypeptide synthetase (NRPS) clusters are SMGCs which produce peptides such as siderophores, the high affinity ferric iron chelating compounds required for iron uptake under aerobic conditions. Armillaria spp. are mostly facultative necrotrophs of woody plants. NRPS-dependent siderophore synthetase (NDSS) clusters of Armillaria spp. and selected Physalacriaceae were investigated using a comparative genomics approach. Siderophore biosynthesis by strains of selected Armillaria spp. was evaluated using CAS and split-CAS assays. At least one NRPS cluster and other clusters were detected in the genomes studied. No correlation was observed between the number and types of SMGCs and reported pathogenicity of the species studied. The genomes contained one NDSS cluster each. All NDSSs were multi-modular with the domain architecture (ATC)3(TC)2. NDSS clusters of the Armillaria spp. showed a high degree of microsynteny. In the genomes of Desarmillaria spp. and Guyanagaster necrorhizus, NDSS clusters were more syntenic with NDSS clusters of Armillaria spp. than to those of the other Physalacriaceae species studied. Three A-domain orthologous groups were identified in the NDSSs, and atypical Stachelhaus codes were predicted for the A3 orthologous group. In vitro biosynthesis of mainly hydroxamate and some catecholate siderophores was observed. Hence, Armillaria spp. generally contain one highly conserved, NDSS cluster although some interspecific variations in the products of these clusters is expected. Results from this study lays the groundwork for future studies to elucidate the molecular biology of fungal phyto-pathogenicity.
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Affiliation(s)
- Deborah L Narh Mensah
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.,Council for Scientific and Industrial Research-Food Research Institute (CSIR-FRI), P. O. Box M20, Accra, Ghana
| | - Brenda D Wingfield
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Martin P A Coetzee
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.
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Okoth DA, Hug JJ, Garcia R, Müller R. Discovery, Biosynthesis and Biological Activity of a Succinylated Myxochelin from the Myxobacterial Strain MSr12020. Microorganisms 2022; 10:microorganisms10101959. [PMID: 36296235 PMCID: PMC9611931 DOI: 10.3390/microorganisms10101959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/07/2022] Open
Abstract
Myxobacteria feature unique biological characteristics, including their capability to glide on the surface, undergo different multicellular developmental stages and produce structurally unique natural products such as the catecholate-type siderophores myxochelins A and B. Herein, we report the isolation, structure elucidation and a proposed biosynthesis of the new congener myxochelin B-succinate from the terrestrial myxobacterial strain MSr12020, featuring a succinyl decoration at its primary amine group. Myxochelin-B-succinate exhibited antibacterial growth inhibition and moderate cytotoxic activity against selected human cancer cell lines. This unique chemical modification of myxochelin B might provide interesting insights for future microbiological studies to understand the biological function and biosynthesis of secondary metabolite succinylation.
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Affiliation(s)
- Dorothy A. Okoth
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Microbial Natural Products, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Helmholtz International Labs, Department of Microbial Natural Products, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
- Department of Chemistry, School of Physical and Biological Sciences, Main campus, Maseno University, Maseno P.O. Box 333-40105, Kenya
| | - Joachim J. Hug
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Microbial Natural Products, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Helmholtz International Labs, Department of Microbial Natural Products, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
| | - Ronald Garcia
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Microbial Natural Products, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Helmholtz International Labs, Department of Microbial Natural Products, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Microbial Natural Products, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Helmholtz International Labs, Department of Microbial Natural Products, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
- Correspondence:
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Brinkmann S, Semmler S, Kersten C, Patras MA, Kurz M, Fuchs N, Hammerschmidt SJ, Legac J, Hammann PE, Vilcinskas A, Rosenthal PJ, Schirmeister T, Bauer A, Schäberle TF. Identification, Characterization, and Synthesis of Natural Parasitic Cysteine Protease Inhibitors: Pentacitidins Are More Potent Falcitidin Analogues. ACS Chem Biol 2022; 17:576-589. [PMID: 35262340 DOI: 10.1021/acschembio.1c00861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protease inhibitors represent a promising therapeutic option for the treatment of parasitic diseases such as malaria and human African trypanosomiasis. Falcitidin was the first member of a new class of inhibitors of falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum. Using a metabolomics dataset of 25 Chitinophaga strains for molecular networking enabled identification of over 30 natural analogues of falcitidin. Based on MS/MS spectra, they vary in their amino acid chain length, sequence, acyl residue, and C-terminal functionalization; therefore, they were grouped into the four falcitidin peptide families A-D. The isolation, characterization, and absolute structure elucidation of two falcitidin-related pentapeptide aldehyde analogues by extensive MS/MS spectrometry and NMR spectroscopy in combination with advanced Marfey's analysis was in agreement with the in silico analysis of the corresponding biosynthetic gene cluster. Total synthesis of chosen pentapeptide analogues followed by in vitro testing against a panel of proteases revealed selective parasitic cysteine protease inhibition and, additionally, low-micromolar inhibition of α-chymotrypsin. The pentapeptides investigated here showed superior inhibitory activity compared to falcitidin.
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Affiliation(s)
- Stephan Brinkmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen 35392, Germany
| | - Sandra Semmler
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen 35392, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Mainz 55128, Germany
| | - Maria A. Patras
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen 35392, Germany
| | - Michael Kurz
- Sanofi-Aventis Deutschland GmbH, R&D, Frankfurt am Main 65926, Germany
| | - Natalie Fuchs
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Mainz 55128, Germany
| | - Stefan J. Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Mainz 55128, Germany
| | - Jenny Legac
- Department of Medicine, University of California, San Francisco, California 94143, United States
| | | | - Andreas Vilcinskas
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen 35392, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen 35392, Germany
| | - Philip J. Rosenthal
- Department of Medicine, University of California, San Francisco, California 94143, United States
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Mainz 55128, Germany
| | - Armin Bauer
- Sanofi-Aventis Deutschland GmbH, R&D, Frankfurt am Main 65926, Germany
| | - Till F. Schäberle
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen 35392, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen 35392, Germany
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Morgan GL, Li K, Crawford DM, Aubé J, Li B. Enzymatic Synthesis of Diverse Heterocycles by a Noncanonical Nonribosomal Peptide Synthetase. ACS Chem Biol 2021; 16:2776-2786. [PMID: 34767712 DOI: 10.1021/acschembio.1c00623] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are typically multimodular enzymes that assemble amino acids or carboxylic acids into complex natural products. Here, we characterize a monomodular NRPS, PvfC, encoded by the Pseudomonas virulence factor (pvf) gene cluster that is essential for virulence and signaling in different bacterial species. PvfC exhibits a unique adenylation-thiolation-reductase (ATR) domain architecture that is understudied in bacteria. We show that the activity of PvfC is essential in the production of seven leucine-derived heterocyclic natural products, including two pyrazines, a pyrazinone, and a rare disubstituted imidazole, as well as three pyrazine N-oxides that require an additional N-oxygenation step. Mechanistic studies reveal that PvfC, without a canonical peptide-forming domain, makes a dipeptide aldehyde intermediate en route to both the pyrazinone and imidazole. Our work identifies a novel biosynthetic route for the production of pyrazinones, an emerging class of signaling molecules and virulence factors. Our discovery also showcases the ability of monomodular NRPSs to generate amino acid- and dipeptide-aldehydes that lead to diverse natural products. The diversity-prone biosynthesis by the pvf-encoded enzymes sets the stage for further understanding the functions of pvf in bacterial cell-to-cell signaling.
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Affiliation(s)
- Gina L. Morgan
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kelin Li
- The Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Drake M. Crawford
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jeffrey Aubé
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- The Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Bo Li
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Wang DG, Niu L, Lin ZM, Wang JJ, Gao DF, Sui HY, Li YZ, Wu C. The Discovery and Biosynthesis of Nicotinic Myxochelins from an Archangium sp. SDU34. JOURNAL OF NATURAL PRODUCTS 2021; 84:2744-2748. [PMID: 34623817 DOI: 10.1021/acs.jnatprod.1c00524] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Myxobacteria are a prolific source of structurally diverse natural products, and one of the best-studied myxobacterial products is the siderophore myxochelin. Herein, we report two new compounds, myxochelins N (1) and O (2), that are nicotinic paralogs of myxochelin A, from the terrestrial myxobacterium Archangium sp. SDU34; 2 is functionalized with a rare 2-oxazolidinone. A precursor-feeding experiment implied that the biosynthesis of 1 or 2 was due to altered substrate specificity of the loading module of MxcE, which likely accepts nicotinic acid and benzoic acid instead of more conventional 2,3-dihydroxybenzoic acid. We also employed a phylogenomic approach to map the evolutionary relationships of the myxochelin biosynthetic gene clusters (BGCs) in all the available myxobacterial genomes, to pave the way for the future discovery of potentially hidden myxochelin derivatives. Although the biological function of 1 and 2 is unclear yet, this work underpins that even extensively studied BGCs in myxobacteria can still produce new chemistry.
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Affiliation(s)
- De-Gao Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Luo Niu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Zhao-Min Lin
- Institute of Medical Science, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, People's Republic of China
| | - Jing-Jing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Dong-Fang Gao
- Institute of Medical Science, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250033, People's Republic of China
| | - Hai-Yan Sui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
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Zhao Y, Wang Y, Xia C, Li X, Ye X, Fan Q, Huang Y, Li Z, Zhu C, Cui Z. Whole-Genome Sequencing of Corallococcus sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior. Genes (Basel) 2021; 12:genes12091421. [PMID: 34573403 PMCID: PMC8466578 DOI: 10.3390/genes12091421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022] Open
Abstract
Corallococcus sp. strain EGB is a Gram-negative myxobacteria isolated from saline soil, and has considerable potential for the biocontrol of phytopathogenic fungi. However, the detailed mechanisms related to development and predatory behavior are unclear. To obtain a comprehensive overview of genetic features, the genome of strain EGB was sequenced, annotated, and compared with 10 other Corallococcus species. The strain EGB genome was assembled as a single circular chromosome of 9.4 Mb with 7916 coding genes. Phylogenomics analysis showed that strain EGB was most closely related to Corallococcus interemptor AB047A, and it was inferred to be a novel species within the Corallococcus genus. Comparative genomic analysis revealed that the pan-genome of Corallococcus genus was large and open. Only a small proportion of genes were specific to strain EGB, and most of them were annotated as hypothetical proteins. Subsequent analyses showed that strain EGB produced abundant extracellular enzymes such as chitinases and β-(1,3)-glucanases, and proteases to degrade the cell-wall components of phytopathogenic fungi. In addition, 35 biosynthetic gene clusters potentially coding for antimicrobial compounds were identified in the strain EGB, and the majority of them were present in the dispensable pan-genome with unexplored metabolites. Other genes related to secretion and regulation were also explored for strain EGB. This study opens new perspectives in the greater understanding of the predatory behavior of strain EGB, and facilitates a potential application in the biocontrol of fungal plant diseases in the future.
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Affiliation(s)
- Yuqiang Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Yanxin Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chengyao Xia
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xu Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiwen Fan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Cancan Zhu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
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Frank NA, Széles M, Akone SH, Rasheed S, Hüttel S, Frewert S, Hamed MM, Herrmann J, Schuler SMM, Hirsch AKH, Müller R. Expanding the Myxochelin Natural Product Family by Nicotinic Acid Containing Congeners. Molecules 2021; 26:4929. [PMID: 34443518 PMCID: PMC8400222 DOI: 10.3390/molecules26164929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022] Open
Abstract
Myxobacteria represent a viable source of chemically diverse and biologically active secondary metabolites. The myxochelins are a well-studied family of catecholate-type siderophores produced by various myxobacterial strains. Here, we report the discovery, isolation, and structure elucidation of three new myxochelins N1-N3 from the terrestrial myxobacterium Corallococcus sp. MCy9049, featuring an unusual nicotinic acid moiety. Precursor-directed biosynthesis (PDB) experiments and total synthesis were performed in order to confirm structures, improve access to pure compounds for bioactivity testing, and to devise a biosynthesis proposal. The combined evaluation of metabolome and genome data covering myxobacteria supports the notion that the new myxochelin congeners reported here are in fact frequent side products of the known myxochelin A biosynthetic pathway in myxobacteria.
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Affiliation(s)
- Nicolas A. Frank
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Márió Széles
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Sergi H. Akone
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Department of Chemistry, Faculty of Science, University of Douala, Douala P.O. Box 24157, Cameroon
| | - Sari Rasheed
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Stephan Hüttel
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Simon Frewert
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Mostafa M. Hamed
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Jennifer Herrmann
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | | | - Anna K. H. Hirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (N.A.F.); (M.S.); (S.H.A.); (S.R.); (S.H.); (S.F.); (M.M.H.); (J.H.); (A.K.H.H.)
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
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Ahearne A, Albataineh H, Dowd SE, Stevens DC. Assessment of Evolutionary Relationships for Prioritization of Myxobacteria for Natural Product Discovery. Microorganisms 2021; 9:microorganisms9071376. [PMID: 34202719 PMCID: PMC8307915 DOI: 10.3390/microorganisms9071376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/03/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023] Open
Abstract
Discoveries of novel myxobacteria have started to unveil the potentially vast phylogenetic diversity within the family Myxococcaceae and have brought about an updated approach to myxobacterial classification. While traditional approaches focused on morphology, 16S gene sequences, and biochemistry, modern methods including comparative genomics have provided a more thorough assessment of myxobacterial taxonomy. Herein, we utilize long-read genome sequencing for two myxobacteria previously classified as Archangium primigenium and Chondrococcus macrosporus, as well as four environmental myxobacteria newly isolated for this study. Average nucleotide identity and digital DNA-DNA hybridization scores from comparative genomics suggest previously classified as A. primigenium to instead be a novel member of the genus Melittangium, C. macrosporus to be a potentially novel member of the genus Corallococcus with high similarity to Corallococcus exercitus, and the four isolated myxobacteria to include another novel Corallococcus species, a novel Pyxidicoccus species, a strain of Corallococcus exiguus, and a potentially novel Myxococcus species with high similarity to Myxococcus stipitatus. We assess the biosynthetic potential of each sequenced myxobacterium and suggest that genus-level conservation of biosynthetic pathways support our preliminary taxonomic assignment. Altogether, we suggest that long-read genome sequencing benefits the classification of myxobacteria and improves determination of biosynthetic potential for prioritization of natural product discovery.
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Affiliation(s)
- Andrew Ahearne
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA; (A.A.); (H.A.)
| | - Hanan Albataineh
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA; (A.A.); (H.A.)
| | - Scot E. Dowd
- MR DNA, Molecular Research LP, Shallowater, TX 79363, USA;
| | - D. Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA; (A.A.); (H.A.)
- Correspondence: ; Tel.: +1-662-915-5730
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13
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Novel Modifications of Nonribosomal Peptides from Brevibacillus laterosporus MG64 and Investigation of Their Mode of Action. Appl Environ Microbiol 2020; 86:AEM.01981-20. [PMID: 32978140 DOI: 10.1128/aem.01981-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023] Open
Abstract
Nonribosomal peptides (NRPs) are a class of secondary metabolites usually produced by microorganisms. They are of paramount importance in different applications, including biocontrol and pharmacy. Brevibacillus spp. are a rich source of NRPs yet have received little attention. In this study, we characterize four novel bogorol variants (bogorols I to L, cationic linear lipopeptides) and four succilins (succilins I to L, containing a succinyl group that is attached to the Orn3/Lys3 in bogorols I to L) from the biocontrol strain Brevibacillus laterosporus MG64. Further investigation revealed that the bogorol family of peptides employs an adenylation pathway for lipoinitiation, different from the usual pattern, which is based on an external ligase and coenzyme A. Moreover, the formation of valinol was proven to be mediated by a terminal reductase domain and a reductase encoded by the bogI gene. Furthermore, succinylation, which is a novel type of modification in the family of bogorols, was discovered. Its occurrence requires a high concentration of the substrate (bogorols), but its responsible enzyme remains unknown. Bogorols display potent activity against both Gram-positive and Gram-negative bacteria. Investigation of their mode of action reveals that bogorols form pores in the cell membrane of both Gram-positive and Gram-negative bacteria. The combination of bogorols and relacidines, another class of NRPs produced by B. laterosporus MG64, displays a synergistic effect on different pathogens, suggesting the great potential of both peptides as well as their producer B. laterosporus MG64 for broad applications. Our study provides a further understanding of the bogorol family of peptides as well as their applications.IMPORTANCE NRPs form a class of secondary metabolites with biocontrol and pharmaceutical potential. This work describes the identification of novel bogorol variants and succinylated bogorols (namely, succilins) and further investigates their biosynthetic pathway and mode of action. Adenylation domain-mediated lipoinitiation of bogorols represents a novel pathway by which NRPs incorporate fatty acid tails. This pathway provides the possibility to engineer the lipid tail of NRPs without identifying a fatty acid coenzyme ligase, which is usually not present in the biosynthetic gene cluster. The terminal reductase domain (TD) and BogI-mediated valinol formation and their effect on the biological activity of bogorols are revealed. Succinylation, which is rarely reported in NRPs, was discovered in the bogorol family of peptides. We demonstrate that bogorols combat bacterial pathogens by forming pores in the cell membrane. We also report the synergistic effect of two natural products (relacidine B and bogorol K) produced by the same strain, which is relevant for competition for a niche.
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14
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Dudomycins: New Secondary Metabolites Produced After Heterologous Expression of an Nrps Cluster from Streptomyces albus ssp. Chlorinus Nrrl B-24108. Microorganisms 2020; 8:microorganisms8111800. [PMID: 33207845 PMCID: PMC7696016 DOI: 10.3390/microorganisms8111800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/04/2020] [Accepted: 11/10/2020] [Indexed: 12/22/2022] Open
Abstract
Since the 1950s, natural products of bacterial origin were systematically developed to be used as drugs with a wide range of medical applications. The available treatment options for many diseases are still not satisfying, wherefore, the discovery of new structures has not lost any of its importance. Beyond the great variety of already isolated and characterized metabolites, Streptomycetes still harbor uninvestigated gene clusters whose products can be accessed using heterologous expression in host organisms. This works presents the discovery of a set of structurally novel secondary metabolites, dudomycins A to D, through the expression of a cryptic NRPS cluster from Streptomyces albus ssp. Chlorinus NRRL B-24108 in the heterologous host strain Streptomyces albus Del14. A minimal set of genes, required for the production of dudomycins, was defined through gene inactivation experiments. This paper also proposes a model for dudomycin biosynthesis.
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15
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Characterization of inthomycin biosynthetic gene cluster revealing new insights into carboxamide formation. Chin J Nat Med 2020; 18:677-683. [PMID: 32928511 DOI: 10.1016/s1875-5364(20)60006-1] [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: 04/25/2020] [Indexed: 11/20/2022]
Abstract
Inthomycins are polyketide antibiotics which contain a terminal carboxamide group and a triene chain. Inthomycin B (1) and its two new analogues 2 and 3 were isolated from the crude extract of Streptomyces pactum L8. Identification of the gene cluster for inthomycin biosynthesis as well as the 15N-labeled glycine incorporation into inthomycins are described. Combined with the gene deletion of the rare P450 domain in the NRPS module, a formation mechanism of carboxamide moiety in inthomycins was proposed via an oxidative release of the assembly chain assisted by the P450 domain.
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16
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Siebert DCB, Sommer R, Pogorevc D, Hoffmann M, Wenzel SC, Müller R, Titz A. Chemical synthesis of tripeptide thioesters for the biotechnological incorporation into the myxobacterial secondary metabolite argyrin via mutasynthesis. Beilstein J Org Chem 2019; 15:2922-2929. [PMID: 31839838 PMCID: PMC6902895 DOI: 10.3762/bjoc.15.286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/20/2019] [Indexed: 11/23/2022] Open
Abstract
The argyrins are secondary metabolites from myxobacteria with antibiotic activity against Pseudomonas aeruginosa. Studying their structure–activity relationship is hampered by the complexity of the chemical total synthesis. Mutasynthesis is a promising approach where simpler and fully synthetic intermediates of the natural product’s biosynthesis can be biotechnologically incorporated. Here, we report the synthesis of a series of tripeptide thioesters as mutasynthons containing the native sequence with a dehydroalanine (Dha) Michael acceptor attached to a sarcosine (Sar) and derivatives. Chemical synthesis of the native sequence ᴅ-Ala-Dha-Sar thioester required revision of the sequential peptide synthesis into a convergent strategy where the thioester with sarcosine was formed before coupling to the Dha-containing dipeptide.
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Affiliation(s)
- David C B Siebert
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), D-66123 Saarbrücken, Germany.,Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany
| | - Roman Sommer
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), D-66123 Saarbrücken, Germany.,Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany
| | - Domen Pogorevc
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany.,Microbial Natural Substances, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), D-66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, D-66123 Saarbrücken, Germany
| | - Michael Hoffmann
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany.,Microbial Natural Substances, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), D-66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, D-66123 Saarbrücken, Germany
| | - Silke C Wenzel
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany.,Microbial Natural Substances, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), D-66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, D-66123 Saarbrücken, Germany
| | - Rolf Müller
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany.,Microbial Natural Substances, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), D-66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, D-66123 Saarbrücken, Germany
| | - Alexander Titz
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), D-66123 Saarbrücken, Germany.,Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany.,Department of Pharmacy, Saarland University, D-66123 Saarbrücken, Germany
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Gregory K, Salvador LA, Akbar S, Adaikpoh BI, Stevens DC. Survey of Biosynthetic Gene Clusters from Sequenced Myxobacteria Reveals Unexplored Biosynthetic Potential. Microorganisms 2019; 7:E181. [PMID: 31238501 PMCID: PMC6616573 DOI: 10.3390/microorganisms7060181] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 01/31/2023] Open
Abstract
Coinciding with the increase in sequenced bacteria, mining of bacterial genomes for biosynthetic gene clusters (BGCs) has become a critical component of natural product discovery. The order Myxococcales, a reputable source of biologically active secondary metabolites, spans three suborders which all include natural product producing representatives. Utilizing the BiG-SCAPE-CORASON platform to generate a sequence similarity network that contains 994 BGCs from 36 sequenced myxobacteria deposited in the antiSMASH database, a total of 843 BGCs with lower than 75% similarity scores to characterized clusters within the MIBiG database are presented. This survey provides the biosynthetic diversity of these BGCs and an assessment of the predicted chemical space yet to be discovered. Considering the mere snapshot of myxobacteria included in this analysis, these untapped BGCs exemplify the potential for natural product discovery from myxobacteria.
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Affiliation(s)
- Katherine Gregory
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Laura A Salvador
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Shukria Akbar
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Barbara I Adaikpoh
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - D Cole Stevens
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
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18
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Zhu M, Wang L, He J. Chemical Diversification Based on Substrate Promiscuity of a Standalone Adenylation Domain in a Reconstituted NRPS System. ACS Chem Biol 2019; 14:256-265. [PMID: 30673204 DOI: 10.1021/acschembio.8b00938] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A nonribosomal peptide synthetase (NRPS) assembly line ( sfa) in Streptomyces thioluteus that directs the formation of the diisonitrile chalkophore SF2768 (1) has been characterized by heterologous expression and directed gene knockouts. Herein, differential metabolic analysis of the heterologous expression strain and the original host led to the isolation of an SF2768 analogue (2, a byproduct of sfa) that possesses N-isovaleryl rather than 3-isocyanobutyryl side chains. The proposed biosynthetic logic of sfa and the structural difference between 1 and 2 suggested substrate promiscuity of the adenylate-forming enzyme SfaB. Further substrate scope investigation of SfaB and a successfully reconstituted NRPS system including a four-enzyme cascade enabled incorporation of diverse carboxylic acid building blocks into peptide scaffolds, and 30 unnatural products were thus generated. This structural diversification strategy based on substrate flexibility of the adenylation domain and in vitro reconstitution can be applied to other adenylation-priming pathways, thus providing a supplementary method for diversity-oriented total synthesis. Additionally, the biocatalytic process of the putative lysine δ-hydroxylase SfaE was validated through the derivatization of two key aldehyde intermediates (2a and 2b), thereby expanding the toolkit of enzymatic C-H bond activation.
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Affiliation(s)
- Mengyi Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijuan Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, P. R. China
| | - Jing He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Engineering Pseudochelin Production in Myxococcus xanthus. Appl Environ Microbiol 2018; 84:AEM.01789-18. [PMID: 30217842 DOI: 10.1128/aem.01789-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/01/2018] [Indexed: 12/15/2022] Open
Abstract
Myxobacteria utilize the catechol natural products myxochelin A and B in order to maintain their iron homeostasis. Recently, the production of these siderophores, along with a new myxochelin derivative named pseudochelin A, was reported for the marine bacterium Pseudoalteromonas piscicida S2040. The latter derivative features a characteristic imidazoline moiety, which was proposed to originate from an intramolecular condensation reaction of the β-aminoethyl amide group in myxochelin B. To identify the enzyme catalyzing this conversion, we compared the myxochelin regulons of two myxobacterial strains that produce solely myxochelin A and B with those of P. piscicida S2040. This approach revealed a gene exclusive to the myxochelin regulon in P. piscicida S2040, coding for an enzyme of the amidohydrolase superfamily. To prove that this enzyme is indeed responsible for the postulated conversion, the reaction was reconstituted in vitro using a hexahistidine-tagged recombinant protein made in Escherichia coli, with myxochelin B as the substrate. To test the production of pseudochelin A under in vivo conditions, the amidohydrolase gene was cloned into the myxobacterial plasmid pZJY156 and placed under the control of a copper-inducible promoter. The resulting vector was introduced into the myxobacterium Myxococcus xanthus DSM 16526, a native producer of myxochelin A and B. Following induction with copper, the myxobacterial expression strain was found to synthesize small quantities of pseudochelin A. Replacement of the copper-inducible promoter with the constitutive pilA promoter led to increased production levels in M. xanthus, which facilitated the isolation and subsequent structural verification of the heterologously produced compound.IMPORTANCE In this study, an enzyme for imidazoline formation in pseudochelin biosynthesis was identified. Evidence for the involvement of this enzyme in the postulated reaction was obtained after in vitro reconstitution. Furthermore, the function of this enzyme was demonstrated in vivo by transferring the corresponding gene into the bacterium Myxococcus xanthus, which thereby became a producer of pseudochelin A. In addition to clarifying the molecular basis of imidazoline formation in siderophore biosynthesis, we describe the heterologous expression of a gene in a myxobacterium without chromosomal integration. Due to its metabolic proficiency, M. xanthus represents an interesting alternative to established host systems for the reconstitution and manipulation of biosynthetic pathways. Since the plasmid used in this study is easily adaptable for the expression of other enzymes as well, we expand the conventional expression strategy for myxobacteria, which is based on the integration of biosynthetic genes into the host genome.
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20
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Mullowney MW, McClure RA, Robey MT, Kelleher NL, Thomson RJ. Natural products from thioester reductase containing biosynthetic pathways. Nat Prod Rep 2018; 35:847-878. [PMID: 29916519 PMCID: PMC6146020 DOI: 10.1039/c8np00013a] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covering: up to 2018 Thioester reductase domains catalyze two- and four-electron reductions to release natural products following assembly on nonribosomal peptide synthetases, polyketide synthases, and their hybrid biosynthetic complexes. This reductive off-loading of a natural product yields an aldehyde or alcohol, can initiate the formation of a macrocyclic imine, and contributes to important intermediates in a variety of biosyntheses, including those for polyketide alkaloids and pyrrolobenzodiazepines. Compounds that arise from reductase-terminated biosynthetic gene clusters are often reactive and exhibit biological activity. Biomedically important examples include the cancer therapeutic Yondelis (ecteinascidin 743), peptide aldehydes that inspired the first therapeutic proteasome inhibitor bortezomib, and numerous synthetic derivatives and antibody drug conjugates of the pyrrolobenzodiazepines. Recent advances in microbial genomics, metabolomics, bioinformatics, and reactivity-based labeling have facilitated the detection of these compounds for targeted isolation. Herein, we summarize known natural products arising from this important category, highlighting their occurrence in Nature, biosyntheses, biological activities, and the technologies used for their detection and identification. Additionally, we review publicly available genomic data to highlight the remaining potential for novel reductively tailored compounds and drug leads from microorganisms. This thorough retrospective highlights various molecular families with especially privileged bioactivity while illuminating challenges and prospects toward accelerating the discovery of new, high value natural products.
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Affiliation(s)
- Michael W Mullowney
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - Ryan A McClure
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
| | - Matthew T Robey
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA. and Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Regan J Thomson
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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21
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Epstein SC, Charkoudian LK, Medema MH. A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences. Stand Genomic Sci 2018; 13:16. [PMID: 30008988 PMCID: PMC6042397 DOI: 10.1186/s40793-018-0318-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/04/2018] [Indexed: 11/18/2022] Open
Abstract
Microorganisms utilize complex enzymatic pathways to biosynthesize structurally complex and pharmacologically relevant molecules. These pathways are encoded by gene clusters and are found in a diverse set of organisms. The Minimum Information about a Biosynthetic Gene cluster repository facilitates standardized and centralized storage of experimental data on these gene clusters and their molecular products, by utilizing user-submitted data to translate scientific discoveries into a format that can be analyzed computationally. This accelerates the processes of connecting genes to chemical structures, understanding biosynthetic gene clusters in the context of environmental diversity, and performing computer-assisted design of synthetic gene clusters. Here, we present a Standard Operating Procedure, Excel templates, a tutorial video, and a collection of relevant review literature to support scientists in their efforts to submit data into MiBIG. Further, we provide tools to integrate gene cluster annotation projects into the classroom environment, including workflows and assessment materials.
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Affiliation(s)
- Samuel C. Epstein
- Department of Chemistry, Haverford College, Haverford, PA 19041-1391 USA
| | | | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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22
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Discovery of small molecule protease inhibitors by investigating a widespread human gut bacterial biosynthetic pathway. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.03.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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23
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Hug JJ, Bader CD, Remškar M, Cirnski K, Müller R. Concepts and Methods to Access Novel Antibiotics from Actinomycetes. Antibiotics (Basel) 2018; 7:E44. [PMID: 29789481 PMCID: PMC6022970 DOI: 10.3390/antibiotics7020044] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/25/2022] Open
Abstract
Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics. Currently uncultured actinobacteria can be made available by bioprospecting extreme or simply habitats other than soil. Furthermore, bioinformatic analysis of genomes reveals most producers to harbour many more biosynthetic gene clusters than compounds identified from any single strain, which translates into a silent biosynthetic potential of the microbial world for the production of yet unknown natural products. This review covers discovery strategies and innovative methods recently employed to access the untapped reservoir of natural products. The focus is the order of actinomycetes although most approaches are similarly applicable to other microbes. Advanced cultivation methods, genomics- and metagenomics-based approaches, as well as modern metabolomics-inspired methods are highlighted to emphasise the interplay of different disciplines to improve access to novel natural products.
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Affiliation(s)
- Joachim J Hug
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Chantal D Bader
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Maja Remškar
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Katarina Cirnski
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
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24
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Ho YTC, Leng DJ, Ghiringhelli F, Wilkening I, Bushell DP, Kostner O, Riva E, Havemann J, Passarella D, Tosin M. Novel chemical probes for the investigation of nonribosomal peptide assembly. Chem Commun (Camb) 2018. [PMID: 28627528 DOI: 10.1039/c7cc02427d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Chemical probes were devised and evaluated for the capture of biosynthetic intermediates involved in the bio-assembly of the nonribosomal peptide echinomycin. Putative intermediate peptide species were isolated and characterised, providing fresh insights into pathway substrate flexibility and paving the way for novel chemoenzymatic approaches towards unnatural peptides.
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Affiliation(s)
- Y T Candace Ho
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Daniel J Leng
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Francesca Ghiringhelli
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK. and Department of Chemistry, Universita' degli Studi di Milano, Via Golgi, 19 20133 Milano, Italy
| | - Ina Wilkening
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Dexter P Bushell
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Otto Kostner
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK. and Institut für Organische Chemie, Universität Wien, Währinger Str., 38 1090 Wien, Austria
| | - Elena Riva
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Judith Havemann
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
| | - Daniele Passarella
- Department of Chemistry, Universita' degli Studi di Milano, Via Golgi, 19 20133 Milano, Italy
| | - Manuela Tosin
- Department of Chemistry, University of Warwick, Library Road, CV4 7AL, UK.
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25
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Wang L, Zhu M, Zhang Q, Zhang X, Yang P, Liu Z, Deng Y, Zhu Y, Huang X, Han L, Li S, He J. Diisonitrile Natural Product SF2768 Functions As a Chalkophore That Mediates Copper Acquisition in Streptomyces thioluteus. ACS Chem Biol 2017; 12:3067-3075. [PMID: 29131568 DOI: 10.1021/acschembio.7b00897] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A nonribosomal peptide synthetase (NRPS) gene cluster (sfa) was identified in Streptomyces thioluteus to direct the biosynthesis of the diisonitrile antibiotic SF2768. Its biosynthetic pathway was reasonably proposed based on bioinformatics analysis, metabolic profiles of mutants, and the elucidation of the intermediate and shunt product structures. Bioinformatics-based alignment found a putative ATP-binding cassette (ABC) transporter related to iron import within the biosynthetic gene cluster, which implied that the product might be a siderophore. However, characterization of the metal-binding properties by high-resolution electrospray ionization mass spectrometry (HR-ESI-MS), metal-ligand titration, thin-layer chromatography (TLC), and chrome azurol S (CAS) assays revealed that the final product SF2768 and its diisonitrile derivatives specifically bind copper, rather than iron, to form stable complexes. Inductively coupled plasma mass spectrometry (ICP-MS) analysis revealed that the intracellular cupric content of S. thioluteus significantly increased upon incubation with the copper-SF2768 complex, direct evidence for the copper acquisition function of SF2768. Further in vivo functional characterization of the transport elements for the copper-SF2768 complexes not only confirmed the chalkophore identity of the compound but also gave initial clues into the copper uptake mechanism of this nonmethanotrophic microorganism.
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Affiliation(s)
- Lijuan Wang
- National
Key Laboratory of Agricultural Microbiology, College of Life Science
and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengyi Zhu
- National
Key Laboratory of Agricultural Microbiology, College of Life Science
and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingbo Zhang
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM
Center for Marine Microbiology, Guangdong Key Laboratory of Marine
Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People’s Republic of China
| | - Xu Zhang
- National
Key Laboratory of Agricultural Microbiology, College of Life Science
and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Panlei Yang
- National
Key Laboratory of Agricultural Microbiology, College of Life Science
and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zihui Liu
- State
Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Yun Deng
- National
Key Laboratory of Agricultural Microbiology, College of Life Science
and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiguang Zhu
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM
Center for Marine Microbiology, Guangdong Key Laboratory of Marine
Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People’s Republic of China
| | - Xueshi Huang
- Institute
of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang 110819, China
| | - Li Han
- Institute
of Microbial Pharmaceuticals, College of Life and Health Sciences, Northeastern University, Shenyang 110819, China
| | - Shengqing Li
- State
Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing He
- National
Key Laboratory of Agricultural Microbiology, College of Life Science
and Technology, Huazhong Agricultural University, Wuhan 430070, China
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26
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von Tesmar A, Hoffmann M, Pippel J, Fayad AA, Dausend-Werner S, Bauer A, Blankenfeldt W, Müller R. Total Biosynthesis of the Pyrrolo[4,2]benzodiazepine Scaffold Tomaymycin on an In Vitro Reconstituted NRPS System. Cell Chem Biol 2017; 24:1216-1227.e8. [PMID: 28890318 DOI: 10.1016/j.chembiol.2017.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/19/2017] [Accepted: 08/01/2017] [Indexed: 11/25/2022]
Abstract
In vitro reconstitution and biochemical analysis of natural product biosynthetic pathways remains a challenging endeavor, especially if megaenzymes of the nonribosomal peptide synthetase (NRPS) type are involved. In theory, all biosynthetic steps may be deciphered using mass spectrometry (MS)-based analyses of both the carrier protein-coupled intermediates and the free intermediates. We here report the "total biosynthesis" of the pyrrolo[4,2]benzodiazepine scaffold tomaymycin using an in vitro reconstituted NRPS system. Proteoforms were analyzed by liquid chromatography (LC)-MS to decipher every step of the biosynthesis on its respective megasynthetase with up to 170 kDa in size. To the best of our knowledge, this is the first report of a comprehensive analysis of virtually all chemical steps involved in the biosynthesis of nonribosomally synthesized natural products. The study includes experiments to determine substrate specificities of the corresponding A-domains in competition assays by analyzing the adenylation step as well as the transfer to the respective carrier protein domain.
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Affiliation(s)
- Alexander von Tesmar
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Michael Hoffmann
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Jan Pippel
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Antoine Abou Fayad
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Stefan Dausend-Werner
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Armin Bauer
- Sanofi-Aventis Deutschland GmbH, R&D Therapeutic Area Infectious Diseases, Industriepark Höchst G878, 65926 Frankfurt am Main, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany
| | - Rolf Müller
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
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27
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Losada AA, Cano-Prieto C, García-Salcedo R, Braña AF, Méndez C, Salas JA, Olano C. Caboxamycin biosynthesis pathway and identification of novel benzoxazoles produced by cross-talk in Streptomyces sp. NTK 937. Microb Biotechnol 2017; 10:873-885. [PMID: 28417606 PMCID: PMC5481532 DOI: 10.1111/1751-7915.12716] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/01/2017] [Accepted: 03/20/2017] [Indexed: 12/13/2022] Open
Abstract
Streptomyces sp. NTK937, producer of benzoxazole antibiotic caboxamycin, produces in addition a methyl ester derivative, O‐methylcaboxamycin. Caboxamycin cluster, comprising one regulatory and nine structural genes, has been delimited, and each gene has been individually inactivated to demonstrate its role in the biosynthetic process. The O‐methyltransferase potentially responsible for O‐methylcaboxamycin synthesis would reside outside this cluster. Five of the genes, cbxR, cbxA, cbxB, cbxD and cbxE, encoding a SARP transcriptional regulator, salicylate synthase, 3‐oxoacyl‐ACP‐synthase, ACP and amidohydrolase, respectively, have been found to be essential for caboxamycin biosynthesis. The remaining five structural genes were found to have paralogues distributed throughout the genome, capable of partaking in the process when their cluster homologue is inactivated. Two of such paralogues, cbxC’ and cbxI’, coding an AMP‐dependent synthetase‐ligase and an anthranilate synthase, respectively, have been identified. However, the other three genes might simultaneously have more than one paralogue, given that cbxF (DAHP synthase), cbxG (2,3‐dihydro‐2,3‐dihydroxybenzoate dehydrogenase) and cbxH (isochorismatase) have three, three and five putative paralogue genes, respectively, of similar function within the genome. As a result of genetic manipulation, a novel benzoxazole (3′‐hydroxycaboxamycin) has been identified in the salicylate synthase‐deficient mutant strain ΔcbxA. 3′‐hydroxycaboxamycin derives from the cross‐talk between the caboxamycin and enterobactin pathways.
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Affiliation(s)
- Armando A Losada
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Carolina Cano-Prieto
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Raúl García-Salcedo
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Alfredo F Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
| | - José A Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006, Oviedo, Spain
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28
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Kurth C, Kage H, Nett M. Siderophores as molecular tools in medical and environmental applications. Org Biomol Chem 2016; 14:8212-27. [PMID: 27492756 DOI: 10.1039/c6ob01400c] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Almost all life forms depend on iron as an essential micronutrient that is needed for electron transport and metabolic processes. Siderophores are low-molecular-weight iron chelators that safeguard the supply of this important metal to bacteria, fungi and graminaceous plants. Although animals and the majority of plants do not utilise siderophores and have alternative means of iron acquisition, siderophores have found important clinical and agricultural applications. In this review, we will highlight the different uses of these iron-chelating molecules.
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Affiliation(s)
- Colette Kurth
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, D-07745 Jena, Germany
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29
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Chiang YM, Ahuja M, Oakley CE, Entwistle R, Asokan A, Zutz C, Wang CCC, Oakley BR. Development of Genetic Dereplication Strains in Aspergillus nidulans Results in the Discovery of Aspercryptin. Angew Chem Int Ed Engl 2016; 55:1662-5. [PMID: 26563584 PMCID: PMC4724294 DOI: 10.1002/anie.201507097] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/04/2015] [Indexed: 11/07/2022]
Abstract
To reduce the secondary metabolite background in Aspergillus nidulans and minimize the rediscovery of compounds and pathway intermediates, we created a "genetic dereplication" strain in which we deleted eight of the most highly expressed secondary metabolite gene clusters (more than 244,000 base pairs deleted in total). This strain allowed us to discover a novel compound that we designate aspercryptin and to propose a biosynthetic pathway for the compound. Interestingly, aspercryptin is formed from compounds produced by two separate gene clusters, one of which makes the well-known product cichorine. This raises the exciting possibility that fungi use differential regulation of expression of secondary metabolite gene clusters to increase the diversity of metabolites they produce.
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Affiliation(s)
- Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan, 71710, Taiwan
| | - Manmeet Ahuja
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
- Industrial Biotechnology Division, Reliance Technology Group, Reliance Industries Limited, Reliance Corporate Park, Thane Belapur Road, Ghansoli, Navi, Mumbai, 400701, India
| | - C Elizabeth Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Ruth Entwistle
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Anabanadam Asokan
- Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66045, USA
| | - Christoph Zutz
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA.
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30
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Chiang YM, Ahuja M, Oakley CE, Entwistle R, Asokan A, Zutz C, Wang CCC, Oakley BR. Development of Genetic Dereplication Strains in Aspergillus nidulans
Results in the Discovery of Aspercryptin. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507097] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy; University of Southern California; Los Angeles CA 90089 USA
- Department of Pharmacy; Chia Nan University of Pharmacy and Science; Tainan 71710 Taiwan
| | - Manmeet Ahuja
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
- Industrial Biotechnology Division, Reliance Technology Group; Reliance Industries Limited, Reliance Corporate Park; Thane Belapur Road, Ghansoli, Navi Mumbai 400701 India
| | - C. Elizabeth Oakley
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
| | - Ruth Entwistle
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
| | - Anabanadam Asokan
- Del Shankel Structural Biology Center; University of Kansas; Lawrence KS 66045 USA
| | - Christoph Zutz
- Institute for Milk Hygiene; University of Veterinary Medicine Vienna; Vienna 1210 Austria
| | - Clay C. C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy; University of Southern California; Los Angeles CA 90089 USA
- Department of Chemistry; University of Southern California; Los Angeles CA 90089 USA
| | - Berl R. Oakley
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
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31
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Korp J, König S, Schieferdecker S, Dahse HM, König GM, Werz O, Nett M. Harnessing Enzymatic Promiscuity in Myxochelin Biosynthesis for the Production of 5-Lipoxygenase Inhibitors. Chembiochem 2015; 16:2445-50. [PMID: 26416255 DOI: 10.1002/cbic.201500446] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 11/10/2022]
Abstract
The siderophore myxochelin A is a potent inhibitor of human 5-lipoxygenase (5-LO). To clarify whether the iron-chelating properties of myxochelin A are responsible for this activity, several analogues of this compound were generated in the native producer Pyxidicoccus fallax by precursor-directed biosynthesis. Testing in a cell-free assay unveiled three derivatives with bioactivity comparable with that of myxochelin A. Furthermore, it became evident that inhibition of 5-LO by myxochelins does not correlate with their iron affinities.
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Affiliation(s)
- Juliane Korp
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Stefanie König
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-Universität Jena, Philosophenweg 14, 07743, Jena, Germany
| | - Sebastian Schieferdecker
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Hans-Martin Dahse
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Gabriele M König
- Institute for Pharmaceutical Biology, Rheinische Friedrich-Wilhelms-Universität Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Oliver Werz
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-Universität Jena, Philosophenweg 14, 07743, Jena, Germany
| | - Markus Nett
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany.
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32
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Sucipto H, Sahner JH, Prusov E, Wenzel SC, Hartmann RW, Koehnke J, Müller R. In vitro reconstitution of α-pyrone ring formation in myxopyronin biosynthesis. Chem Sci 2015; 6:5076-5085. [PMID: 29308173 PMCID: PMC5724707 DOI: 10.1039/c5sc01013f] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/14/2015] [Indexed: 12/22/2022] Open
Abstract
Myxopyronins are α-pyrone antibiotics produced by the terrestrial bacterium Myxococcus fulvus Mx f50 and possess antibacterial activity against Gram-positive and Gram-negative pathogens. They target the bacterial RNA polymerase (RNAP) "switch region" as non-competitive inhibitors and display no cross-resistance to the established RNAP inhibitor rifampicin. Recent analysis of the myxopyronin biosynthetic pathway led to the hypothesis that this secondary metabolite is produced from two separate polyketide parts, which are condensed by the stand-alone ketosynthase MxnB. Using in vitro assays we show that MxnB catalyzes a unique condensation reaction forming the α-pyrone ring of myxopyronins from two activated acyl chains in form of their β-keto intermediates. MxnB is able to accept thioester substrates coupled to either N-acetylcysteamine (NAC) or a specific carrier protein (CP). The turnover rate of MxnB for substrates bound to CP was 12-fold higher than for NAC substrates, demonstrating the importance of protein-protein interactions in polyketide synthase (PKS) systems. The crystal structure of MxnB reveals the enzyme to be an unusual member of the ketosynthase group capable of binding and condensing two long alkyl chains bound to carrier proteins. The geometry of the two binding tunnels supports the biochemical data and allows us to propose an order of reaction, which is supported by the identification of novel myxopyronin congeners in the extract of the producer strain. Insights into the mechanism of this unique condensation reaction do not only expand our knowledge regarding the thiolase enzyme family but also opens up opportunities for PKS bioengineering to achieve directed structural modifications.
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Affiliation(s)
- H Sucipto
- Department of Microbial Natural Products , Helmholtz Institute for Pharmaceutical Research Saarland , Building C2 3 , 66123 Saarbrücken , Germany .
| | - J H Sahner
- Department of Drug Design and Optimization , Helmholtz Institute for Pharmaceutical Research Saarland , Pharmaceutical and Medicinal Chemistry , Saarland University , Building C2 3 , 66123 Saarbrücken , Germany
| | - E Prusov
- Helmholtz Centre for Infection Research , Inhoffenstrasse 7 , 38124 Braunschweig , Germany
| | - S C Wenzel
- Department of Microbial Natural Products , Helmholtz Institute for Pharmaceutical Research Saarland , Building C2 3 , 66123 Saarbrücken , Germany .
| | - R W Hartmann
- Department of Drug Design and Optimization , Helmholtz Institute for Pharmaceutical Research Saarland , Pharmaceutical and Medicinal Chemistry , Saarland University , Building C2 3 , 66123 Saarbrücken , Germany
| | - J Koehnke
- Workgroup Structural Biology of Biosynthetic Enzymes , Helmholtz Institute for Pharmaceutical Research Saarland , Building C2 2 , 66123 Saarbrücken , Germany .
| | - R Müller
- Department of Microbial Natural Products , Helmholtz Institute for Pharmaceutical Research Saarland , Building C2 3 , 66123 Saarbrücken , Germany .
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Barajas JF, Phelan RM, Schaub AJ, Kliewer JT, Kelly PJ, Jackson DR, Luo R, Keasling JD, Tsai SC. Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols. ACTA ACUST UNITED AC 2015; 22:1018-29. [PMID: 26235055 DOI: 10.1016/j.chembiol.2015.06.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/05/2015] [Accepted: 06/22/2015] [Indexed: 01/22/2023]
Abstract
The terminal reductase (R) domain from the non-ribosomal peptide synthetase (NRPS) module MxaA in Stigmatella aurantiaca Sga15 catalyzes a non-processive four-electron reduction to produce the myxalamide family of secondary metabolites. Despite widespread use in nature, a lack of structural and mechanistic information concerning reductive release from polyketide synthase (PKS) and NRPS assembly lines principally limits our ability to redesign R domains with altered or improved activity. Here we report crystal structures for MxaA R, both in the absence and, for the first time, in the presence of the NADPH cofactor. Molecular dynamics simulations were employed to provide a deeper understanding of this domain and further identify residues critical for structural integrity, substrate binding, and catalysis. Aggregate computational and structural findings provided a basis for mechanistic investigations and, in the process, delivered a rationally altered variant with improved activity toward highly reduced substrates.
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Affiliation(s)
- Jesus F Barajas
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Ryan M Phelan
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94270, USA
| | - Andrew J Schaub
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Jaclyn T Kliewer
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Peter J Kelly
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - David R Jackson
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Jay D Keasling
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94270, USA; Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.
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34
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Keller L, Plaza A, Dubiella C, Groll M, Kaiser M, Müller R. Macyranones: Structure, Biosynthesis, and Binding Mode of an Unprecedented Epoxyketone that Targets the 20S Proteasome. J Am Chem Soc 2015; 137:8121-30. [PMID: 26050527 DOI: 10.1021/jacs.5b03833] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In our screening efforts to identify unique scaffolds from myxobacteria for the drug discovery process, we used LC-SPE-NMR-MS techniques to isolate six linear peptides, termed macyranone A-F, from Cystobacter fuscus MCy9118. The macyranones are characterized by a rare 2-methylmalonamide moiety and an α-amino ketone fragment including an α',β'-epoxyketone in macyranone A. Gene disruption experiments confirmed the biosynthetic gene cluster of the macyranones as PKS/NRPS hybrid. Detailed in silico and phylogenetic analysis unraveled that the biosynthesis involves two conspicuous amide bond formations accomplished by an amidotransferase and a unique condensation domain. The gene cluster provides further insights into the formation of the powerful epoxyketone residue involving an acyl-CoA dehydrogenase and an unconventional free-standing thioesterase. Macyranone A was found to inhibit the chymotrypsin-like activity of the yeast 20S proteasome with an IC50 of 5.9 nM and the human constitutive proteasome and immunoproteasome with IC50 values of 21 and 15 nM, respectively. The β5 subunit of the 20S proteasome was characterized as target by X-ray crystallography revealing an irreversible binding mode similar to the natural product epoxomicin. The presence of the methylmalonamide residue facilitates the stabilization of macyranone A with the active β5 subunit of the proteasome. Macyranone A exhibits a potent inhibitory effect against the parasites Trypanosoma brucei rhodesiense and Leishmania donovani with IC50 values of 1.55 and 0.22 μM, respectively.
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Affiliation(s)
- Lena Keller
- †Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.,∥German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig 38124, Germany
| | - Alberto Plaza
- †Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.,∥German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig 38124, Germany
| | - Christian Dubiella
- ⊥Center for Integrated Protein Science Munich (CIPSM), Department für Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Michael Groll
- ⊥Center for Integrated Protein Science Munich (CIPSM), Department für Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany
| | - Marcel Kaiser
- §Swiss Tropical and Public Health Institute (Swiss TPH), Socinstraße 57, CH-4002 Basel, Switzerland.,‡University of Basel, Petersplatz 1, CH-4003 Basel, Switzerland
| | - Rolf Müller
- †Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.,∥German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig 38124, Germany
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Alonzo DA, Magarvey NA, Schmeing TM. Characterization of cereulide synthetase, a toxin-producing macromolecular machine. PLoS One 2015; 10:e0128569. [PMID: 26042597 PMCID: PMC4455996 DOI: 10.1371/journal.pone.0128569] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 04/28/2015] [Indexed: 01/14/2023] Open
Abstract
Cereulide synthetase is a two-protein nonribosomal peptide synthetase system that produces a potent emetic toxin in virulent strains of Bacillus cereus. The toxin cereulide is a depsipeptide, as it consists of alternating aminoacyl and hydroxyacyl residues. The hydroxyacyl residues are derived from keto acid substrates, which cereulide synthetase selects and stereospecifically reduces with imbedded ketoreductase domains before incorporating them into the growing depsipeptide chain. We present an in vitro biochemical characterization of cereulide synthetase. We investigate the kinetics and side chain specificity of α-keto acid selection, evaluate the requirement of an MbtH-like protein for adenylation domain activity, assay the effectiveness of vinylsulfonamide inhibitors on ester-adding modules, perform NADPH turnover experiments and evaluate in vitro depsipeptide biosynthesis. This work also provides biochemical insight into depsipeptide-synthesizing nonribosomal peptide synthetases responsible for other bioactive molecules such as valinomycin, antimycin and kutzneride.
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Affiliation(s)
- Diego A. Alonzo
- Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada
| | - Nathan A. Magarvey
- Department of Chemistry & Chemical Biology, McMaster University, M.G. DeGroote Institute for Infectious Disease Research, 1200 Main St. W, Hamilton, Ontario L8N 3Z5, Canada
| | - T. Martin Schmeing
- Department of Biochemistry, McGill University, Montréal, QC H3G 0B1, Canada
- Groupe de Recherche Axé sur la Structure des Protéines (GRASP), McGill University, Montréal, QC H3G 0B1, Canada
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Abstract
Microbes produce a huge array of secondary metabolites endowed with important ecological functions. These molecules, which can be catalogued as natural products, have long been exploited in medical fields as antibiotics, anticancer and anti-infective agents. Recent years have seen considerable advances in elucidating natural-product biosynthesis and many drugs used today are natural products or natural-product derivatives. The major contribution to recent knowledge came from application of genomics to secondary metabolism and was facilitated by all relevant genes being organised in a contiguous DNA segment known as gene cluster. Clustering of genes regulating biosynthesis in bacteria is virtually universal. Modular gene clusters can be mixed and matched during evolution to generate structural diversity in natural products. Biosynthesis of many natural products requires the participation of complex molecular machines known as polyketide synthases and non-ribosomal peptide synthetases. Discovery of new evolutionary links between the polyketide synthase and fatty acid synthase pathways may help to understand the selective advantages that led to evolution of secondary-metabolite biosynthesis within bacteria. Secondary metabolites confer selective advantages, either as antibiotics or by providing a chemical language that allows communication among species, with other organisms and their environment. Herewith, we discuss these aspects focusing on the most clinically relevant bioactive molecules, the thiotemplated modular systems that include polyketide synthases, non-ribosomal peptide synthetases and fatty acid synthases. We begin by describing the evolutionary and physiological role of marine natural products, their structural/functional features, mechanisms of action and biosynthesis, then turn to genomic and metagenomic approaches, highlighting how the growing body of information on microbial natural products can be used to address fundamental problems in environmental evolution and biotechnology.
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Biosynthesis of crocacin involves an unusual hydrolytic release domain showing similarity to condensation domains. ACTA ACUST UNITED AC 2014; 21:855-65. [PMID: 24981773 DOI: 10.1016/j.chembiol.2014.05.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/12/2014] [Accepted: 05/15/2014] [Indexed: 11/20/2022]
Abstract
The crocacins are potent antifungal and cytotoxic natural compounds from myxobacteria of the genus Chondromyces. Although total synthesis approaches have been reported, the molecular and biochemical basis guiding the formation of the linear crocacin scaffold has remained unknown. Along with the identification and functional analysis of the crocacin biosynthetic gene cluster from Chondromyces crocatus Cm c5, we here present the identification and biochemical characterization of an unusual chain termination domain homologous to condensation domains responsible for hydrolytic release of the product from the assembly line. In particular, gene inactivation studies and in vitro experiments using the heterologously produced domain CroK-C2 confirm this surprising role giving rise to the linear carboxylic acid. Additionally, we determined the kinetic parameters of CroK-C2 by monitoring hydrolytic cleavage of the substrate mimic N-acetylcysteaminyl-crocacin B using an innovative high-performance liquid chromatography mass spectrometry-based assay.
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38
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Müller R, Wink J. Future potential for anti-infectives from bacteria - how to exploit biodiversity and genomic potential. Int J Med Microbiol 2013; 304:3-13. [PMID: 24119567 DOI: 10.1016/j.ijmm.2013.09.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The early stages of antibiotic development include the identification of novel hit compounds. Since actinomycetes and myxobacteria are still the most important natural sources of active metabolites, we provide an overview on these producers and discuss three of the most promising approaches toward finding novel anti-infectives from microorganisms. These are defined as the use of biodiversity to find novel producers, the variation of culture conditions and induction of silent genes, and the exploitation of the genomic potential of producers via "genome mining". Challenges that exist beyond compound discovery are outlined in the last section.
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Affiliation(s)
- Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), P.O. Box 151150, 66041 Saarbrücken, Germany; Helmholtz Centre for Infectious Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Joachim Wink
- Helmholtz Centre for Infectious Research (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany.
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Masschelein J, Mattheus W, Gao LJ, Moons P, Van Houdt R, Uytterhoeven B, Lamberigts C, Lescrinier E, Rozenski J, Herdewijn P, Aertsen A, Michiels C, Lavigne R. A PKS/NRPS/FAS hybrid gene cluster from Serratia plymuthica RVH1 encoding the biosynthesis of three broad spectrum, zeamine-related antibiotics. PLoS One 2013; 8:e54143. [PMID: 23349809 PMCID: PMC3547906 DOI: 10.1371/journal.pone.0054143] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 12/06/2012] [Indexed: 11/21/2022] Open
Abstract
Serratia plymuthica strain RVH1, initially isolated from an industrial food processing environment, displays potent antimicrobial activity towards a broad spectrum of Gram-positive and Gram-negative bacterial pathogens. Isolation and subsequent structure determination of bioactive molecules led to the identification of two polyamino antibiotics with the same molecular structure as zeamine and zeamine II as well as a third, closely related analogue, designated zeamine I. The gene cluster encoding the biosynthesis of the zeamine antibiotics was cloned and sequenced and shown to encode FAS, PKS as well as NRPS related enzymes in addition to putative tailoring and export enzymes. Interestingly, several genes show strong homology to the pfa cluster of genes involved in the biosynthesis of long chain polyunsaturated fatty acids in marine bacteria. We postulate that a mixed FAS/PKS and a hybrid NRPS/PKS assembly line each synthesize parts of the backbone that are linked together post-assembly in the case of zeamine and zeamine I. This interaction reflects a unique interplay between secondary lipid and secondary metabolite biosynthesis. Most likely, the zeamine antibiotics are produced as prodrugs that undergo activation in which a nonribosomal peptide sequence is cleaved off.
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Affiliation(s)
- Joleen Masschelein
- Division of Gene Technology, KU Leuven, Heverlee, Belgium
- Laboratory of Food Microbiology, KU Leuven, Heverlee, Belgium
| | | | - Ling-Jie Gao
- Interface Valorisation Platform, KU Leuven, Leuven, Belgium
| | - Pieter Moons
- Laboratory of Food Microbiology, KU Leuven, Heverlee, Belgium
| | - Rob Van Houdt
- Laboratory of Food Microbiology, KU Leuven, Heverlee, Belgium
| | | | | | - Eveline Lescrinier
- Laboratory for Medicinal Chemistry, Rega Institute for Medicinal Research, Leuven, Belgium
| | - Jef Rozenski
- Laboratory for Medicinal Chemistry, Rega Institute for Medicinal Research, Leuven, Belgium
| | - Piet Herdewijn
- Interface Valorisation Platform, KU Leuven, Leuven, Belgium
- Laboratory for Medicinal Chemistry, Rega Institute for Medicinal Research, Leuven, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology, KU Leuven, Heverlee, Belgium
| | - Chris Michiels
- Laboratory of Food Microbiology, KU Leuven, Heverlee, Belgium
| | - Rob Lavigne
- Division of Gene Technology, KU Leuven, Heverlee, Belgium
- * E-mail:
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40
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Wyatt MA, Mok MCY, Junop M, Magarvey NA. Heterologous expression and structural characterisation of a pyrazinone natural product assembly line. Chembiochem 2012; 13:2408-15. [PMID: 23070851 DOI: 10.1002/cbic.201200340] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Indexed: 11/07/2022]
Abstract
Through a number of strategies nonribosomal peptide assembly lines give rise to a metabolic diversity not possible by ribosomal synthesis. One distinction within nonribosomal assembly is that products are elaborated on an enzyme-tethered substrate, and their release is enzyme catalysed. Reductive release by NAD(P)H-dependent catalysts is one observed nonribosomal termination and release strategy. Here we probed the selectivity of a terminal reductase domain by using a full-length heterologously expressed nonribosomal peptide synthetase for the dipeptide aureusimine and were able to generate 17 new analogues. Further, we generated an X-ray structure of aureusimine terminal reductase to gain insight into the structural details associated with this enzymatic domain.
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Affiliation(s)
- Morgan A Wyatt
- Michael G. Degroote Institute for Infectious Disease Research, McMaster University, 1200 Main St. W, Hamilton ON, L8N 3Z5, Canada
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41
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ZHU LP, Li ZF, HAN K, LI SG, LI YZ. Novel Characters of Myxobacterial Modular Natural Product Assembly Lines*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2011.00325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Simpson TJ. Genetic and biosynthetic studies of the fungal prenylated xanthone shamixanthone and related metabolites in Aspergillus spp. revisited. Chembiochem 2012; 13:1680-8. [PMID: 22730213 DOI: 10.1002/cbic.201200014] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Revised: 05/07/2012] [Indexed: 11/08/2022]
Abstract
Biosynthetic genes for the prenylated xanthone shamixanthone have been identified in the Aspergillus nidulans genome; based on assignment of putative functions from sequence analyses and selected gene deletions, a pathway was proposed leading from the anthraquinone emodin via the benzophenone carboxylic acid monodictyphenone and the xanthone emericellin to shamixanthone. Several aspects of this proposed pathway are inconsistent with previously identified biosynthetic intermediates: the anthraquinone chrysophanol and the benzophenone aldehyde derivatives arugosins F and A/B, isotopic labelling studies and chemical precedents. A new pathway is presented that provides a full rationale for the results of the gene deletion studies and reconciles them with previous biosynthetic results, and is in accord with established chemical and biosynthetic mechanisms. The importance of interpreting genetic information in terms of established biosynthetic events is discussed.
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Affiliation(s)
- Thomas J Simpson
- University of Bristol, School of Chemistry, Cantock's Close, Bristol, BS8 1TS, UK.
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43
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Seyedsayamdost MR, Traxler MF, Zheng SL, Kolter R, Clardy J. Structure and biosynthesis of amychelin, an unusual mixed-ligand siderophore from Amycolatopsis sp. AA4. J Am Chem Soc 2011; 133:11434-7. [PMID: 21699219 PMCID: PMC3144690 DOI: 10.1021/ja203577e] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Actinobacteria generate a large number of structurally diverse small molecules with potential therapeutic value. Genomic analyses of this productive group of bacteria show that their genetic potential to manufacture small molecules exceeds their observed ability by roughly an order of magnitude, and this revelation has prompted a number of studies to identify members of the unknown majority. As a potential window into this cryptic secondary metabolome, pairwise assays for developmental interactions within a set of 20 sequenced actinomycetes were carried out. These assays revealed that Amycolatopsis sp. AA4, a so-called “rare” actinomycete, produces a novel siderophore, amychelin, which alters the developmental processes of several neighboring streptomycetes. Using this phenotype as an assay, we isolated amychelin and solved its structure by NMR and MS methods coupled with an X-ray crystallographic analysis of its Fe-complex. The iron binding affinity of amychelin was determined using EDTA competition assays, and a biosynthetic cluster was identified and annotated to provide a tentative biosynthetic scheme for amychelin.
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Affiliation(s)
- Mohammad R Seyedsayamdost
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Carr G, Seyedsayamdost MR, Chandler JR, Greenberg EP, Clardy J. Sources of diversity in bactobolin biosynthesis by Burkholderia thailandensis E264. Org Lett 2011; 13:3048-51. [PMID: 21615115 PMCID: PMC3111747 DOI: 10.1021/ol200922s] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Indexed: 11/30/2022]
Abstract
A series of deletion mutants in the recently identified bactobolin biosynthetic pathway defined the roles of several key biosynthetic enzymes and showed how promiscuity in three enzyme systems allows this cluster to produce multiple products. Studies on the deletion mutants also led to four new bactobolin analogs that provide additional structure-activity relationships for this interesting antibiotic family.
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45
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Biosynthesis of the immunosuppressants FK506, FK520, and rapamycin involves a previously undescribed family of enzymes acting on chorismate. Proc Natl Acad Sci U S A 2011; 108:4776-81. [PMID: 21383123 DOI: 10.1073/pnas.1015773108] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The macrocyclic polyketides FK506, FK520, and rapamycin are potent immunosuppressants that prevent T-cell proliferation through initial binding to the immunophilin FKBP12. Analogs of these molecules are of considerable interest as therapeutics in both metastatic and inflammatory disease. For these polyketides the starter unit for chain assembly is (4R,5R)-4,5-dihydroxycyclohex-1-enecarboxylic acid derived from the shikimate pathway. We show here that the first committed step in its formation is hydrolysis of chorismate to form (4R,5R)-4,5-dihydroxycyclohexa-1,5-dienecarboxylic acid. This chorismatase activity is encoded by fkbO in the FK506 and FK520 biosynthetic gene clusters, and by rapK in the rapamycin gene cluster of Streptomyces hygroscopicus. Purified recombinant FkbO (from FK520) efficiently catalyzed the chorismatase reaction in vitro, as judged by HPLC-MS and NMR analysis. Complementation using fkbO from either the FK506 or the FK520 gene cluster of a strain of S. hygroscopicus specifically deleted in rapK (BIOT-4010) restored rapamycin production, as did supplementation with (4R,5R)-4,5-dihydroxycyclohexa-1,5-dienecarboxylic acid. Although BIOT-4010 produced no rapamycin, it did produce low levels of BC325, a rapamycin analog containing a 3-hydroxybenzoate starter unit. This led us to identify the rapK homolog hyg5 as encoding a chorismatase/3-hydroxybenzoate synthase. Similar enzymes in other bacteria include the product of the bra8 gene from the pathway to the terpenoid natural product brasilicardin. Expression of either hyg5 or bra8 in BIOT-4010 led to increased levels of BC325. Also, purified Hyg5 catalyzed the predicted conversion of chorismate into 3-hydroxybenzoate. FkbO, RapK, Hyg5, and Bra8 are thus founder members of a previously unrecognized family of enzymes acting on chorismate.
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46
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Zhu G, Shi X, Cai X. The reductase domain in a Type I fatty acid synthase from the apicomplexan Cryptosporidium parvum: restricted substrate preference towards very long chain fatty acyl thioesters. BMC BIOCHEMISTRY 2010; 11:46. [PMID: 21092192 PMCID: PMC2995488 DOI: 10.1186/1471-2091-11-46] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Accepted: 11/22/2010] [Indexed: 12/30/2022]
Abstract
Background The apicomplexan Cryptosporidium parvum genome possesses a 25-kb intronless open reading frame (ORF) that predicts a multifunctional Type I fatty acid synthase (CpFAS1) with at least 21 enzymatic domains. Although the architecture of CpFAS1 resembles those of bacterial polyketide synthases (PKSs), this megasynthase is predicted to function as a fatty acyl elongase as our earlier studies have indicated that the N-terminal loading unit (acyl-[ACP] ligase) prefers using intermediate to long chain fatty acids as substrates, and each of the three internal elongation modules contains a complete set of enzymes to produce a saturated fatty acyl chain. Although the activities of almost all domains were confirmed using recombinant proteins, that of the C-terminal reductase domain (CpFAS1-R) was yet undetermined. In fact, there were no published studies to report the kinetic features of any reductase domains in bacterial PKSs using purified recombinant or native proteins. Results In the present study, the identity of CpFAS1-R as a reductase is confirmed by in silico analysis on sequence similarity and characteristic motifs. Phylogenetic analysis based on the R-domains supports a previous notion on the bacterial origin of apicomplexan Type I FAS/PKS genes. We also developed a novel assay using fatty acyl-CoAs as substrates, and determined that CpFAS1-R could only utilize very long chain fatty acyl-CoAs as substrates (i.e., with activity on C26 > C24 > C22 > C20, but no activity on C18 and C16). It was capable of using both NADPH and NADH as electron donors, but prefers NADPH to NADH. The activity of CpFAS1-R displayed allosteric kinetics towards C26 hexacosanoyl CoA as a substrate (h = 2.0; Vmax = 32.8 nmol min-1 mg-1 protein; and K50 = 0.91 mM). Conclusions We have confirmed the activity of CpFAS1-R by directly assaying its substrate preference and kinetic parameters, which is for the first time for a Type I FAS, PKS or non-ribosomal peptide synthase (NRPS) reductase domain. The restricted substrate preference towards very long chain fatty acyl thioesters may be an important feature for this megasynthase to avoid the release of product(s) with undesired lengths.
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Affiliation(s)
- Guan Zhu
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4467, USA.
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Abstract
Natural product biosynthetic pathways have evolved enzymes with myriad activities that represent an expansive array of chemical transformations for constructing secondary metabolites. Recently, harnessing the biosynthetic potential of these enzymes through chemoenzymatic synthesis has provided a powerful tool that often rivals the most sophisticated methodologies in modern synthetic chemistry and provides new opportunities for accessing chemical diversity. Herein, we describe our research efforts with enzymes from a broad collection of biosynthetic systems, highlighting recent progress in this exciting field.
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Affiliation(s)
- Jonathan D. Mortison
- Life Sciences Institute, Department of Chemistry and Department of Medicinal Chemistry, 210 Washtenaw Avenue, University of Michigan, Ann Arbor, Michigan 48109
| | - David H. Sherman
- Life Sciences Institute, Department of Chemistry and Department of Medicinal Chemistry, 210 Washtenaw Avenue, University of Michigan, Ann Arbor, Michigan 48109
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Binz TM, Maffioli SI, Sosio M, Donadio S, Müller R. Insights into an unusual nonribosomal peptide synthetase biosynthesis: identification and characterization of the GE81112 biosynthetic gene cluster. J Biol Chem 2010; 285:32710-32719. [PMID: 20710026 DOI: 10.1074/jbc.m110.146803] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The GE81112 tetrapeptides (1-3) represent a structurally unique class of antibiotics, acting as specific inhibitors of prokaryotic protein synthesis. Here we report the cloning and sequencing of the GE81112 biosynthetic gene cluster from Streptomyces sp. L-49973 and the development of a genetic manipulation system for Streptomyces sp. L-49973. The biosynthetic gene cluster for the tetrapeptide antibiotic GE81112 (getA-N) was identified within a 61.7-kb region comprising 29 open reading frames (open reading frames), 14 of which were assigned to the biosynthetic gene cluster. Sequence analysis revealed the GE81112 cluster to consist of six nonribosomal peptide synthetase (NRPS) genes encoding incomplete di-domain NRPS modules and a single free standing NRPS domain as well as genes encoding other biosynthetic and modifying proteins. The involvement of the cloned gene cluster in GE81112 biosynthesis was confirmed by inactivating the NRPS gene getE resulting in a GE81112 production abolished mutant. In addition, we characterized the NRPS A-domains from the pathway by expression in Escherichia coli and in vitro enzymatic assays. The previously unknown stereochemistry of most chiral centers in GE81112 was established from a combined chemical and biosynthetic approach. Taken together, these findings have allowed us to propose a rational model for GE81112 biosynthesis. The results further open the door to developing new derivatives of these promising antibiotic compounds by genetic engineering.
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Affiliation(s)
- Tina M Binz
- From the Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), and Department of Pharmaceutical Biotechnology, Saarland University, Campus C2 3, Saarbrücken 66123, Germany
| | | | | | | | - Rolf Müller
- From the Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), and Department of Pharmaceutical Biotechnology, Saarland University, Campus C2 3, Saarbrücken 66123, Germany.
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Manavalan B, Murugapiran SK, Lee G, Choi S. Molecular modeling of the reductase domain to elucidate the reaction mechanism of reduction of peptidyl thioester into its corresponding alcohol in non-ribosomal peptide synthetases. BMC STRUCTURAL BIOLOGY 2010; 10:1. [PMID: 20067617 PMCID: PMC2835699 DOI: 10.1186/1472-6807-10-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 01/12/2010] [Indexed: 11/19/2022]
Abstract
Background Nonribosomal peptide synthetases (NRPSs) are multienzymatic, multidomain megasynthases involved in the biosynthesis of pharmaceutically important nonribosomal peptides. The peptaibol synthetase from Trichoderma virens (TPS) is an important member of the NRPS family that exhibits antifungal properties. The majority of the NRPSs terminate peptide synthesis with the thioesterase (TE) domain, which either hydrolyzes the thioester linkage, releasing the free peptic acid, or catalyzes the intramolecular macrocyclization to produce a macrolactone product. TPS is an important NRPS that does not encompass a TE domain, but rather a reductase domain (R domain) to release the mature peptide product reductively with the aid of a NADPH cofactor. However, the catalytic mechanism of the reductase domain has not yet been elucidated. Results We present here a three-dimensional (3D) model of the reductase domain based on the crystal structure of vestitone reductase (VR). VR belongs to the short-chain dehydrogenase/reductase (SDR) superfamily and is responsible for the nicotinamide dinucleotide phosphate (NADPH)-dependent reduction of the substrate into its corresponding secondary alcohol product. The binding sites of the probable linear substrates, alamethicin, trichotoxin, antiamoebin I, chrysopermin C and gramicidin, were identified within the modeled R domain using multiple docking approaches. The docking results of the ligand in the active site of the R domain showed that reductase side chains have a high affinity towards ligand binding, while the thioester oxygen of each substrate forms a hydrogen bond with the OH group of Tyr176 and the thiol group of the substrate is closer to the Glu220. The modeling and docking studies revealed the reaction mechanism of reduction of thioester into a primary alcohol. Conclusion Peptaibol biosynthesis incorporates a single R domain, which appears to catalyze the four-electron reduction reaction of a peptidyl carrier protein (PCP)-bound peptide to its corresponding primary alcohol. Analysis of R domains present in the non-redundant (nr) database of the NCBI showed that the R domain always resides in the last NRPS module and is involved in either a two or four-electron reduction reaction.
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Roberts AA, Ryan KS, Moore BS, Gulder TA. Total (bio)synthesis: strategies of nature and of chemists. Top Curr Chem (Cham) 2010; 297:149-203. [PMID: 21495259 PMCID: PMC3109256 DOI: 10.1007/128_2010_79] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The biosynthetic pathways to a number of natural products have been reconstituted in vitro using purified enzymes. Many of these molecules have also been synthesized by organic chemists. Here we compare the strategies used by nature and by chemists to reveal the underlying logic and success of each total synthetic approach for some exemplary molecules with diverse biosynthetic origins.
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