1
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Einsiedler M, Lamm K, Ohlrogge JF, Schuler S, Richter IJ, Lübken T, Gulder TAM. Product Selectivity in Baeyer-Villiger Monooxygenase-Catalyzed Bacterial Alkaloid Core Structure Maturation. J Am Chem Soc 2024; 146:16203-16212. [PMID: 38829274 PMCID: PMC11177316 DOI: 10.1021/jacs.4c04115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/05/2024]
Abstract
Baeyer-Villiger monooxygenases (BVMOs) play crucial roles in the core-structure modification of natural products. They catalyze lactone formation by selective oxygen insertion into a carbon-carbon bond adjacent to a carbonyl group (Baeyer-Villiger oxidation, BVO). The homologous bacterial BVMOs, BraC and PxaB, thereby process bicyclic dihydroindolizinone substrates originating from a bimodular nonribosomal peptide synthetase (BraB or PxaA). While both enzymes initially catalyze the formation of oxazepine-dione intermediates following the identical mechanism, the final natural product spectrum diverges. For the pathway involving BraC, the exclusive formation of lipocyclocarbamates, the brabantamides, was reported. The pathway utilizing PxaB solely produces pyrrolizidine alkaloids, the pyrrolizixenamides. Surprisingly, replacing pxaB within the pyrrolizixenamide biosynthetic pathway by braC does not change the product spectrum to brabantamides. Factors controlling this product selectivity have remained elusive. In this study, we set out to solve this puzzle by combining the total synthesis of crucial pathway intermediates and anticipated products with in-depth functional in vitro studies on both recombinant BVMOs. This work shows that the joint oxazepine-dione intermediate initially formed by both BVMOs leads to pyrrolizixenamides upon nonenzymatic hydrolysis, decarboxylative ring contraction, and dehydration. Brabantamide biosynthesis is enzyme-controlled, with BraC efficiently transforming all the accepted substrates into its cognate final product scaffold. PxaB, in contrast, shows only considerable activity toward brabantamide formation for the substrate analog with a natural brabantamide-type side chain structure, revealing substrate-controlled product selectivity.
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Affiliation(s)
- Manuel Einsiedler
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Natural Product Biotechnology, Helmholtz
Centre for Infection Research (HZI) and Department of Pharmacy at
Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Chair
of Technical Biochemistry, Technische Universität
Dresden, Bergstraße
66, 01069 Dresden, Germany
| | - Katharina Lamm
- Chair
of Technical Biochemistry, Technische Universität
Dresden, Bergstraße
66, 01069 Dresden, Germany
| | - Jonas F. Ohlrogge
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Natural Product Biotechnology, Helmholtz
Centre for Infection Research (HZI) and Department of Pharmacy at
Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Chair
of Technical Biochemistry, Technische Universität
Dresden, Bergstraße
66, 01069 Dresden, Germany
| | - Sebastian Schuler
- Chair
of Technical Biochemistry, Technische Universität
Dresden, Bergstraße
66, 01069 Dresden, Germany
| | - Ivana J. Richter
- Chair
of Technical Biochemistry, Technische Universität
Dresden, Bergstraße
66, 01069 Dresden, Germany
| | - Tilo Lübken
- Chair
of Organic Chemistry I, Technische Universität
Dresden, Bergstraße 66, 01069 Dresden, Germany
| | - Tobias A. M. Gulder
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Natural Product Biotechnology, Helmholtz
Centre for Infection Research (HZI) and Department of Pharmacy at
Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Chair
of Technical Biochemistry, Technische Universität
Dresden, Bergstraße
66, 01069 Dresden, Germany
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2
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Wang S, Wu K, Tang YJ, Deng H. Dehydroamino acid residues in bioactive natural products. Nat Prod Rep 2024; 41:273-297. [PMID: 37942836 PMCID: PMC10880069 DOI: 10.1039/d3np00041a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Indexed: 11/10/2023]
Abstract
Covering: 2000 to up to 2023α,β-Dehydroamino acids (dhAAs) are unsaturated nonproteinogenic amino acids found in a wide array of naturally occurring peptidyl metabolites, predominantly those from bacteria. Other organisms, such as fungi, higher plants and marine invertebrates, have also been found to produce dhAA-containing peptides. The α,β-unsaturation in dhAAs has profound effects on the properties of these molecules. They display significant synthetic flexibility, readily undergoing reactions such as Michael additions, transition-metal-catalysed cross-couplings, and cycloadditions. These residues in peptides/proteins also exhibit great potential in bioorthogonal applications using click chemistry. Peptides containing contiguous dhAA residues have been extensively investigated in the field of foldamers, self-assembling supermolecules that mimic biomacromolecules such as proteins to fold into well-defined conformations. dhAA residues in these peptidyl materials tend to form a 2.05-helix. As a result, stretches of dhAA residues arrange in an extended conformation. In particular, peptidyl foldamers containing β-enamino acid units display interesting conformational, electronic, and supramolecular aggregation properties that can be modulated by light-dependent E-Z isomerization. Among approximately 40 dhAAs found in the natural product inventory, dehydroalanine (Dha) and dehydrobutyrine (Dhb) are the most abundant. Dha is the simplest dehydro-α-amino acid, or α-dhAA, without any geometrical isomers, while its re-arranged isomer, 3-aminoacrylic acid (Aaa or ΔβAla), is the simplest dehydro-β-amino acid, or β-enamino acid, and displays E/Z isomerism. Dhb is the simplest α-dhAA that exhibits E/Z isomerism. The Z-isomer of Dhb (Z-Dhb) is sterically favourable and is present in the majority of naturally occurring peptides containing Dhb residues. Dha and Z-Dhb motifs are commonly found in ribosomally synthesized and post-translationally modified peptides (RiPPs). In the last decade, the formation of Dha and Dhb motifs in RiPPs has been extensively investigated, which will be briefly discussed in this review. The formation of other dhAA residues in natural products (NPs) is, however, less understood. In this review, we will discuss recent advances in the biosynthesis of peptidyl NPs containing unusual dhAA residues and cryptic dhAA residues. The proposed biosynthetic pathways of these natural products will also be discussed.
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Affiliation(s)
- Shan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Kewen Wu
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
| | - Ya-Jie Tang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
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3
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Pang L, Yao D, Gao F, Bian X, Zhang Y, Zhong G. Biosyntheses of azetidine-containing natural products. Org Biomol Chem 2023; 21:7242-7254. [PMID: 37642579 DOI: 10.1039/d3ob01205k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Azetidine is a four-membered polar heterocycle including a basic secondary amine, and is characterized by its high ring-strain energy, strong molecular rigidity and satisfactory stability. As a result, azetidine exhibits great challenges in its chemical synthesis and biosynthesis, which may explain the limited number of azetidine-containing natural products uncovered to date. In particular, the biosynthetic mechanisms of naturally occurring azetidines are poorly understood. Only some of them have been intensively investigated and few reviews have been published for the summarization of azetidine biosynthesis. In this review, we provide a comprehensive description of the biosyntheses of all the azetidine-containing natural products, especially the biosyntheses of azetidine moieties. We hope that this review will draw much attention to the biosynthetic research of the largely unexplored azetidine moieties as well as the discovery of novel azetidine-containing natural products in the near future.
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Affiliation(s)
- Linlin Pang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Daichen Yao
- School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Fenghui Gao
- School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Xiaoying Bian
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology and Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Guannan Zhong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
- Suzhou Research Institute of Shandong University, Suzhou 215123, China
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4
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Patteson JB, Fortinez CM, Putz AT, Rodriguez-Rivas J, Bryant LH, Adhikari K, Weigt M, Schmeing TM, Li B. Structure and Function of a Dehydrating Condensation Domain in Nonribosomal Peptide Biosynthesis. J Am Chem Soc 2022; 144:14057-14070. [PMID: 35895935 DOI: 10.1021/jacs.1c13404] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dehydroamino acids are important structural motifs and biosynthetic intermediates for natural products. Many bioactive natural products of nonribosomal origin contain dehydroamino acids; however, the biosynthesis of dehydroamino acids in most nonribosomal peptides is not well understood. Here, we provide biochemical and bioinformatic evidence in support of the role of a unique class of condensation domains in dehydration (CmodAA). We also obtain the crystal structure of a CmodAA domain, which is part of the nonribosomal peptide synthetase AmbE in the biosynthesis of the antibiotic methoxyvinylglycine. Biochemical analysis reveals that AmbE-CmodAA modifies a peptide substrate that is attached to the donor carrier protein. Mutational studies of AmbE-CmodAA identify several key residues for activity, including four residues that are mostly conserved in the CmodAA subfamily. Alanine mutation of these conserved residues either significantly increases or decreases AmbE activity. AmbE exhibits a dimeric conformation, which is uncommon and could enable transfer of an intermediate between different protomers. Our discovery highlights a central dehydrating function for CmodAA domains that unifies dehydroamino acid biosynthesis in diverse nonribosomal peptide pathways. Our work also begins to shed light on the mechanism of CmodAA domains. Understanding CmodAA domain function may facilitate identification of new natural products that contain dehydroamino acids and enable engineering of dehydroamino acids into nonribosomal peptides.
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Affiliation(s)
- Jon B Patteson
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Camille Marie Fortinez
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, Canada H3G 0B1
| | - Andrew T Putz
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Juan Rodriguez-Rivas
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biologie Computationnelle et Quantitative - LCQB, Paris 75005, France
| | - L Henry Bryant
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kamal Adhikari
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, Canada H3G 0B1
| | - Martin Weigt
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biologie Computationnelle et Quantitative - LCQB, Paris 75005, France
| | - T Martin Schmeing
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, Canada H3G 0B1
| | - Bo Li
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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5
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ClpP inhibitors are produced by a widespread family of bacterial gene clusters. Nat Microbiol 2022; 7:451-462. [PMID: 35246663 DOI: 10.1038/s41564-022-01073-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/31/2022] [Indexed: 11/08/2022]
Abstract
The caseinolytic protease (ClpP) is part of a highly conserved proteolytic complex whose disruption can lead to antibacterial activity but for which few specific inhibitors have been discovered. Specialized metabolites produced by bacteria have been shaped by evolution for specific functions, making them a potential source of selective ClpP inhibitors. Here, we describe a target-directed genome mining strategy for discovering ClpP-interacting compounds by searching for biosynthetic gene clusters that contain duplicated copies of ClpP as putative antibiotic resistance genes. We identify a widespread family of ClpP-associated clusters that are known to produce pyrrolizidine alkaloids but whose connection to ClpP has never been made. We show that previously characterized molecules do not affect ClpP function but are shunt metabolites derived from the genuine product of these gene clusters, a reactive covalent ClpP inhibitor. Focusing on one such cryptic gene cluster from Streptomyces cattleya, we identify the relevant inhibitor, which we name clipibicyclene, and show that it potently and selectively inactivates ClpP. Finally, we solve the crystal structure of clipibicyclene-modified Escherichia coli ClpP. Clipibicyclene's discovery reveals the authentic function of a family of natural products whose specificity for ClpP and abundance in nature illuminate the role of eco-evolutionary forces during bacterial competition.
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6
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Wenski SL, Thiengmag S, Helfrich EJ. Complex peptide natural products: Biosynthetic principles, challenges and opportunities for pathway engineering. Synth Syst Biotechnol 2022; 7:631-647. [PMID: 35224231 PMCID: PMC8842026 DOI: 10.1016/j.synbio.2022.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/03/2023] Open
Abstract
Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical properties. As a result, many peptides have entered the clinics for various applications. Two main routes for the biosynthesis of complex peptides have evolved in nature: ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic pathways and non-ribosomal peptide synthetases (NRPSs). Insights into both bioorthogonal peptide biosynthetic strategies led to the establishment of universal principles for each of the two routes. These universal rules can be leveraged for the targeted identification of novel peptide biosynthetic blueprints in genome sequences and used for the rational engineering of biosynthetic pathways to produce non-natural peptides. In this review, we contrast the key principles of both biosynthetic routes and compare the different biochemical strategies to install the most frequently encountered peptide modifications. In addition, the influence of the fundamentally different biosynthetic principles on past, current and future engineering approaches is illustrated. Despite the different biosynthetic principles of both peptide biosynthetic routes, the arsenal of characterized peptide modifications encountered in RiPP and NRPS systems is largely overlapping. The continuous expansion of the biocatalytic toolbox of peptide modifying enzymes for both routes paves the way towards the production of complex tailor-made peptides and opens up the possibility to produce NRPS-derived peptides using the ribosomal route and vice versa.
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Affiliation(s)
- Sebastian L. Wenski
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
| | - Sirinthra Thiengmag
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
| | - Eric J.N. Helfrich
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
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7
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Fang Q, Wu L, Urwald C, Mugat M, Wang S, Kyeremeh K, Philips C, Law S, Zhou Y, Deng H. Genomic scanning enabling discovery of a new antibacterial bicyclic carbamate-containing alkaloid. Synth Syst Biotechnol 2021; 6:12-19. [PMID: 33553705 PMCID: PMC7820566 DOI: 10.1016/j.synbio.2021.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/02/2021] [Accepted: 01/08/2021] [Indexed: 01/13/2023] Open
Abstract
Non-ribosomal peptides are a group of structurally diverse natural products with various important therapeutic and agrochemical applications. Bacterial pyrrolizidine alkaloids (PAs), containing a scaffold of two fused five-membered ring system with a nitrogen atom at the bridgehead, have been found to originate from a multidomain non-ribosomal peptide synthetase to generate indolizidine intermediates, followed by multistep oxidation, catalysed by single Bayer-Villiger (BV) enzymes, to yield PA scaffolds. Although bacterial PAs are rare in natural product inventory, bioinformatics analysis suggested that the biosynthetic gene clusters (BGCs) that are likely to be responsible for the production of PA-like metabolites are widely distributed in bacterial genomes. However, most of the strains containing PA-like BGCs are not deposited in the public domain, therefore preventing further assessment of the chemical spaces of this group of bioactive metabolites. Here, we report a genomic scanning strategy to assess the potential of PA metabolites production in our culture collection without prior knowledge of genome information. Among the strains tested, we found fifteen contain the key BV enzymes that are likely to be involved in the last step of PA ring formation. Subsequently one-strain-many-compound (OSMAC) method, supported by a combination of HR-MS, NMR, SMART 2.0 technology, and GNPS analysis, allowed identification and characterization of a new [5 + 7] heterobicyclic carbamate, legoncarbamate, together with five known PAs, bohemamine derivatives, from Streptomyces sp. CT37, a Ghanaian soil isolate. The absolute stereochemistry of legoncarbamate was determined by comparison of measured and calculated ECD spectra. Legoncarbamate displays antibacterial activity against E. coli ATCC 25922 with an MIC value of 3.1 μg/mL. Finally, a biosynthetic model of legoncarbamate and other bohemamines was proposed based on the knowledge we have gained so far.
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Affiliation(s)
- Qing Fang
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, UK
| | - Linrui Wu
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, UK
| | - Caroline Urwald
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, UK
- ENSAIA, 2 avenue de la forêt de Haye, 54505 vandœuvre lès Nancy, France
| | - Morgane Mugat
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, UK
- ENSAIA, 2 avenue de la forêt de Haye, 54505 vandœuvre lès Nancy, France
| | - Shan Wang
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, UK
| | - Kwaku Kyeremeh
- Department of Chemistry, University of Ghana, P.O. Box LG56, Legon-Accra, Ghana
| | - Carol Philips
- NCIMB Ltd, Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen, AB21 9YA, Scotland, UK
| | - Samantha Law
- NCIMB Ltd, Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen, AB21 9YA, Scotland, UK
| | - Yongjun Zhou
- Research Centre for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Hai Deng
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, UK
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8
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Girard L, Höfte M, De Mot R. Lipopeptide families at the interface between pathogenic and beneficial Pseudomonas-plant interactions. Crit Rev Microbiol 2020; 46:397-419. [PMID: 32885723 DOI: 10.1080/1040841x.2020.1794790] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Lipopeptides (LPs) are a prominent class of molecules among the steadily growing spectrum of specialized metabolites retrieved from Pseudomonas, in particular soil-dwelling and plant-associated isolates. Among the multiple LP families, pioneering research focussed on phytotoxic and antimicrobial cyclic lipopeptides (CLPs) of the ubiquitous plant pathogen Pseudomonas syringae (syringomycin and syringopeptin). Their non-ribosomal peptide synthetases (NRPSs) are embedded in biosynthetic gene clusters (BGCs) that are tightly co-clustered on a pathogenicity island. Other members of the P. syringae group (Pseudomonas cichorii) and some species of the Pseudomonas asplenii group and Pseudomonas fluorescens complex have adopted these biosynthetic strategies to co-produce their own mycin and peptin variants, in some strains supplemented with an analogue of the P. syringae linear LP (LLP), syringafactin. This capacity is not confined to phytopathogens but also occurs in some biocontrol strains, which indicates that these LP families not solely function as general virulence factors. We address this issue by scrutinizing the structural diversity and bioactivities of LPs from the mycin, peptin, and factin families in a phylogenetic and evolutionary perspective. BGC functional organization (including associated regulatory and transport genes) and NRPS modular architectures in known and candidate LP producers were assessed by genome mining.
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Affiliation(s)
- Léa Girard
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Heverlee-Leuven, Belgium
| | - Monica Höfte
- Department of Plants and Crops, Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Heverlee-Leuven, Belgium
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9
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Draft Genome Sequence of Cyclic Lipopeptide Producer Pseudomonas sp. Strain SWRI103, Isolated from Wheat Rhizosphere. Microbiol Resour Announc 2020; 9:9/27/e00538-20. [PMID: 32616641 PMCID: PMC7330243 DOI: 10.1128/mra.00538-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The draft genome sequence of wheat rhizosphere isolate Pseudomonas sp. strain SWRI103 is reported. This strain carries several gene clusters encoding nonribosomal peptide synthetases (NRPSs), including a system for cyclic lipopeptide (CLP) production, and genes for carotenoid biosynthesis. The draft genome sequence of wheat rhizosphere isolate Pseudomonas sp. strain SWRI103 is reported. This strain carries several gene clusters encoding nonribosomal peptide synthetases (NRPSs), including a system for cyclic lipopeptide (CLP) production, and genes for carotenoid biosynthesis.
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10
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Liu L, Li S, Sun R, Qin X, Ju J, Zhang C, Duan Y, Huang Y. Activation and Characterization of Bohemamine Biosynthetic Gene Cluster from Streptomyces sp. CB02009. Org Lett 2020; 22:4614-4619. [PMID: 32463693 DOI: 10.1021/acs.orglett.0c01224] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bohemamines (BHMs) are bacterial alkaloids containing a pyrrolizidine core with two unusual methyl groups. Herein we report the activation of BHMs biosynthesis using a ribosome engineering approach. Characterization of the bhm gene cluster reveals that nonribosomal peptide synthetase BhmJ and Baeyer-Villiger monooxygenase BhmK are responsible for the formation of the pyrrolizidine core, which is further methylated on C-7 by methyltransferase BhmG. The 9-methyl group of BHMs is instead originated from a nonproteinogenic amino acid (2S,5S)-5-methylproline.
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Affiliation(s)
- Ling Liu
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China
| | - Sainan Li
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China
| | - Runze Sun
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China
| | - Xiangjing Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Jianhua Ju
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, 410011, Hunan, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410011, Hunan, China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, 410013, Hunan, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410011, Hunan, China
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11
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Shi YM, Bode HB. Chemical language and warfare of bacterial natural products in bacteria-nematode-insect interactions. Nat Prod Rep 2019; 35:309-335. [PMID: 29359226 DOI: 10.1039/c7np00054e] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: up to November 2017 Organismic interaction is one of the fundamental principles for survival in any ecosystem. Today, numerous examples show the interaction between microorganisms like bacteria and higher eukaryotes that can be anything between mutualistic to parasitic/pathogenic symbioses. There is also increasing evidence that microorganisms are used by higher eukaryotes not only for the supply of essential factors like vitamins but also as biological weapons to protect themselves or to kill other organisms. Excellent examples for such systems are entomopathogenic nematodes of the genera Heterorhabditis and Steinernema that live in mutualistic symbiosis with bacteria of the genera Photorhabdus and Xenorhabdus, respectively. Although these systems have been used successfully in organic farming on an industrial scale, it was only shown during the last 15 years that several different natural products (NPs) produced by the bacteria play key roles in the complex life cycle of the bacterial symbionts, the nematode host and the insect prey that is killed by and provides nutrients for the nematode-bacteria pair. Since the bacteria can switch from mutualistic to pathogenic lifestyle, interacting with two different types of higher eukaryotes, and since the full system with all players can be established in the lab, they are promising model systems to elucidate the natural function of microbial NPs. This review summarizes the current knowledge as well as open questions for NPs from Photorhabdus and Xenorhabdus and tries to assign their roles in the tritrophic relationship.
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Affiliation(s)
- Yi-Ming Shi
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main 60438, Germany
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12
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Patteson JB, Lescallette AR, Li B. Discovery and Biosynthesis of Azabicyclene, a Conserved Nonribosomal Peptide in Pseudomonas aeruginosa. Org Lett 2019; 21:4955-4959. [PMID: 31247735 DOI: 10.1021/acs.orglett.9b01383] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Azabicyclene, an azetidine-containing natural product, was identified using quorum-sensing molecules to upregulate expression of a gene cluster highly conserved in the human pathogen Pseudomonas aeruginosa. Mutational studies of the gene cluster revealed essential genes for biosynthesis, including an unusual nonribosomal peptide synthetase. Reconstitution of this enzyme in vitro identified key biosynthetic intermediates. This work demonstrates a useful strategy for discovering quorum-sensing-regulated natural products. It sets the stage for understanding the biosynthesis and bioactivity of azabicyclene.
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Affiliation(s)
- Jon B Patteson
- Department of Chemistry , University of North Carolina at Chapel Hill CB 3290, Chapel Hill , North Carolina 27599-3290 , United States
| | - Adam R Lescallette
- Department of Chemistry , University of North Carolina at Chapel Hill CB 3290, Chapel Hill , North Carolina 27599-3290 , United States
| | - Bo Li
- Department of Chemistry , University of North Carolina at Chapel Hill CB 3290, Chapel Hill , North Carolina 27599-3290 , United States
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13
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Hong Z, Bolard A, Giraud C, Prévost S, Genta‐Jouve G, Deregnaucourt C, Häussler S, Jeannot K, Li Y. Azetidine‐Containing Alkaloids Produced by a Quorum‐Sensing Regulated Nonribosomal Peptide Synthetase Pathway in
Pseudomonas aeruginosa. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201809981] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zhilai Hong
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM)Muséum National d'Histoire Naturelle (MNHN)Centre National de la Recherche Scientifique (CNRS), CP 54 57 rue Cuvier 75005 Paris France
| | - Arnaud Bolard
- Laboratoire de BactériologieCentre National de Référence (CNR) de la Résistance aux Antibiotiques, Centre Hospitalier Régional Universitaire (CHRU) de Besançon, UMR4269 “Chrono-Environnement” Boulevard Fleming 25030 Besançon France
| | - Caroline Giraud
- U2RM Stress/VirulenceNormandy University, UNICAEN 14000 Caen France
| | - Sébastien Prévost
- Laboratoire de Synthèse Organique, UMR 7652CNRS, Ecole PolytechniqueENSTA ParisTechUniversité Paris-Saclay 828 Bd des Maréchaux 91128 Palaiseau France
| | - Grégory Genta‐Jouve
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM)Muséum National d'Histoire Naturelle (MNHN)Centre National de la Recherche Scientifique (CNRS), CP 54 57 rue Cuvier 75005 Paris France
- C-TAC, UMR 8638, CNRSFaculté de Pharmacie de ParisUniversité Paris Descartes, Sorbonne Paris Cité 4 Avenue de l'Observatoire 75006 Paris France
| | - Christiane Deregnaucourt
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM)Muséum National d'Histoire Naturelle (MNHN)Centre National de la Recherche Scientifique (CNRS), CP 54 57 rue Cuvier 75005 Paris France
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORECentre for Experimental and Clinical Infection Research Hannover Germany
- Department of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
| | - Katy Jeannot
- Laboratoire de BactériologieCentre National de Référence (CNR) de la Résistance aux Antibiotiques, Centre Hospitalier Régional Universitaire (CHRU) de Besançon, UMR4269 “Chrono-Environnement” Boulevard Fleming 25030 Besançon France
| | - Yanyan Li
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM)Muséum National d'Histoire Naturelle (MNHN)Centre National de la Recherche Scientifique (CNRS), CP 54 57 rue Cuvier 75005 Paris France
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14
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Hong Z, Bolard A, Giraud C, Prévost S, Genta-Jouve G, Deregnaucourt C, Häussler S, Jeannot K, Li Y. Azetidine-Containing Alkaloids Produced by a Quorum-Sensing Regulated Nonribosomal Peptide Synthetase Pathway in Pseudomonas aeruginosa. Angew Chem Int Ed Engl 2019; 58:3178-3182. [PMID: 30548135 DOI: 10.1002/anie.201809981] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/08/2018] [Indexed: 12/26/2022]
Abstract
Pseudomonas aeruginosa displays an impressive metabolic versatility, which ensures its survival in diverse environments. Reported herein is the identification of rare azetidine-containing alkaloids from P. aeruginosa PAO1, termed azetidomonamides, which are derived from a conserved, quorum-sensing regulated nonribosomal peptide synthetase (NRPS) pathway. Biosynthesis of the azetidine motif has been elucidated by gene inactivation, feeding experiments, and biochemical characterization in vitro, which involves a new S-adenosylmethionine-dependent enzyme to produce azetidine 2-carboxylic acid as an unusual building block of NRPS. The mutants of P. aeruginosa unable to produce azetidomonamides had an advantage in growth at high cell density in vitro and displayed rapid virulence in Galleria mellonella model, inferring functional roles of azetidomonamides in the host adaptation. This work opens the avenue to study the biological functions of azetidomonamides and related compounds in pathogenic and environmental bacteria.
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Affiliation(s)
- Zhilai Hong
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Arnaud Bolard
- Laboratoire de Bactériologie, Centre National de Référence (CNR) de la Résistance aux Antibiotiques, Centre Hospitalier Régional Universitaire (CHRU) de Besançon, UMR4269 "Chrono-Environnement", Boulevard Fleming, 25030, Besançon, France
| | - Caroline Giraud
- U2RM Stress/Virulence, Normandy University, UNICAEN, 14000, Caen, France
| | - Sébastien Prévost
- Laboratoire de Synthèse Organique, UMR 7652, CNRS, Ecole Polytechnique, ENSTA ParisTech, Université Paris-Saclay, 828 Bd des Maréchaux, 91128, Palaiseau, France
| | - Grégory Genta-Jouve
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), CP 54, 57 rue Cuvier, 75005, Paris, France.,C-TAC, UMR 8638, CNRS, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, 4 Avenue de l'Observatoire, 75006, Paris, France
| | - Christiane Deregnaucourt
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Katy Jeannot
- Laboratoire de Bactériologie, Centre National de Référence (CNR) de la Résistance aux Antibiotiques, Centre Hospitalier Régional Universitaire (CHRU) de Besançon, UMR4269 "Chrono-Environnement", Boulevard Fleming, 25030, Besançon, France
| | - Yanyan Li
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), CP 54, 57 rue Cuvier, 75005, Paris, France
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15
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Dockerty P, Edens JG, Tol MB, Morales Angeles D, Domenech A, Liu Y, Hirsch AKH, Veening JW, Scheffers DJ, Witte MD. Bicyclic enol cyclocarbamates inhibit penicillin-binding proteins. Org Biomol Chem 2018; 15:894-910. [PMID: 28045164 DOI: 10.1039/c6ob01664b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Natural products form attractive leads for the development of chemical probes and drugs. The antibacterial lipopeptide Brabantamide A contains an unusual enol cyclocarbamate and we used this scaffold as inspiration for the synthesis of a panel of enol cyclocarbamate containing compounds. By equipping the scaffold with different groups, we identified structural features that are essential for antibacterial activity. Some of the derivatives block incorporation of hydroxycoumarin carboxylic acid-amino d-alanine into the newly synthesized peptidoglycan. Activity-based protein-profiling experiments revealed that the enol carbamates inhibit a specific subset of penicillin-binding proteins in B. subtilis and S. pneumoniae.
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Affiliation(s)
- Paul Dockerty
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.
| | - Jerre G Edens
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.
| | - Menno B Tol
- Molecular Microbiology, Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Danae Morales Angeles
- Molecular Microbiology, Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Arnau Domenech
- Molecular Genetics, Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Yun Liu
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.
| | - Anna K H Hirsch
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.
| | - Jan-Willem Veening
- Molecular Genetics, Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Dirk-Jan Scheffers
- Molecular Microbiology, Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Martin D Witte
- Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.
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16
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Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
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Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
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17
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Draft Genome Sequence of
Streptomyces silvensis
ATCC 53525, a Producer of Novel Hormone Antagonists. GENOME ANNOUNCEMENTS 2016; 4:4/1/e00001-16. [PMID: 26893408 PMCID: PMC4759055 DOI: 10.1128/genomea.00001-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Streptomyces silvensis produces nonribosomal peptides that act as antagonists of the human oxytocin and vasopressin receptors. Here, we present the genome sequence of S. silvensis ATCC 53525 and demonstrate that this organism possesses a number of additional biosynthetic gene clusters and might be a promising source for genome-guided drug discovery efforts.
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18
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Johnston CW, Skinnider MA, Wyatt MA, Li X, Ranieri MRM, Yang L, Zechel DL, Ma B, Magarvey NA. An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products. Nat Commun 2015; 6:8421. [PMID: 26412281 PMCID: PMC4598715 DOI: 10.1038/ncomms9421] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 08/19/2015] [Indexed: 12/04/2022] Open
Abstract
Bacterial natural products are a diverse and valuable group of small molecules, and genome sequencing indicates that the vast majority remain undiscovered. The prediction of natural product structures from biosynthetic assembly lines can facilitate their discovery, but highly automated, accurate, and integrated systems are required to mine the broad spectrum of sequenced bacterial genomes. Here we present a genome-guided natural products discovery tool to automatically predict, combinatorialize and identify polyketides and nonribosomal peptides from biosynthetic assembly lines using LC–MS/MS data of crude extracts in a high-throughput manner. We detail the directed identification and isolation of six genetically predicted polyketides and nonribosomal peptides using our Genome-to-Natural Products platform. This highly automated, user-friendly programme provides a means of realizing the potential of genetically encoded natural products. Microbial natural products represent a large reservoir of potential pharmaceutical agents. Here, Johnston et al. describe a computer-automated programme for connecting genome sequences with identified and isolated natural products.
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Affiliation(s)
- Chad W Johnston
- Department of Biochemistry &Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research; McMaster University, Hamilton, Ontario, Canada L8N 3Z5.,Department of Chemistry &Chemical Biology, M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Michael A Skinnider
- Department of Biochemistry &Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research; McMaster University, Hamilton, Ontario, Canada L8N 3Z5.,Department of Chemistry &Chemical Biology, M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Morgan A Wyatt
- Department of Biochemistry &Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research; McMaster University, Hamilton, Ontario, Canada L8N 3Z5.,Department of Chemistry &Chemical Biology, M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Xiang Li
- Department of Biochemistry &Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research; McMaster University, Hamilton, Ontario, Canada L8N 3Z5.,Department of Chemistry &Chemical Biology, M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Michael R M Ranieri
- Department of Biochemistry &Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research; McMaster University, Hamilton, Ontario, Canada L8N 3Z5.,Department of Chemistry &Chemical Biology, M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Lian Yang
- The David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - David L Zechel
- Department of Chemistry; Queens University, Kingston, Ontario, Canada K7L 3N6
| | - Bin Ma
- The David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Nathan A Magarvey
- Department of Biochemistry &Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research; McMaster University, Hamilton, Ontario, Canada L8N 3Z5.,Department of Chemistry &Chemical Biology, M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
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19
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Schimming O, Challinor VL, Tobias NJ, Adihou H, Grün P, Pöschel L, Richter C, Schwalbe H, Bode HB. Structure, Biosynthesis, and Occurrence of Bacterial Pyrrolizidine Alkaloids. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504877] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Schimming O, Challinor VL, Tobias NJ, Adihou H, Grün P, Pöschel L, Richter C, Schwalbe H, Bode HB. Structure, Biosynthesis, and Occurrence of Bacterial Pyrrolizidine Alkaloids. Angew Chem Int Ed Engl 2015; 54:12702-5. [PMID: 26465655 DOI: 10.1002/anie.201504877] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Indexed: 12/24/2022]
Abstract
Pyrrolizidine alkaloids (PAs) are widespread plant natural products with potent toxicity and bioactivity. Herein, the identification of bacterial PAs from entomopathogenic bacteria using differential analysis by 2D NMR spectroscopy (DANS) and mass spectrometry is described. Their biosynthesis was elucidated to involve a non-ribosomal peptide synthetase. The occurrence of these biosynthesis gene clusters in Gram-negative and Gram-positive bacteria indicates an important biological function in bacteria.
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Affiliation(s)
- Olivia Schimming
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany) http://www.bio.uni-frankfurt.de/48050101
| | - Victoria L Challinor
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany) http://www.bio.uni-frankfurt.de/48050101
| | - Nicholas J Tobias
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany) http://www.bio.uni-frankfurt.de/48050101
| | - Hélène Adihou
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany) http://www.bio.uni-frankfurt.de/48050101
| | - Peter Grün
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany) http://www.bio.uni-frankfurt.de/48050101
| | - Laura Pöschel
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany) http://www.bio.uni-frankfurt.de/48050101
| | - Christian Richter
- Institut für Organische und Chemische Biologie, Zentrum für Biomolekulare Magnetische Resonanz, Goethe Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Harald Schwalbe
- Institut für Organische und Chemische Biologie, Zentrum für Biomolekulare Magnetische Resonanz, Goethe Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany) http://www.bio.uni-frankfurt.de/48050101. .,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main (Germany).
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21
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Huang S, Tabudravu J, Elsayed SS, Travert J, Peace D, Tong MH, Kyeremeh K, Kelly SM, Trembleau L, Ebel R, Jaspars M, Yu Y, Deng H. Discovery of a Single Monooxygenase that Catalyzes Carbamate Formation and Ring Contraction in the Biosynthesis of the Legonmycins. Angew Chem Int Ed Engl 2015. [PMID: 26206556 DOI: 10.1002/anie.201502902] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Pyrrolizidine alkaloids (PAs) are a group of natural products with important biological activities. The discovery and characterization of the multifunctional FAD-dependent enzyme LgnC is now described. The enzyme is shown to convert indolizidine intermediates into pyrrolizidines through an unusual ring expansion/contraction mechanism, and catalyze the biosynthesis of new bacterial PAs, the so-called legonmycins. By genome-driven analysis, heterologous expression, and gene inactivation, the legonmycins were also shown to originate from non-ribosomal peptide synthetases (NRPSs). The biosynthetic origin of bacterial PAs has thus been disclosed for the first time.
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Affiliation(s)
- Sheng Huang
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071 (P.R. China)
| | - Jioji Tabudravu
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | | | - Jeanne Travert
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | - Doe Peace
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | - Ming Him Tong
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | - Kwaku Kyeremeh
- Department of Chemistry, University of Ghana, P.O. Box LG56, Legon-Accra (Ghana)
| | - Sharon M Kelly
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ (UK)
| | | | - Rainer Ebel
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | - Marcel Jaspars
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071 (P.R. China).
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen (UK).
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22
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Huang S, Tabudravu J, Elsayed SS, Travert J, Peace D, Tong MH, Kyeremeh K, Kelly SM, Trembleau L, Ebel R, Jaspars M, Yu Y, Deng H. Discovery of a Single Monooxygenase that Catalyzes Carbamate Formation and Ring Contraction in the Biosynthesis of the Legonmycins. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502902] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Van Der Voort M, Meijer HJG, Schmidt Y, Watrous J, Dekkers E, Mendes R, Dorrestein PC, Gross H, Raaijmakers JM. Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds. Front Microbiol 2015. [PMID: 26217324 PMCID: PMC4493835 DOI: 10.3389/fmicb.2015.00693] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The plant microbiome represents an enormous untapped resource for discovering novel genes and bioactive compounds. Previously, we isolated Pseudomonas sp. SH-C52 from the rhizosphere of sugar beet plants grown in a soil suppressive to the fungal pathogen Rhizoctonia solani and showed that its antifungal activity is, in part, attributed to the production of the chlorinated 9-amino-acid lipopeptide thanamycin (Mendes et al., 2011). To get more insight into its biosynthetic repertoire, the genome of Pseudomonas sp. SH-C52 was sequenced and subjected to in silico, mutational and functional analyses. The sequencing revealed a genome size of 6.3 Mb and 5579 predicted ORFs. Phylogenetic analysis placed strain SH-C52 within the Pseudomonas corrugata clade. In silico analysis for secondary metabolites revealed a total of six non-ribosomal peptide synthetase (NRPS) gene clusters, including the two previously described NRPS clusters for thanamycin and the 2-amino acid antibacterial lipopeptide brabantamide. Here we show that thanamycin also has activity against an array of other fungi and that brabantamide A exhibits anti-oomycete activity and affects phospholipases of the late blight pathogen Phytophthora infestans. Most notably, mass spectrometry led to the discovery of a third lipopeptide, designated thanapeptin, with a 22-amino-acid peptide moiety. Seven structural variants of thanapeptin were found with varying degrees of activity against P. infestans. Of the remaining four NRPS clusters, one was predicted to encode for yet another and unknown lipopeptide with a predicted peptide moiety of 8-amino acids. Collectively, these results show an enormous metabolic potential for Pseudomonas sp. SH-C52, with at least three structurally diverse lipopeptides, each with a different antimicrobial activity spectrum.
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Affiliation(s)
| | - Harold J G Meijer
- Laboratory of Phytopathology, Wageningen University Wageningen, Netherlands
| | - Yvonne Schmidt
- Institute for Pharmaceutical Biology, University of Bonn Bonn, Germany
| | - Jeramie Watrous
- Departments of Pharmacology and Chemistry and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego San Diego, CA, USA
| | - Ester Dekkers
- Laboratory of Phytopathology, Wageningen University Wageningen, Netherlands
| | - Rodrigo Mendes
- Laboratory of Phytopathology, Wageningen University Wageningen, Netherlands ; Brazilian Agricultural Research Corporation, Embrapa Environment Jaguariuna, Brazil
| | - Pieter C Dorrestein
- Departments of Pharmacology and Chemistry and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego San Diego, CA, USA
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen Tübingen, Germany
| | - Jos M Raaijmakers
- Laboratory of Phytopathology, Wageningen University Wageningen, Netherlands ; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
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24
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Schmidt Y, van der Voort M, Crüsemann M, Piel J, Josten M, Sahl HG, Miess H, Raaijmakers JM, Gross H. Biosynthetic origin of the antibiotic cyclocarbamate brabantamide A (SB-253514) in plant-associated Pseudomonas. Chembiochem 2014; 15:259-66. [PMID: 24436210 DOI: 10.1002/cbic.201300527] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Indexed: 11/07/2022]
Abstract
Within the framework of our genome-based program to discover new antibiotic lipopeptides from Pseudomonads, brabantamides A-C were isolated from plant-associated Pseudomonas sp. SH-C52. Brabantamides A-C displayed moderate to high in vitro activities against Gram-positive bacterial pathogens. Their shared structure is unique in that they contain a 5,5-bicyclic carbamate scaffold. Here, the biosynthesis of brabantamide A (SB-253514) was studied by a combination of bioinformatics, feeding experiments with isotopically labelled precursors and in vivo and in vitro functional analysis of enzymes encoded in the biosynthetic pathway. The studies resulted in the deduction of all biosynthetic building blocks of brabantamide A and revealed an unusual feature of this metabolite: its biosynthesis occurs via an initially formed linear di-lipopeptide that is subsequently rearranged by a novel FAD-dependent Baeyer-Villiger monooxygenase.
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Metagenomic approaches for exploiting uncultivated bacteria as a resource for novel biosynthetic enzymology. ACTA ACUST UNITED AC 2013; 20:636-47. [PMID: 23706630 DOI: 10.1016/j.chembiol.2013.04.011] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 03/28/2013] [Accepted: 04/16/2013] [Indexed: 12/24/2022]
Abstract
Most biologically active microbial natural products are known from strains that can be isolated and cultivated in the laboratory. However, the genomics era has revealed that cultured bacteria represent a mere fraction of total estimated bacterial biodiversity. With the development of community genomics, termed metagenomics, the uncultivated majority became accessible for functional analysis. Through metagenomic studies, novel biocatalysts and biosynthetic pathways are being discovered at a pace previously not possible using traditional molecular biology techniques. Additionally, the study of uncultivated bacteria has provided valuable insights into previously overlooked biocatalysts from cultured strains. This perspective highlights recent discoveries from metagenomics of uncultivated bacteria and discusses the impact of those findings on the field of natural products.
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