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Präve L, Seyfert CE, Bozhüyük KAJ, Racine E, Müller R, Bode HB. Investigation of the Odilorhabdin Biosynthetic Gene Cluster Using NRPS Engineering. Angew Chem Int Ed Engl 2024; 63:e202406389. [PMID: 38801753 DOI: 10.1002/anie.202406389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024]
Abstract
The recently identified natural product NOSO-95A from entomopathogenic Xenorhabdus bacteria, derived from a biosynthetic gene cluster (BGC) encoding a non-ribosomal peptide synthetase (NRPS), was the first member of the odilorhabdin class of antibiotics. This class exhibits broad-spectrum antibiotic activity and inspired the development of the synthetic derivative NOSO-502, which holds potential as a new clinical drug by breaking antibiotic resistance. While the mode of action of odilorhabdins was broadly investigated, their biosynthesis pathway remained poorly understood. Here we describe the heterologous production of NOSO-95A in Escherichia coli after refactoring the complete BGC. Since the production titer was low, NRPS engineering was applied to uncover the underlying biosynthetic principles. For this, modules of the odilorhabdin NRPS fused to other synthetases were co-expressed with candidate hydroxylases encoded in the BGC allowing the characterization of the biosynthesis of three unusual amino acids and leading to the identification of a prodrug-activation mechanism by deacylation. Our work demonstrates the application of NRPS engineering as a blueprint to mechanistically elucidate large or toxic NRPS and provides the basis to generate novel odilorhabdin analogues with improved properties in the future.
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Affiliation(s)
- Leonard Präve
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Carsten E Seyfert
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Department of Pharmacy, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Hannover-Braunschweig, Germany
| | - Kenan A J Bozhüyük
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438, Frankfurt, Germany
- Myria Biosciences AG, Hochbergerstrasse 60 C, 4057, Basel, Switzerland
- Present address: Synthetic Biology of Microbial Natural Products (SIMS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, 66123, Saarbrücken, Germany
| | - Emilie Racine
- Nosopharm, 226 rue Georges Besse, 30000, Nîmes, France
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Department of Pharmacy, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Hannover-Braunschweig, Germany
| | - Helge B Bode
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438, Frankfurt, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043, Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043, Marburg, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt, Germany
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2
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Bozhüyük KAJ, Präve L, Kegler C, Schenk L, Kaiser S, Schelhas C, Shi YN, Kuttenlochner W, Schreiber M, Kandler J, Alanjary M, Mohiuddin TM, Groll M, Hochberg GKA, Bode HB. Evolution-inspired engineering of nonribosomal peptide synthetases. Science 2024; 383:eadg4320. [PMID: 38513038 DOI: 10.1126/science.adg4320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/09/2024] [Indexed: 03/23/2024]
Abstract
Many clinically used drugs are derived from or inspired by bacterial natural products that often are produced through nonribosomal peptide synthetases (NRPSs), megasynthetases that activate and join individual amino acids in an assembly line fashion. In this work, we describe a detailed phylogenetic analysis of several bacterial NRPSs that led to the identification of yet undescribed recombination sites within the thiolation (T) domain that can be used for NRPS engineering. We then developed an evolution-inspired "eXchange Unit between T domains" (XUT) approach, which allows the assembly of NRPS fragments over a broad range of GC contents, protein similarities, and extender unit specificities, as demonstrated for the specific production of a proteasome inhibitor designed and assembled from five different NRPS fragments.
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Affiliation(s)
- Kenan A J Bozhüyük
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Myria Biosciences AG, Tech Park Basel, Hochbergstrasse 60C, 4057 Basel, Switzerland
| | - Leonard Präve
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Carsten Kegler
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Leonie Schenk
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Sebastian Kaiser
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Christian Schelhas
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
| | - Yan-Ni Shi
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Wolfgang Kuttenlochner
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Max Schreiber
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Joshua Kandler
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - T M Mohiuddin
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
| | - Helge B Bode
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) & Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt, Germany
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3
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Zhang Y, Li H, Wang F, Liu C, Reddy GVP, Li H, Li Z, Sun Y, Zhao Z. Discovery of a new highly pathogenic toxin involved in insect sepsis. Microbiol Spectr 2023; 11:e0142223. [PMID: 37787562 PMCID: PMC10715044 DOI: 10.1128/spectrum.01422-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/07/2023] [Indexed: 10/04/2023] Open
Abstract
IMPORTANCE As a current biocontrol resource, entomopathogenic nematodes and their symbiotic bacterium can produce many toxin factors to trigger insect sepsis, having the potential to promote sustainable pest management. In this study, we found Steinernema feltiae and Xenorhabdus bovienii were highly virulent against the insects. After infective juvenile injection, Galleria mellonella quickly turned black and softened with increasing esterase activity. Simultaneously, X. bovienii attacked hemocytes and released toxic components, resulting in extensive hemolysis and sepsis. Then, we applied high-resolution mass spectrometry-based metabolomics and found multiple substances were upregulated in the host hemolymph. We found extremely hazardous actinomycin D produced via 3-hydroxyanthranilic acid metabolites. Moreover, a combined transcriptomic analysis revealed that gene expression of proteins associated with actinomycin D was upregulated. Our research revealed actinomycin D might be responsible for the infestation activity of X. bovienii, indicating a new direction for exploring the sepsis mechanism and developing novel biotic pesticides.
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Affiliation(s)
- Yuan Zhang
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hao Li
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China
| | - Fang Wang
- Institute of Plant Protection, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, China
| | - Chang Liu
- Institute of Plant Protection, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, China
| | - Gadi V. P. Reddy
- Department of Entomology, Lousiana State University, Baton Rouge, Los Angeles, USA
| | - Hu Li
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, China Agricultural University, Sanya, China
| | - Zhihong Li
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, China Agricultural University, Sanya, China
| | - Yucheng Sun
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zihua Zhao
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, China Agricultural University, Sanya, China
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Meesil W, Muangpat P, Sitthisak S, Rattanarojpong T, Chantratita N, Machado RAR, Shi YM, Bode HB, Vitta A, Thanwisai A. Genome mining reveals novel biosynthetic gene clusters in entomopathogenic bacteria. Sci Rep 2023; 13:20764. [PMID: 38007490 PMCID: PMC10676414 DOI: 10.1038/s41598-023-47121-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/09/2023] [Indexed: 11/27/2023] Open
Abstract
The discovery of novel bioactive compounds produced by microorganisms holds significant potential for the development of therapeutics and agrochemicals. In this study, we conducted genome mining to explore the biosynthetic potential of entomopathogenic bacteria belonging to the genera Xenorhabdus and Photorhabdus. By utilizing next-generation sequencing and bioinformatics tools, we identified novel biosynthetic gene clusters (BGCs) in the genomes of the bacteria, specifically plu00736 and plu00747. These clusters were identified as unidentified non-ribosomal peptide synthetase (NRPS) and unidentified type I polyketide synthase (T1PKS) clusters. These BGCs exhibited unique genetic architecture and encoded several putative enzymes and regulatory elements, suggesting its involvement in the synthesis of bioactive secondary metabolites. Furthermore, comparative genome analysis revealed that these BGCs were distinct from previously characterized gene clusters, indicating the potential for the production of novel compounds. Our findings highlighted the importance of genome mining as a powerful approach for the discovery of biosynthetic gene clusters and the identification of novel bioactive compounds. Further investigations involving expression studies and functional characterization of the identified BGCs will provide valuable insights into the biosynthesis and potential applications of these bioactive compounds.
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Affiliation(s)
- Wipanee Meesil
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Paramaporn Muangpat
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Sutthirat Sitthisak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
- Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Triwit Rattanarojpong
- Department of Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10400, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Yi-Ming Shi
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe University, Frankfurt, 60438, Frankfurt am Main, Germany
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Helge B Bode
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe University, Frankfurt, 60438, Frankfurt am Main, Germany
- Chemical Biology, Department of Chemistry, Philipps University Marburg, 35032, Marburg, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- SYNMIKRO (Zentrum für Synthetische Mikrobiologie), 35032, Marburg, Germany
| | - Apichat Vitta
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
- Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
- Center of Excellence for Biodiversity, Faculty of Sciences, Naresuan University, Phitsanulok, 65000, Thailand
| | - Aunchalee Thanwisai
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand.
- Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand.
- Center of Excellence for Biodiversity, Faculty of Sciences, Naresuan University, Phitsanulok, 65000, Thailand.
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5
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Awori RM, Hendre P, Amugune NO. The genome of a steinernematid-associated Pseudomonas piscis bacterium encodes the biosynthesis of insect toxins. Access Microbiol 2023; 5:000659.v3. [PMID: 37970093 PMCID: PMC10634486 DOI: 10.1099/acmi.0.000659.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/15/2023] [Indexed: 11/17/2023] Open
Abstract
Several species of soil-dwelling Steinernema nematodes are used in the biocontrol of crop pests, due to their natural capacity to kill diverse lepidopteran species. Although this insect-killing trait is known to be augmented by the nematodes' Xenorhabdus endosymbionts, the role of other steinernematid-associated bacterial genera in the nematode lifecycle remains unclear. This genomic study aimed to determine the potential of Pseudomonas piscis to contribute to the entomopathogenicity of its Steinernema host. Insect larvae were infected with three separate Steinernema cultures. From each of the three treatments, the prevalent bacteria in the haemocoel of cadavers, four days post-infection, were isolated. These three bacterial isolates were morphologically characterised. DNA was extracted from each of the three bacterial isolates and used for long-read genome sequencing and assembly. Assemblies were used to delineate species and identify genes that encode insect toxins, antimicrobials, and confer antibiotic resistance. We assembled three complete genomes. Through digital DNA-DNA hybridisation analyses, we ascertained that the haemocoels of insect cadavers previously infected with Steinernema sp. Kalro, Steinernema sp. 75, and Steinernema sp. 97 were dominated by Xenorhabdus griffiniae Kalro, Pseudomonas piscis 75, and X. griffiniae 97, respectively. X. griffiniae Kalro and X. griffiniae 97 formed a subspecies with other X. griffiniae symbionts of steinernematids from Kenya. P. piscis 75 phylogenetically clustered with pseudomonads that are characterised by high insecticidal activity. The P. piscis 75 genome encoded the production pathway of insect toxins such as orfamides and rhizoxins, antifungals such as pyrrolnitrin and pyoluteorin, and the broad-spectrum antimicrobial 2,4-diacetylphloroglucinol. The P. piscis 75 genome encoded resistance to over ten classes of antibiotics, including cationic lipopeptides. Steinernematid-associated P. piscis bacteria hence have the biosynthetic potential to contribute to nematode entomopathogenicity.
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Affiliation(s)
- Ryan Musumba Awori
- Elakistos Biosciences, P. O. Box 19301-00100, Nairobi, Kenya
- International Centre for Research on Agroforestry, P. O. Box 30677-00100, Nairobi, Kenya
| | - Prasad Hendre
- International Centre for Research on Agroforestry, P. O. Box 30677-00100, Nairobi, Kenya
| | - Nelson O. Amugune
- Department of Biology, University of Nairobi, P. O. Box 30197-00100, Nairobi, Kenya
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Fodor A, Hess C, Ganas P, Boros Z, Kiss J, Makrai L, Dublecz K, Pál L, Fodor L, Sebestyén A, Klein MG, Tarasco E, Kulkarni MM, McGwire BS, Vellai T, Hess M. Antimicrobial Peptides (AMP) in the Cell-Free Culture Media of Xenorhabdus budapestensis and X. szentirmaii Exert Anti-Protist Activity against Eukaryotic Vertebrate Pathogens including Histomonas meleagridis and Leishmania donovani Species. Antibiotics (Basel) 2023; 12:1462. [PMID: 37760758 PMCID: PMC10525888 DOI: 10.3390/antibiotics12091462] [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: 07/31/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Anti-microbial peptides provide a powerful toolkit for combating multidrug resistance. Combating eukaryotic pathogens is complicated because the intracellular drug targets in the eukaryotic pathogen are frequently homologs of cellular structures of vital importance in the host organism. The entomopathogenic bacteria (EPB), symbionts of entomopathogenic-nematode species, release a series of non-ribosomal templated anti-microbial peptides. Some may be potential drug candidates. The ability of an entomopathogenic-nematode/entomopathogenic bacterium symbiotic complex to survive in a given polyxenic milieu is a coevolutionary product. This explains that those gene complexes that are responsible for the biosynthesis of different non-ribosomal templated anti-microbial protective peptides (including those that are potently capable of inactivating the protist mammalian pathogen Leishmania donovanii and the gallinaceous bird pathogen Histomonas meleagridis) are co-regulated. Our approach is based on comparative anti-microbial bioassays of the culture media of the wild-type and regulatory mutant strains. We concluded that Xenorhabdus budapestensis and X. szentirmaii are excellent sources of non-ribosomal templated anti-microbial peptides that are efficient antagonists of the mentioned pathogens. Data on selective cytotoxicity of different cell-free culture media encourage us to forecast that the recently discovered "easy-PACId" research strategy is suitable for constructing entomopathogenic-bacterium (EPB) strains producing and releasing single, harmless, non-ribosomal templated anti-microbial peptides with considerable drug, (probiotic)-candidate potential.
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Affiliation(s)
- András Fodor
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter. sétány 1C, H-1117 Budapest, Hungary; (Z.B.); (T.V.)
| | - Claudia Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine (Vetmeduni Vienna), 1210 Vienna, Austria; (C.H.); (P.G.)
| | - Petra Ganas
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine (Vetmeduni Vienna), 1210 Vienna, Austria; (C.H.); (P.G.)
| | - Zsófia Boros
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter. sétány 1C, H-1117 Budapest, Hungary; (Z.B.); (T.V.)
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Páter Károly utca 1, H-2100 Gödöllő, Hungary;
| | - János Kiss
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Páter Károly utca 1, H-2100 Gödöllő, Hungary;
| | | | - Károly Dublecz
- Institute of Physiology and Nutrition, Georgikon Campus, Hungarian University of Agriculture and Life Sciences (MATE), Deák Ferenc utca 16, H-8360 Keszthely, Hungary; (K.D.); (L.P.)
| | - László Pál
- Institute of Physiology and Nutrition, Georgikon Campus, Hungarian University of Agriculture and Life Sciences (MATE), Deák Ferenc utca 16, H-8360 Keszthely, Hungary; (K.D.); (L.P.)
| | - László Fodor
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, H-1143 Budapest, Hungary;
| | - Anna Sebestyén
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, H-1085 Budapest, Hungary;
| | - Michael G. Klein
- USDA-ARS & Department of Entomology, The Ohio State University, 13416 Claremont Ave, Cleveland, OH 44130, USA;
| | - Eustachio Tarasco
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy;
| | - Manjusha M. Kulkarni
- Division of Infectious Diseases, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA; (M.M.K.); (B.S.M.)
| | - Bradford S. McGwire
- Division of Infectious Diseases, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA; (M.M.K.); (B.S.M.)
| | - Tibor Vellai
- Department of Genetics, Institute of Biology, Eötvös Loránd University, Pázmány Péter. sétány 1C, H-1117 Budapest, Hungary; (Z.B.); (T.V.)
| | - Michael Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine (Vetmeduni Vienna), 1210 Vienna, Austria; (C.H.); (P.G.)
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7
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XENOFOOD—An Autoclaved Feed Supplement Containing Autoclavable Antimicrobial Peptides—Exerts Anticoccidial GI Activity, and Causes Bursa Enlargement, but Has No Detectable Harmful Effects in Broiler Cockerels despite In Vitro Detectable Cytotoxicity on LHM Cells. Pathogens 2023; 12:pathogens12030458. [PMID: 36986380 PMCID: PMC10059668 DOI: 10.3390/pathogens12030458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023] Open
Abstract
Entomopathogenic bacteria are obligate symbionts of entomopathogenic nematode (EPN) species. These bacteria biosynthesize and release non-ribosomal-templated hybrid peptides (NR-AMPs), with strong, and large-spectral antimicrobial potential, capable of inactivating pathogens belonging to different prokaryote, and eukaryote taxa. The cell-free conditioned culture media (CFCM) of Xenorhabdus budapestensis and X. szentirmaii efficiently inactivate poultry pathogens like Clostridium, Histomonas, and Eimeria. To learn whether a bio-preparation containing antimicrobial peptides of Xenorhabdus origin with accompanying (in vitro detectable) cytotoxic effects could be considered a safely applicable preventive feed supplement, we conducted a 42-day feeding experiment on freshly hatched broiler cockerels. XENOFOOD (containing autoclaved X. budapestensis, and X. szentirmaii cultures developed on chicken food) were consumed by the birds. The XENOFOOD exerted detectable gastrointestinal (GI) activity (reducing the numbers of the colony-forming Clostridium perfringens units in the lower jejunum. No animal was lost in the experiment. Neither the body weight, growth rate, feed-conversion ratio, nor organ-weight data differed between the control (C) and treated (T) groups, indicating that the XENOFOOD diet did not result in any detectable adverse effects. We suppose that the parameters indicating a moderate enlargement of bursas of Fabricius (average weight, size, and individual bursa/spleen weight-ratios) in the XENOFOOD-fed group must be an indirect indication that the bursa-controlled humoral immune system neutralized the cytotoxic ingredients of the XENOFOOD in the blood, not allowing to reach their critical cytotoxic concentration in the sensitive tissues.
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Abd-Elgawad MMM. Xenorhabdus spp.: An Overview of the Useful Facets of Mutualistic Bacteria of Entomopathogenic Nematodes. Life (Basel) 2022; 12:1360. [PMID: 36143397 PMCID: PMC9503066 DOI: 10.3390/life12091360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 12/17/2022] Open
Abstract
Mounting concern over the misuse of chemical pesticides has sparked broad interest for safe and effective alternatives to control plant pests and pathogens. Xenorhabdus bacteria, as pesticidal symbionts of the entomopathogenic nematodes Steinernema species, can contribute to this solution with a treasure trove of insecticidal compounds and an ability to suppress a variety of plant pathogens. As many challenges face sound exploitation of plant-phytonematode interactions, a full useful spectrum of such interactions should address nematicidal activity of Xenorhabdus. Steinernema-Xenorhabdus complex or Xenorhabdus individually should be involved in mechanisms underlying the favorable side of plant-nematode interactions in emerging cropping systems. Using Xenorhabdus bacteria should earnestly be harnessed to control not only phytonematodes, but also other plant pests and pathogens within integrated pest management plans. This review highlights the significance of fitting Xenorhabdus-obtained insecticidal, nematicidal, fungicidal, acaricidal, pharmaceutical, antimicrobial, and toxic compounds into existing, or arising, holistic strategies, for controlling many pests/pathogens. The widespread utilization of Xenorhabdus bacteria, however, has been slow-going, due to costs and some issues with their commercial processing. Yet, advances have been ongoing via further mastering of genome sequencing, discovering more of the beneficial Xenorhabdus species/strains, and their successful experimentations for pest control. Their documented pathogenicity to a broad range of arthropods and pathogens and versatility bode well for useful industrial products. The numerous beneficial traits of Xenorhabdus bacteria can facilitate their integration with other tactics for better pest/disease management programs.
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Affiliation(s)
- Mahfouz M M Abd-Elgawad
- Plant Pathology Department, Agricultural and Biological Research Division, National Research Centre, El-Behooth St., Dokki, Giza 12622, Egypt
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9
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Fodor A, Gualtieri M, Zeller M, Tarasco E, Klein MG, Fodor AM, Haynes L, Lengyel K, Forst SA, Furgani GM, Karaffa L, Vellai T. Type Strains of Entomopathogenic Nematode-Symbiotic Bacterium Species, Xenorhabdus szentirmaii (EMC) and X. budapestensis (EMA), Are Exceptional Sources of Non-Ribosomal Templated, Large-Target-Spectral, Thermotolerant-Antimicrobial Peptides (by Both), and Iodinin (by EMC). Pathogens 2022; 11:pathogens11030342. [PMID: 35335666 PMCID: PMC8950435 DOI: 10.3390/pathogens11030342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 01/26/2023] Open
Abstract
Antimicrobial multidrug resistance (MDR) is a global challenge, not only for public health, but also for sustainable agriculture. Antibiotics used in humans should be ruled out for use in veterinary or agricultural settings. Applying antimicrobial peptide (AMP) molecules, produced by soil-born organisms for protecting (soil-born) plants, seems a preferable alternative. The natural role of peptide-antimicrobials, produced by the prokaryotic partner of entomopathogenic-nematode/bacterium (EPN/EPB) symbiotic associations, is to sustain monoxenic conditions for the EPB in the gut of the semi-anabiotic infective dauer juvenile (IJ) EPN. They keep pathobiome conditions balanced for the EPN/EPB complex in polyxenic (soil, vanquished insect cadaver) niches. Xenorhabdus szentirmaii DSM16338(T) (EMC), and X. budapestensis DSM16342(T) (EMA), are the respective natural symbionts of EPN species Steinernema rarum and S. bicornutum. We identified and characterized both of these 15 years ago. The functional annotation of the draft genome of EMC revealed 71 genes encoding non-ribosomal peptide synthases, and polyketide synthases. The large spatial Xenorhabdus AMP (fabclavine), was discovered in EMA, and its biosynthetic pathway in EMC. The AMPs produced by EMA and EMC are promising candidates for controlling MDR prokaryotic and eukaryotic pathogens (bacteria, oomycetes, fungi, protozoa). EMC releases large quantity of iodinin (1,6-dihydroxyphenazine 5,10-dioxide) in a water-soluble form into the media, where it condenses to form spectacular water-insoluble, macroscopic crystals. This review evaluates the scientific impact of international research on EMA and EMC.
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Affiliation(s)
- András Fodor
- Department of Genetics, Eötvös University, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary; (A.M.F.); (K.L.); or (G.M.F.); or (T.V.)
- Department of Genetics, University of Szeged, Középfasor 52, H-6726 Szeged, Hungary
- Correspondence: ; Tel.: +36-(30)-490-9294
| | - Maxime Gualtieri
- Nosopharm, 110 Allée Charles Babbage, Espace Innovation 2, 30000 Nîmes, France;
| | - Matthias Zeller
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA;
| | - Eustachio Tarasco
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy;
- Institute for Sustainable Plant Protection of CNR, Via Amendola 122/D, 70126 Bari, Italy
| | - Michael G. Klein
- USDA-ARS & Department of Entomology, The Ohio State University, 13416 Claremont Ave, Cleveland, OH 44130, USA;
| | - Andrea M. Fodor
- Department of Genetics, Eötvös University, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary; (A.M.F.); (K.L.); or (G.M.F.); or (T.V.)
| | - Leroy Haynes
- Department of Chemistry, The College of Wooster, Wooster, OH 44691, USA;
| | - Katalin Lengyel
- Department of Genetics, Eötvös University, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary; (A.M.F.); (K.L.); or (G.M.F.); or (T.V.)
- National Institute of Pharmacy and Nutrition (NIPN), Zrinyi utca 3, H-1051 Budapest, Hungary
| | - Steven A. Forst
- Department of Biological Sciences, University of Wisconsin-Milwaukee, P.O. Box 413, Milwaukee, WI 53201, USA;
| | - Ghazala M. Furgani
- Department of Genetics, Eötvös University, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary; (A.M.F.); (K.L.); or (G.M.F.); or (T.V.)
- Department of Plant Protection, Faculty of Agriculture, University of Tripoli, Tripoli P.O. Box 13793, Libya
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem Tér 1, H-4032 Debrecen, Hungary;
- Institute of Metagenomics, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Tibor Vellai
- Department of Genetics, Eötvös University, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary; (A.M.F.); (K.L.); or (G.M.F.); or (T.V.)
- MTA-ELTE Genetics Research Group, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary
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10
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Santos-Aberturas J, Vior NM. Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them. Antibiotics (Basel) 2022; 11:195. [PMID: 35203798 PMCID: PMC8868522 DOI: 10.3390/antibiotics11020195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.
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Affiliation(s)
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich NR7 4UH, UK
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11
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Li JH, Cho W, Hamchand R, Oh J, Crawford JM. A Conserved Nonribosomal Peptide Synthetase in Xenorhabdus bovienii Produces Citrulline-Functionalized Lipopeptides. JOURNAL OF NATURAL PRODUCTS 2021; 84:2692-2699. [PMID: 34581573 PMCID: PMC9970011 DOI: 10.1021/acs.jnatprod.1c00573] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The entomopathogenic bacterium Xenorhabdus bovienii exists in a mutualistic relationship with nematodes of the genus Steinernema. Free-living infective juveniles of Steinernema prey on insect larvae and regurgitate X. bovienii within the hemocoel of a host larva. X. bovienii subsequently produces a complex array of specialized metabolites and effector proteins that kill the insect and regulate various aspects of the trilateral symbiosis. While Xenorhabdus species are rich producers of secondary metabolites, many of their biosynthetic gene clusters remain uncharacterized. Here, we describe a nonribosomal peptide synthetase (NRPS) identified through comparative genomics analysis that is widely conserved in Xenorhabdus species. Heterologous expression of this NRPS gene from X. bovienii in E. coli led to the discovery of a family of lipo-tripeptides that chromatographically appear as pairs, containing either a C-terminal carboxylic acid or carboxamide. Coexpression of the NRPS with the leupeptin protease inhibitor pathway enhanced production, facilitating isolation and characterization efforts. The new lipo-tripeptides were also detected in wild-type X. bovienii cultures. These metabolites, termed bovienimides, share an uncommon C-terminal d-citrulline residue. The NRPS lacked a dedicated chain termination domain, resulting in product diversification and release from the assembly line through reactions with ammonia, water, or exogenous alcohols.
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Affiliation(s)
- Jhe-Hao Li
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Wooyoung Cho
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Randy Hamchand
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Joonseok Oh
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, United States
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12
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Li B, Qiu D, Wang S. Complete Genome Sequence Data of Xenorhabdus budapestensis Strain C72, a Candidate Biological Control Agent from China. PLANT DISEASE 2021; 105:3276-3278. [PMID: 33970680 DOI: 10.1094/pdis-04-21-0701-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Xenorhabdus budapestensis strain C72 isolated from the entomopathogenic nematode of Steinernema bicornutum possesses an excellent biocontrol effect on southern corn leaf blight. However, its genomic information is lacking. Here, we report a high-quality complete and annotated genome sequence of X. budapestensis strain C72. Fifteen secondary metabolite biosynthetic gene clusters are identified in the genome, which are responsible for the production of a diverse group of antimicrobial compounds to help host plants against agricultural pathogenic diseases. This genome sequence could contribute to investigations of the molecular basis underlying the biocontrol activity of this Xenorhabdus strain.
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Affiliation(s)
- Bo Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, B-5030 Gembloux, Belgium
| | - Dewen Qiu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuangchao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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13
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Watzel J, Duchardt-Ferner E, Sarawi S, Bode HB, Wöhnert J. Cooperation between a T Domain and a Minimal C-Terminal Docking Domain to Enable Specific Assembly in a Multiprotein NRPS. Angew Chem Int Ed Engl 2021; 60:14171-14178. [PMID: 33876501 PMCID: PMC8251938 DOI: 10.1002/anie.202103498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 01/27/2023]
Abstract
Non-ribosomal peptide synthetases (NRPS) produce natural products from amino acid building blocks. They often consist of multiple polypeptide chains which assemble in a specific linear order via specialized N- and C-terminal docking domains (N/C DDs). Typically, docking domains function independently from other domains in NRPS assembly. Thus, docking domain replacements enable the assembly of "designer" NRPS from proteins that normally do not interact. The multiprotein "peptide-antimicrobial-Xenorhabdus" (PAX) peptide-producing PaxS NRPS is assembled from the three proteins PaxA, PaxB and PaxC. Herein, we show that the small C DD of PaxA cooperates with its preceding thiolation (T1 ) domain to bind the N DD of PaxB with very high affinity, establishing a structural and thermodynamical basis for this unprecedented docking interaction, and we test its functional importance in vivo in a truncated PaxS assembly line. Similar docking interactions are apparently present in other NRPS systems.
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Affiliation(s)
- Jonas Watzel
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Sepas Sarawi
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Helge B Bode
- Department of Natural Products in Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt am Main, Germany.,Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
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14
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Watzel J, Duchardt‐Ferner E, Sarawi S, Bode HB, Wöhnert J. Kooperation zwischen T‐Domäne und minimaler C‐terminaler Docking‐Domäne für funktionelle Proteininteraktionen in Multiprotein‐NRPS. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jonas Watzel
- Molekulare Biotechnologie Institut für Molekulare Biowissenschaften Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Elke Duchardt‐Ferner
- Institut für Molekulare Biowissenschaften und Biomolekulares Magnetresonanz Zentrum (BMRZ) Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Sepas Sarawi
- Institut für Molekulare Biowissenschaften und Biomolekulares Magnetresonanz Zentrum (BMRZ) Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
- Molekulare Biotechnologie Institut für Molekulare Biowissenschaften Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Helge B. Bode
- Abteilung Naturstoffe in organismischen Interaktionen Max-Planck-Institut für terrestrische Mikrobiologie 35043 Marburg Deutschland
- Senckenberg Gesellschaft für Naturforschung 60325 Frankfurt am Main Deutschland
- Molekulare Biotechnologie Institut für Molekulare Biowissenschaften Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften und Biomolekulares Magnetresonanz Zentrum (BMRZ) Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
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15
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Booysen E, Dicks LMT. Does the Future of Antibiotics Lie in Secondary Metabolites Produced by Xenorhabdus spp.? A Review. Probiotics Antimicrob Proteins 2021; 12:1310-1320. [PMID: 32844362 DOI: 10.1007/s12602-020-09688-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The over-prescription of antibiotics for treatment of infections is primarily to blame for the increase in bacterial resistance. Added to the problem is the slow rate at which novel antibiotics are discovered and the many processes that need to be followed to classify antimicrobials safe for medical use. Xenorhabdus spp. of the family Enterobacteriaceae, mutualistically associated with entomopathogenic nematodes of the genus Steinernema, produce a variety of antibacterial peptides, including bacteriocins, depsipeptides, xenocoumacins and PAX (peptide antimicrobial-Xenorhabdus) peptides, plus additional secondary metabolites with antibacterial and antifungal activity. The secondary metabolites of some strains are active against protozoa and a few have anti-carcinogenic properties. It is thus not surprising that nematodes invaded by a single strain of a Xenorhabdus species are not infected by other microorganisms. In this review, the antimicrobial compounds produced by Xenorhabdus spp. are listed and the gene clusters involved in synthesis of these secondary metabolites are discussed. We also review growth conditions required for increased production of antimicrobial compounds.
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Affiliation(s)
- E Booysen
- Department of Microbiology, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - L M T Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch, 7600, South Africa.
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16
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Booysen E, Rautenbach M, Stander MA, Dicks LMT. Profiling the Production of Antimicrobial Secondary Metabolites by Xenorhabdus khoisanae J194 Under Different Culturing Conditions. Front Chem 2021; 9:626653. [PMID: 33859975 PMCID: PMC8042232 DOI: 10.3389/fchem.2021.626653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
Species from the genus Xenorhabdus, endosymbiotic bacteria of Steinernema nematodes, produce several antibacterial and antifungal compounds, some of which are anti-parasitic. In this study, we report on the effect growth conditions have on the production of antimicrobial compounds produced by Xenorhabdus khoisanae J194. The strain was cultured in aerated and non-aerated broth, respectively, and on solid media. Production of antimicrobial compounds was detected after 24 h of growth in liquid media, with highest levels recorded after 96 h. Highest antimicrobial activity was obtained from cells cultured on solid media. By using ultraperformance liquid chromatography linked to mass spectrometry and HPLC, a plethora of known Xenorhabdus compounds were identified. These compounds are the PAX lipopeptides (PAX 1', PAX 3', PAX 5, and PAX 7E), xenocoumacins and xenoamicins. Differences observed in the MS-MS fractionation patterns collected in this study, when compared to previous studies indicated that this strain produces novel xenoamicins. Three novel antimicrobial compounds, khoicin, xenopep and rhabdin, were identified and structurally characterized based on MS-MS fractionation patterns, amino acid analysis and whole genome analysis. The various compounds produced under the three different conditions indicates that the secondary metabolism of X. khoisanae J194 may be regulated by oxygen, water activity or both. Based on these findings X. khoisanae J194 produce a variety of antimicrobial compounds that may have application in disease control.
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Affiliation(s)
- Elzaan Booysen
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Marina Rautenbach
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Marietjie A Stander
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa.,LCMS Central Analytical Facility, Stellenbosch University, Stellenbosch, South Africa
| | - Leon M T Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
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17
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Vo TD, Spahn C, Heilemann M, Bode HB. Microbial Cationic Peptides as a Natural Defense Mechanism against Insect Antimicrobial Peptides. ACS Chem Biol 2021; 16:447-451. [PMID: 33596038 DOI: 10.1021/acschembio.0c00794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria produce a plethora of specialized metabolites (SM), with the ecological function of most of them not known. A major group of SM are peptides derived from nonribosomal peptide synthetases (NRPS). In entomopathogenic bacteria of the genus Xenorhabdus, PAX (peptide-antimicrobial-Xenorhabdus) were described as NRPS-derived lipopeptides, which show antimicrobial activities against bacteria and fungi. We analyzed the production of PAX in Xenorhabdus doucetiae and found the majority bound to the cells. We derivatized PAX with fluorophores and show binding to cells when added externally using super-resolution microscopy. Externally added PAX in X. doucetiae and E. coli as well as inducible PAX production in X. doucetiae showed a protective effect against various antimicrobial peptides (AMPs) from insects, where they are used as a defense mechanism against pathogens. Because AMPs are often positively charged, our results suggest a PAX-induced repulsive force due to positive charge at the bacterial cell wall.
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Affiliation(s)
- Tien Duy Vo
- Fachbereich Biowissenschaften, Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main 60438, Germany
| | - Christoph Spahn
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe-Universität Frankfurt, Frankfurt am Main 60438, Germany
| | - Mike Heilemann
- Single Molecule Biophysics, Institute of Physical and Theoretical Chemistry, Goethe-Universität Frankfurt, Frankfurt am Main 60438, Germany
| | - Helge B. Bode
- Fachbereich Biowissenschaften, Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main 60438, Germany
- Buchmann Institute for Life Sciences (BMLS), Goethe-Universität Frankfurt, Frankfurt am Main 60438, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt 60325, Germany
- Max-Planck-Institute for Terrestrial Microbiology, Marburg 35043, Germany
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18
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Moyer TB, Parsley NC, Sadecki PW, Schug WJ, Hicks LM. Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products. Nat Prod Rep 2021; 38:489-509. [PMID: 32929442 PMCID: PMC7956910 DOI: 10.1039/d0np00046a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: Up to July 2020Ribosomal antimicrobial peptide (AMP) natural products, also known as ribosomally synthesized and post-translationally modified peptides (RiPPs) or host defense peptides, demonstrate potent bioactivities and impressive complexity that complicate molecular and biological characterization. Tandem mass spectrometry (MS) has rapidly accelerated bioactive peptide sequencing efforts, yet standard workflows insufficiently address intrinsic AMP diversity. Herein, orthogonal approaches to accelerate comprehensive and accurate molecular characterization without the need for prior isolation are reviewed. Chemical derivatization, proteolysis (enzymatic and chemical cleavage), multistage MS fragmentation, and separation (liquid chromatography and ion mobility) strategies can provide complementary amino acid composition and post-translational modification data to constrain sequence solutions. Examination of two complex case studies, gomesin and styelin D, highlights the practical implementation of the proposed approaches. Finally, we emphasize the importance of heterogeneous AMP peptidoforms that confer varying biological function, an area that warrants significant further development.
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Affiliation(s)
- Tessa B Moyer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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19
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Kegler C, Bode HB. Artificial Splitting of a Non-Ribosomal Peptide Synthetase by Inserting Natural Docking Domains. Angew Chem Int Ed Engl 2020; 59:13463-13467. [PMID: 32329545 PMCID: PMC7496407 DOI: 10.1002/anie.201915989] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/18/2020] [Indexed: 12/13/2022]
Abstract
The interaction in multisubunit non‐ribosomal peptide synthetases (NRPSs) is mediated by docking domains that ensure the correct subunit‐to‐subunit interaction. We introduced natural docking domains into the three‐module xefoampeptide synthetase (XfpS) to create two to three artificial NRPS XfpS subunits. The enzymatic performance of the split biosynthesis was measured by absolute quantification of the products by HPLC‐ESI‐MS. The connecting role of the docking domains was probed by deleting integral parts of them. The peptide production data was compared to soluble protein amounts of the NRPS using SDS‐PAGE. Reduced peptide synthesis was not a result of reduced soluble NRPS concentration but a consequence of the deletion of vital docking domain parts. Splitting the xefoampeptide biosynthesis polypeptide by introducing docking domains was feasible and resulted in higher amounts of product in one of the two tested split‐module cases compared to the full‐length wild‐type enzyme.
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Affiliation(s)
- Carsten Kegler
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Helge B Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, 60438, Frankfurt, Germany.,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt, Germany
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20
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Kegler C, Bode HB. Artificial Splitting of a Non‐Ribosomal Peptide Synthetase by Inserting Natural Docking Domains. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Carsten Kegler
- Molekulare Biotechnologie, Fachbereich Biowissenschaften Goethe Universität Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt am Main Germany
| | - Helge B. Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften Goethe Universität Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt am Main Germany
- Buchmann Institute for Molecular Life Sciences (BMLS) Goethe-Universität Frankfurt 60438 Frankfurt Germany
- Senckenberg Gesellschaft für Naturforschung Senckenberganlage 25 60325 Frankfurt Germany
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21
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Wenski SL, Cimen H, Berghaus N, Fuchs SW, Hazir S, Bode HB. Fabclavine diversity in Xenorhabdus bacteria. Beilstein J Org Chem 2020; 16:956-965. [PMID: 32461774 PMCID: PMC7214866 DOI: 10.3762/bjoc.16.84] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
The global threat of multiresistant pathogens has to be answered by the development of novel antibiotics. Established antibiotic applications are often based on so-called secondary or specialized metabolites (SMs), identified in large screening approaches. To continue this successful strategy, new sources for bioactive compounds are required, such as the bacterial genera Xenorhabdus or Photorhabdus. In these strains, fabclavines are widely distributed SMs with a broad-spectrum bioactivity. Fabclavines are hybrid SMs derived from nonribosomal peptide synthetases (NRPS), polyunsaturated fatty acid (PUFA), and polyketide synthases (PKS). Selected Xenorhabdus and Photorhabdus mutant strains were generated applying a chemically inducible promoter in front of the suggested fabclavine (fcl) biosynthesis gene cluster (BGC), followed by the analysis of the occurring fabclavines. Subsequently, known and unknown derivatives were identified and confirmed by MALDI-MS and MALDI-MS2 experiments in combination with an optimized sample preparation. This led to a total number of 22 novel fabclavine derivatives in eight strains, increasing the overall number of fabclavines to 32. Together with the identification of fabclavines as major antibiotics in several entomopathogenic strains, our work lays the foundation for the rapid fabclavine identification and dereplication as the basis for future work of this widespread and bioactive SM class.
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Affiliation(s)
- Sebastian L Wenski
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Harun Cimen
- Adnan Menderes University, Faculty of Arts and Sciences, Department of Biology, 09010 Aydin, Turkey
| | - Natalie Berghaus
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Sebastian W Fuchs
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Selcuk Hazir
- Adnan Menderes University, Faculty of Arts and Sciences, Department of Biology, 09010 Aydin, Turkey
| | - Helge B Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
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22
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Watzel J, Hacker C, Duchardt-Ferner E, Bode HB, Wöhnert J. A New Docking Domain Type in the Peptide-Antimicrobial-Xenorhabdus Peptide Producing Nonribosomal Peptide Synthetase from Xenorhabdus bovienii. ACS Chem Biol 2020; 15:982-989. [DOI: 10.1021/acschembio.9b01022] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jonas Watzel
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Carolin Hacker
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Helge B. Bode
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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Bode E, Heinrich AK, Hirschmann M, Abebew D, Shi Y, Vo TD, Wesche F, Shi Y, Grün P, Simonyi S, Keller N, Engel Y, Wenski S, Bennet R, Beyer S, Bischoff I, Buaya A, Brandt S, Cakmak I, Çimen H, Eckstein S, Frank D, Fürst R, Gand M, Geisslinger G, Hazir S, Henke M, Heermann R, Lecaudey V, Schäfer W, Schiffmann S, Schüffler A, Schwenk R, Skaljac M, Thines E, Thines M, Ulshöfer T, Vilcinskas A, Wichelhaus TA, Bode HB. Promoter Activation in Δhfq Mutants as an Efficient Tool for Specialized Metabolite Production Enabling Direct Bioactivity Testing. Angew Chem Int Ed Engl 2019; 58:18957-18963. [PMID: 31693786 PMCID: PMC6972681 DOI: 10.1002/anie.201910563] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Indexed: 12/02/2022]
Abstract
Natural products (NPs) from microorganisms have been important sources for discovering new therapeutic and chemical entities. While their corresponding biosynthetic gene clusters (BGCs) can be easily identified by gene-sequence-similarity-based bioinformatics strategies, the actual access to these NPs for structure elucidation and bioactivity testing remains difficult. Deletion of the gene encoding the RNA chaperone, Hfq, results in strains losing the production of most NPs. By exchanging the native promoter of a desired BGC against an inducible promoter in Δhfq mutants, almost exclusive production of the corresponding NP from the targeted BGC in Photorhabdus, Xenorhabdus and Pseudomonas was observed including the production of several new NPs derived from previously uncharacterized non-ribosomal peptide synthetases (NRPS). This easyPACId approach (easy Promoter Activated Compound Identification) facilitates NP identification due to low interference from other NPs. Moreover, it allows direct bioactivity testing of supernatants containing secreted NPs, without laborious purification.
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Bode E, Heinrich AK, Hirschmann M, Abebew D, Shi Y, Vo TD, Wesche F, Shi Y, Grün P, Simonyi S, Keller N, Engel Y, Wenski S, Bennet R, Beyer S, Bischoff I, Buaya A, Brandt S, Cakmak I, Çimen H, Eckstein S, Frank D, Fürst R, Gand M, Geisslinger G, Hazir S, Henke M, Heermann R, Lecaudey V, Schäfer W, Schiffmann S, Schüffler A, Schwenk R, Skaljac M, Thines E, Thines M, Ulshöfer T, Vilcinskas A, Wichelhaus TA, Bode HB. Promoter Activation in Δ
hfq
Mutants as an Efficient Tool for Specialized Metabolite Production Enabling Direct Bioactivity Testing. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910563] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Zhang S, Liu Q, Han Y, Han J, Yan Z, Wang Y, Zhang X. Nematophin, an Antimicrobial Dipeptide Compound From Xenorhabdus nematophila YL001 as a Potent Biopesticide for Rhizoctonia solani Control. Front Microbiol 2019; 10:1765. [PMID: 31440217 PMCID: PMC6693444 DOI: 10.3389/fmicb.2019.01765] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/16/2019] [Indexed: 11/13/2022] Open
Abstract
This study was conducted to purify and identify metabolites of antimicrobial activity against phytopathogens from Xenorhabdus nematophila YL001. Three dipeptide compounds were purified from its cell-free cultural broth and identified as (±)-nematophin, cyclo (L-Pro-Gly), and N, N'-dimethyl-cyclo (L-Phe-L-Leu). Nematophin demonstrated a wider antifungal spectrum than the other two compounds. It also exhibited strong inhibitory effects on mycelial growth of Rhizoctonia solani and Phytophthora infestans with EC50 values of 40.00 and 51.25 μg/ml, respectively. Its (S)-configuration structure [(+)-nematophin] was also synthesized and exhibited higher antimicrobial activity than the enantiomeric mixture. The detached leaf assay revealed that nematophin possessed significant preventive and curative efficacy against R. solani on broad bean leaves showing corresponding control efficacies of 93.01 and 94.93% at 1,000 μg/ml, comparable to those of a chemical fungicide (carbendazim) at 500 μg/ml. Additionally, the pot experiments indicated that nematophin could effectively inhibit the disease extension on rice and broad bean plants caused by R. solani. Nematophin also exerted some adverse influences on the sclerotial development of R. solani by dramatically suppressing their formation and maturation at 40.00 μg/ml, as well as their germination at 15.00 μg/ml. Morphological and ultrastructural observations showed that the hyphae of R. solani became twisted, shriveled, and deformed at the growing points after exposure to nematophin at 40.00 μg/ml, and that the subcellular fractions also became abnormal concurrently, especially the mitochondrial structure. These results indicate that nematophin has great potential to be used as a bio-pesticide in agricultural production.
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Affiliation(s)
- Shujing Zhang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Research and Development Center of Biorational Pesticides, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Qi Liu
- Plant Quarantine and Protection Bureau of Zhumadian, Zhumadian, China
| | - Yunfei Han
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Research and Development Center of Biorational Pesticides, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jinghua Han
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Research and Development Center of Biorational Pesticides, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Zhiqiang Yan
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Research and Development Center of Biorational Pesticides, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Yonghong Wang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Research and Development Center of Biorational Pesticides, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Xing Zhang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Research and Development Center of Biorational Pesticides, College of Plant Protection, Northwest A&F University, Yangling, China
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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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MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools. Metabolites 2019; 9:metabo9070144. [PMID: 31315242 PMCID: PMC6680503 DOI: 10.3390/metabo9070144] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 12/17/2022] Open
Abstract
Metabolomics has started to embrace computational approaches for chemical interpretation of large data sets. Yet, metabolite annotation remains a key challenge. Recently, molecular networking and MS2LDA emerged as molecular mining tools that find molecular families and substructures in mass spectrometry fragmentation data. Moreover, in silico annotation tools obtain and rank candidate molecules for fragmentation spectra. Ideally, all structural information obtained and inferred from these computational tools could be combined to increase the resulting chemical insight one can obtain from a data set. However, integration is currently hampered as each tool has its own output format and efficient matching of data across these tools is lacking. Here, we introduce MolNetEnhancer, a workflow that combines the outputs from molecular networking, MS2LDA, in silico annotation tools (such as Network Annotation Propagation or DEREPLICATOR), and the automated chemical classification through ClassyFire to provide a more comprehensive chemical overview of metabolomics data whilst at the same time illuminating structural details for each fragmentation spectrum. We present examples from four plant and bacterial case studies and show how MolNetEnhancer enables the chemical annotation, visualization, and discovery of the subtle substructural diversity within molecular families. We conclude that MolNetEnhancer is a useful tool that greatly assists the metabolomics researcher in deciphering the metabolome through combination of multiple independent in silico pipelines.
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Dreyer J, Rautenbach M, Booysen E, van Staden AD, Deane SM, Dicks LMT. Xenorhabdus khoisanae SB10 produces Lys-rich PAX lipopeptides and a Xenocoumacin in its antimicrobial complex. BMC Microbiol 2019; 19:132. [PMID: 31195965 PMCID: PMC6567599 DOI: 10.1186/s12866-019-1503-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 05/31/2019] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Xenorhabdus spp. live in close symbiosis with nematodes of the Steinernema genus. Steinernema nematodes infect an insect larva and release their symbionts into the haemocoel of the insect. Once released into the haemocoel, the bacteria produce bioactive compounds to create a semi-exclusive environment by inhibiting the growth of bacteria, yeasts and molds. The antimicrobial compounds thus far identified are xenocoumacins, xenortides, xenorhabdins, indole derivatives, xenoamicins, bicornutin and a number of antimicrobial peptides. The latter may be linear peptides such as the bacteriocins xenocin and xenorhabdicin, rhabdopeptides and cabanillasin, or cyclic, such as PAX lipopeptides, taxlllaids, xenobactin and szentiamide. Thus far, production of antimicrobial compounds have been reported for Xenorhabdus nematophila, Xenorhabdus budapestensis, Xenorhabdus cabanillasii, Xenorhabdus kozodoii, Xenorhabdus szentirmaii, Xenorhabdus doucetiae, Xenorhabdus mauleonii, Xenorhabdus indica and Xenorhabdus bovienii. Here we describe, for the first time, PAX lipopeptides and xenocoumacin 2 produced by Xenorhabdus khoisanae. These compounds were identified using ultraperformance liquid chromatography, linked to high resolution electrospray ionisation mass spectrometry and tandem mass spectrometry. RESULTS Cell-free supernatants of X. khoisanae SB10 were heat stable and active against Bacillus subtilis subsp. subtilis, Escherichia coli and Candida albicans. Five lysine-rich lipopeptides from the PAX group were identified in HPLC fractions, with PAX1' and PAX7 present in the highest concentrations. Three novel PAX7 peptides with putative enoyl modifications and two linear analogues of PAX1' were also detected. A small antibiotic compound, yellow in colour and λmax of 314 nm, was recovered from the HPLC fractions and identified as xenocoumacin 2. The PAX lipopeptides and xenocoumacin 2 correlated with the genes and gene clusters in the genome of X. khoisanae SB10. CONCLUSION With UPLC-MS and MSe analyses of compounds in the antimicrobial complex of X. khoisanae SB10, a number of PAX peptides and a xenocoumacin were identified. The combination of pure PAX1' peptide with xenocoumacin 2 resulted in high antimicrobial activity. Many of the fractions did, however, contain labile compounds and some fractions were difficult to resolve. It is thus possible that strain SB10 may produce more antimicrobial compounds than reported here, as suggested by the APE Ec biosynthetic complex. Further research is required to develop these broad-spectrum antimicrobial compounds into drugs that may be used in the fight against microbial infections.
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Affiliation(s)
- J Dreyer
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - M Rautenbach
- BIOPEP Peptide Group, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
| | - E Booysen
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - A D van Staden
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - S M Deane
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - L M T Dicks
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
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Modification and de novo design of non-ribosomal peptide synthetases using specific assembly points within condensation domains. Nat Chem 2019; 11:653-661. [PMID: 31182822 DOI: 10.1038/s41557-019-0276-z] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 04/26/2019] [Indexed: 11/09/2022]
Abstract
Non-ribosomal peptide synthetases (NRPSs) are giant enzyme machines that activate amino acids in an assembly line fashion. As NRPSs are not restricted to the incorporation of the 20 proteinogenic amino acids, their efficient manipulation would enable microbial production of a diverse range of peptides; however, the structural requirements for reprogramming NRPSs to facilitate the production of new peptides are not clear. Here we describe a new fusion point inside the condensation domains of NRPSs that results in the development of the exchange unit condensation domain (XUC) concept, which enables the efficient production of peptides, even containing non-natural amino acids, in yields up to 280 mg l-1. This allows the generation of more specific NRPSs, reducing the number of unwanted peptide derivatives, but also the generation of peptide libraries. The XUC might therefore be suitable for the future optimization of peptide production and the identification of bioactive peptide derivatives for pharmaceutical and other applications.
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30
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Cai X, Zhao L, Bode HB. Reprogramming Promiscuous Nonribosomal Peptide Synthetases for Production of Specific Peptides. Org Lett 2019; 21:2116-2120. [DOI: 10.1021/acs.orglett.9b00395] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xiaofeng Cai
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Lei Zhao
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Helge B. Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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Dreyer J, Malan AP, Dicks LMT. Bacteria of the Genus Xenorhabdus, a Novel Source of Bioactive Compounds. Front Microbiol 2018; 9:3177. [PMID: 30619229 PMCID: PMC6305712 DOI: 10.3389/fmicb.2018.03177] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/07/2018] [Indexed: 12/04/2022] Open
Abstract
The genus Xenorhabdus of the family Enterobacteriaceae, are mutualistically associated with entomopathogenic nematodes of the genus Steinernema. Although most of the associations are species-specific, a specific Xenorhabdus sp. may infect more than one Steinernema sp. During the Xenorhabdus-Steinernema life cycle, insect larvae are infected and killed, while both mutualists produce bioactive compounds. These compounds act synergistically to ensure reproduction and proliferation of the nematodes and bacteria. A single strain of Xenorhabdus may produce a variety of antibacterial and antifungal compounds, some of which are also active against insects, nematodes, protozoa, and cancer cells. Antimicrobial compounds produced by Xenorhabdus spp. have not been researched to the same extent as other soil bacteria and they may hold the answer to novel antibacterial and antifungal compounds. This review summarizes the bioactive secondary metabolites produced by Xenorhabdus spp. and their application in disease control. Gene regulation and increasing the production of a few of these antimicrobial compounds are discussed. Aspects limiting future development of these novel bioactive compounds are also pointed out.
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Affiliation(s)
- Jönike Dreyer
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Antoinette P. Malan
- Department of Conservation Ecology and Entomology, Stellenbosch University, Stellenbosch, South Africa
| | - Leon M. T. Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
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Xue Y, Wang M, Zhao P, Quan C, Li X, Wang L, Gao W, Li J, Zu X, Fu D, Feng S, Li P. Gram-negative bacilli-derived peptide antibiotics developed since 2000. Biotechnol Lett 2018; 40:1271-1287. [PMID: 29968134 DOI: 10.1007/s10529-018-2589-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/27/2018] [Indexed: 11/24/2022]
Abstract
Gram-negative bacilli such as Pseudomonas spp., Pseudoalteromonas sp., Angiococcus sp., Archangium sp., Burkholderia spp., Chromobacterium sp., Chondromyces sp., Cystobacter sp., Jahnella sp., Janthinobacterium sp., Lysobacter spp., Paraliomyxa sp., Photobacterium spp., Photorhabdus sp., Pontibacter sp., Ruegeria sp., Serratia sp., Sorangium sp., Sphingomonas sp., and Xenorhabdus spp. produce an enormous array of short peptides of 30 residues or fewer that are potential pharmaceutical drugs and/or biocontrol agents. The need for novel lead antibiotic compounds is urgent due to increasing drug resistance, and this review summarises 150 Gram-negative bacilli-derived compounds reported since 2000, including 40 cyclic lipopeptides from Pseudomonas spp.; nine aromatic peptides; eight glycopeptides; 45 different cyclic lipopeptides; 24 linear lipopeptides; eight thiopeptides; one lasso peptide; ten typical cyclic peptides; and five standard linear peptides. The current and potential therapeutic applications of these peptides, including structures and antituberculotic, anti-cyanobacterial, antifungal, antibacterial, antiviral, insecticidal, and antiprotozoal activities are discussed.
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Affiliation(s)
- Yun Xue
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Mengya Wang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Pengchao Zhao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China.
| | - Chunshan Quan
- Department of Life Science, Dalian Nationalities University, Dalian, 116600, China
| | - Xin Li
- Life Science College, Yuncheng University, Yuncheng, 044000, China
| | - Lina Wang
- Department of Oncology, Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, China
| | - Weina Gao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Jinghua Li
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xiangyang Zu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Dongliao Fu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Shuxiao Feng
- College of Chemical Engineering and Pharmacy, Henan University of Science and Technology, Luoyang, 471023, China
| | - Ping Li
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
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Zhang S, Fang X, Tang Q, Ge J, Wang Y, Zhang X. CpxR negatively regulates the production of xenocoumacin 1, a dihydroisocoumarin derivative produced by Xenorhabdus nematophila. Microbiologyopen 2018; 8:e00674. [PMID: 29888873 PMCID: PMC6391269 DOI: 10.1002/mbo3.674] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 05/07/2018] [Accepted: 05/19/2018] [Indexed: 11/10/2022] Open
Abstract
Xenocoumacin 1 (Xcn1), a major antimicrobial compound produced by Xenorhabdus nematophila, has great potential for use in agricultural productions. In this study, we evaluated the effects of CpxR, a global response regulator associated with the mutualism and pathogenesis of X. nematophila, on the antimicrobial activity and Xcn1 production. The mutation of cpxR could promote the production of Xcn1 significantly with its level in ΔcpxR mutant being 3.07 times higher than that in the wild type. Additionally, the expression levels of xcnA‐L genes, which are responsible for the production of Xcn1, were increased in ΔcpxR mutant while the expression levels of xcnMN, which are required for the conversion of Xcn1 into Xcn2 was reduced. Noticeably, Xcn2 was also enhanced on account of the conversion of excessive Xcn1 in spite of low expression levels of xcnM and xcnN in ΔcpxR mutant. The transcriptional levels of ompR and lrp, encoding the global response regulators OmpR and Lrp which negatively and positively regulate the production of Xcn1 were concurrently decreased and increased, respectively. Correspondingly, ΔcpxR mutant also exhibited increased antimicrobial activities in vitro and in vivo. Together, these findings suggest that CpxR negatively regulates xcnA‐L genes expression while positively regulating xcnMN expression in X. nematophila YL001, which led to a high yield of Xcn1 in ΔcpxR mutant.
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Affiliation(s)
- Shujing Zhang
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A &F University, Yangling, Shaanxi, China
| | - Xiangling Fang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.,School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, Western Australia, Australia
| | - Qian Tang
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A &F University, Yangling, Shaanxi, China
| | - Jing Ge
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A &F University, Yangling, Shaanxi, China
| | - Yonghong Wang
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A &F University, Yangling, Shaanxi, China
| | - Xing Zhang
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A &F University, Yangling, Shaanxi, China
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Guo S, Zhang S, Fang X, Liu Q, Gao J, Bilal M, Wang Y, Zhang X. Regulation of antimicrobial activity and xenocoumacins biosynthesis by pH in Xenorhabdus nematophila. Microb Cell Fact 2017; 16:203. [PMID: 29141647 PMCID: PMC5688692 DOI: 10.1186/s12934-017-0813-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/08/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Xenocoumacin 1 (Xcn1) and Xenocoumacin 2 (Xcn2) are the main antimicrobial compounds produced by Xenorhabdus nematophila. Culture conditions, including pH, had remarkably distinct effects on the antimicrobial activity of X. nematophila. However, the regulatory mechanism of pH on the antimicrobial activity and antibiotic production of this bacterium is still lacking. RESULTS With the increase of initial pH, the antimicrobial activity of X. nematophila YL001 was improved. The levels of Xcn1 and nematophin at pH 8.5 were significantly (P < 0.05) higher than that at pH 5.5 and 7.0. In addition, the expression of xcnA-L, which are responsible for the production of Xcn1 was increased and the expression of xcnMN, which are required for the conversion of Xcn1 to Xcn2 was reduced at pH 8.5. Also, the expression of ompR and cpxR were decreased at pH 8.5. CONCLUSION The alkaline pH environment was found to be beneficial for the production of Xcn1 and nematophin, which in turn led to high antimicrobial activity of X. nematophila at pH 8.5.
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Affiliation(s)
- Shuqi Guo
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shujing Zhang
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Xiangling Fang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.,School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Qi Liu
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Jiangtao Gao
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yonghong Wang
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China. .,Shaanxi Research Center of Biopesticide Engineering and Technology, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China.
| | - Xing Zhang
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China.,Shaanxi Research Center of Biopesticide Engineering and Technology, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
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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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A New Member of the Growing Family of Contact-Dependent Growth Inhibition Systems in Xenorhabdus doucetiae. PLoS One 2016; 11:e0167443. [PMID: 27907104 PMCID: PMC5131962 DOI: 10.1371/journal.pone.0167443] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 11/14/2016] [Indexed: 12/29/2022] Open
Abstract
Xenorhabdus is a bacterial symbiont of entomopathogenic Steinernema nematodes and is pathogenic for insects. Its life cycle involves a stage inside the insect cadaver, in which it competes for environmental resources with microorganisms from soil and the insect gut. Xenorhabdus is, thus, a useful model for identifying new interbacterial competition systems. For the first time, in an entomopathogenic bacterium, Xenorhabdus doucetiae strain FRM16, we identified a cdi-like locus. The cdi loci encode contact-dependent inhibition (CDI) systems composed of proteins from the two-partner secretion (TPS) family. CdiB is the outer membrane protein and CdiA is the toxic exoprotein. An immunity protein, CdiI, protects bacteria against inhibition. We describe here the growth inhibition effect of the toxic C-terminus of CdiA from X. doucetiae FRM16, CdiA-CTFRM16, following its production in closely and distantly related enterobacterial species. CdiA-CTFRM16 displayed Mg2+-dependent DNase activity, in vitro. CdiA-CTFRM16-mediated growth inhibition was specifically neutralized by CdiIFRM16. Moreover, the cdi FRM16 locus encodes an ortholog of toxin-activating proteins C that we named CdiCFRM16. In addition to E. coli, the cdiBCAI-type locus was found to be widespread in environmental bacteria interacting with insects, plants, rhizospheres and soils. Phylogenetic tree comparisons for CdiB, CdiA and CdiC suggested that the genes encoding these proteins had co-evolved. By contrast, the considerable variability of CdiI protein sequences suggests that the cdiI gene is an independent evolutionary unit. These findings further characterize the sparsely described cdiBCAI-type locus.
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Hillman K, Goodrich-Blair H. Are you my symbiont? Microbial polymorphic toxins and antimicrobial compounds as honest signals of beneficial symbiotic defensive traits. Curr Opin Microbiol 2016; 31:184-190. [DOI: 10.1016/j.mib.2016.04.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/11/2016] [Accepted: 04/13/2016] [Indexed: 11/28/2022]
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Okinyo-Owiti DP, Young L, Burnett PGG, Reaney MJT. New flaxseed orbitides: Detection, sequencing, and (15)N incorporation. Biopolymers 2016; 102:168-75. [PMID: 24408479 DOI: 10.1002/bip.22459] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 12/20/2013] [Accepted: 12/23/2013] [Indexed: 11/07/2022]
Abstract
Three new orbitides (cyclolinopeptides 17, 18, and 19) were identified in flaxseed (Linum usitatissimum L.) extracts without any form of purification. Their structures were elucidated by a combination of (15) N-labeling experiments and extensive tandem mass spectrometry (MS/MS) with electrospray ionization (ESI). Putative linear peptide sequences of the new orbitides were used as the query in the Basic Local Alignment Search Tool (BLAST) searches of flax genome database. These searches returned linear sequences for the putative precursors of cyclolinopeptides 17 and 19 among others. Cyclolinopeptide 18 contains MetO (O) and is not directly encoded, but is a product of post-translation modification of the Met present in 17. The identification of precursor proteins in flax mRNA transcripts and DNA sequences confirmed the occurrence and amino acid sequences of these orbitides as [1-9-NαC]-MLKPFFFWI, [1-9-NαC]-OLKPFFFWI, and [1-9-NαC]-GIPPFWLTL for cyclolinopeptides 17, 18, and 19, respectively.
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Affiliation(s)
- Denis P Okinyo-Owiti
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
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Abstract
Despite the importance of microbial natural products for human health, only a few bacterial genera have been mined for the new natural products needed to overcome the urgent threat of antibiotic resistance. This is surprising, given that genome sequencing projects have revealed that the capability to produce natural products is not a rare feature among bacteria. Even the bacteria occurring in the human microbiome produce potent antibiotics, and thus potentially are an untapped resource for novel compounds, potentially with new activities. This review highlights examples of bacteria that should be considered new sources of natural products, including anaerobes, pathogens, and symbionts of humans, insects, and nematodes. Exploitation of these producer strains, combined with advances in modern natural product research methodology, has the potential to open the way for a new golden age of microbial therapeutics.
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Affiliation(s)
- Victoria L Challinor
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Frankfurt am Main, Germany
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Antimicrobials and the Natural Biology of a Bacterial-Nematode Symbiosis. ADVANCES IN ENVIRONMENTAL MICROBIOLOGY 2016. [DOI: 10.1007/978-3-319-28068-4_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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41
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Rinkel J, Dickschat JS. Recent highlights in biosynthesis research using stable isotopes. Beilstein J Org Chem 2015; 11:2493-508. [PMID: 26734097 PMCID: PMC4685789 DOI: 10.3762/bjoc.11.271] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/23/2015] [Indexed: 02/03/2023] Open
Abstract
The long and successful history of isotopic labeling experiments within natural products research has both changed and deepened our understanding of biosynthesis. As demonstrated in this article, the usage of isotopes is not at all old-fashioned, but continues to give important insights into biosynthetic pathways of secondary metabolites. This review with 85 cited references is structured by separate discussions of compounds from different classes including polyketides, non-ribosomal peptides, their hybrids, terpenoids, and aromatic compounds formed via the shikimate pathway. The text does not aim at a comprehensive overview, but instead a selection of recent important examples of isotope usage within biosynthetic studies is presented, with a special emphasis on mechanistic surprises.
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Affiliation(s)
- Jan Rinkel
- Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
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Role of secondary metabolites in establishment of the mutualistic partnership between Xenorhabdus nematophila and the entomopathogenic nematode Steinernema carpocapsae. Appl Environ Microbiol 2014; 81:754-64. [PMID: 25398871 DOI: 10.1128/aem.02650-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Xenorhabdus nematophila engages in a mutualistic partnership with the nematode Steinernema carpocapsae, which invades insects, migrates through the gut, and penetrates into the hemocoel (body cavity). We showed previously that during invasion of Manduca sexta, the gut microbe Staphylococcus saprophyticus appeared transiently in the hemocoel, while Enterococcus faecalis proliferated as X. nematophila became dominant. X. nematophila produces diverse secondary metabolites, including the major water-soluble antimicrobial xenocoumacin. Here, we study the role of X. nematophila antimicrobials in interspecies competition under biologically relevant conditions using strains lacking either xenocoumacin (ΔxcnKL strain), xenocoumacin and the newly discovered antibiotic F (ΔxcnKL:F strain), or all ngrA-derived secondary metabolites (ngrA strain). Competition experiments were performed in Grace's insect medium, which is based on lepidopteran hemolymph. S. saprophyticus was eliminated when inoculated into growing cultures of either the ΔxcnKL strain or ΔxcnKL:F strain but grew in the presence of the ngrA strain, indicating that ngrA-derived antimicrobials, excluding xenocoumacin or antibiotic F, were required to eliminate the competitor. In contrast, S. saprophyticus was eliminated when coinjected into M. sexta with either the ΔxcnKL or ngrA strain, indicating that ngrA-derived antimicrobials were not required to eliminate the competitor in vivo. E. faecalis growth was facilitated when coinjected with either of the mutant strains. Furthermore, nematode reproduction in M. sexta naturally infected with infective juveniles colonized with the ngrA strain was markedly reduced relative to the level of reproduction when infective juveniles were colonized with the wild-type strain. These findings provide new insights into interspecies competition in a host environment and suggest that ngrA-derived compounds serve as signals for in vivo nematode reproduction.
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Kronenwerth M, Bozhüyük KAJ, Kahnt AS, Steinhilber D, Gaudriault S, Kaiser M, Bode HB. Characterisation of taxlllaids A-G; natural products from Xenorhabdus indica. Chemistry 2014; 20:17478-87. [PMID: 25351611 DOI: 10.1002/chem.201403979] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Indexed: 01/06/2023]
Abstract
Six new lipodepsipeptides and an additional linear derivative named taxlllaids A-G (1-7) have been identified in the entomopathogenic bacterium Xenorhabdus indica. The structures of the main compounds have been solved by detailed NMR spectroscopic analysis and the structures of minor derivatives were elucidated by a combination of labelling experiments and detailed MS experiments. The absolute configuration of the taxlllaids was deduced by using the advanced Marfey method and analysis of the biosynthesis gene cluster showing the presence of epimerisation domains, which was subsequently proved to be correct by solid-phase peptide synthesis of all taxlllaids. The exchange of a single amino acid in the adenylation domain was shown to be responsible for substrate promiscuity of the third A domain, resulting in the incorporation of leucine, phenylalanine or tyrosine. Bioactivity testing revealed the taxlllaids to be weakly active against Plasmodium falciparum and against a number of eukaryotic cell lines.
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Affiliation(s)
- Max Kronenwerth
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Johann Wolfgang Goethe-Universität Frankfurt am Main, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany), Fax: (+49) 69-798-29527
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Reimer D, Nollmann FI, Schultz K, Kaiser M, Bode HB. Xenortide Biosynthesis by Entomopathogenic Xenorhabdus nematophila. JOURNAL OF NATURAL PRODUCTS 2014; 77:1976-1980. [PMID: 25080196 DOI: 10.1021/np500390b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The biosynthesis gene cluster of the xenortides and a new derivative, xenortide D, which is produced in only trace amounts, was identified in Xenorhabdus nematophila. The structure of xenortide D was elucidated using a combination of labeling experiments followed by MS analysis and was confirmed by synthesis. Bioactivity tests revealed a weak activity of tryptamine-carrying xenortides against Plasmodium falciparum and Trypanosoma brucei.
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Affiliation(s)
- Daniela Reimer
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt , 60438 Frankfurt am Main, Germany
| | - Friederike I Nollmann
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt , 60438 Frankfurt am Main, Germany
| | - Katharina Schultz
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt , 60438 Frankfurt am Main, Germany
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute , Parasite Chemotherapy Socinstraße 57, P.O. Box, CH-4002 Basel, Switzerland
| | - Helge B Bode
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt , 60438 Frankfurt am Main, Germany
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45
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Genilloud O. The re-emerging role of microbial natural products in antibiotic discovery. Antonie Van Leeuwenhoek 2014; 106:173-88. [PMID: 24923558 DOI: 10.1007/s10482-014-0204-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 05/23/2014] [Indexed: 11/28/2022]
Abstract
New classes of antibacterial compounds are urgently needed to respond to the high frequency of occurrence of resistances to all major classes of known antibiotics. Microbial natural products have been for decades one of the most successful sources of drugs to treat infectious diseases but today, the emerging unmet clinical need poses completely new challenges to the discovery of novel candidates with the desired properties to be developed as antibiotics. While natural products discovery programs have been gradually abandoned by the big pharma, smaller biotechnology companies and research organizations are taking over the lead in the discovery of novel antibacterials. Recent years have seen new approaches and technologies being developed and integrated in a multidisciplinary effort to further exploit microbial resources and their biosynthetic potential as an untapped source of novel molecules. New strategies to isolate novel species thought to be uncultivable, and synthetic biology approaches ranging from genome mining of microbial strains for cryptic biosynthetic pathways to their heterologous expression have been emerging in combination with high throughput sequencing platforms, integrated bioinformatic analysis, and on-site analytical detection and dereplication tools for novel compounds. These different innovative approaches are defining a completely new framework that is setting the bases for the future discovery of novel chemical scaffolds that should foster a renewed interest in the identification of novel classes of natural product antibiotics from the microbial world.
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Affiliation(s)
- Olga Genilloud
- Fundación MEDINA, Avda Conocimiento 3, Parque Tecnológico Ciencias de la Salud, 18016, Granada, Spain,
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Ogier JC, Pagès S, Bisch G, Chiapello H, Médigue C, Rouy Z, Teyssier C, Vincent S, Tailliez P, Givaudan A, Gaudriault S. Attenuated virulence and genomic reductive evolution in the entomopathogenic bacterial symbiont species, Xenorhabdus poinarii. Genome Biol Evol 2014; 6:1495-513. [PMID: 24904010 PMCID: PMC4079199 DOI: 10.1093/gbe/evu119] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Bacteria of the genus Xenorhabdus are symbionts of soil entomopathogenic nematodes of the genus Steinernema. This symbiotic association constitutes an insecticidal complex active against a wide range of insect pests. Unlike other Xenorhabdus species, Xenorhabdus poinarii is avirulent when injected into insects in the absence of its nematode host. We sequenced the genome of the X. poinarii strain G6 and the closely related but virulent X. doucetiae strain FRM16. G6 had a smaller genome (500–700 kb smaller) than virulent Xenorhabdus strains and lacked genes encoding potential virulence factors (hemolysins, type 5 secretion systems, enzymes involved in the synthesis of secondary metabolites, and toxin–antitoxin systems). The genomes of all the X. poinarii strains analyzed here had a similar small size. We did not observe the accumulation of pseudogenes, insertion sequences or decrease in coding density usually seen as a sign of genomic erosion driven by genetic drift in host-adapted bacteria. Instead, genome reduction of X. poinarii seems to have been mediated by the excision of genomic blocks from the flexible genome, as reported for the genomes of attenuated free pathogenic bacteria and some facultative mutualistic bacteria growing exclusively within hosts. This evolutionary pathway probably reflects the adaptation of X. poinarii to specific host.
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Affiliation(s)
- Jean-Claude Ogier
- INRA, UMR Diversité, Génomes et Interactions Microorganismes-Insectes (DGIMI), Montpellier, FranceUniversité Montpellier 2, UMR Diversité, Génomes et Interactions Microorganismes-Insectes (DGIMI), France
| | - Sylvie Pagès
- INRA, UMR Diversité, Génomes et Interactions Microorganismes-Insectes (DGIMI), Montpellier, FranceUniversité Montpellier 2, UMR Diversité, Génomes et Interactions Microorganismes-Insectes (DGIMI), France
| | - Gaëlle Bisch
- INRA, UMR Diversité, Génomes et Interactions Microorganismes-Insectes (DGIMI), Montpellier, FranceUniversité Montpellier 2, UMR Diversité, Génomes et Interactions Microorganismes-Insectes (DGIMI), France
| | - Hélène Chiapello
- INRA Toulouse Midi-Pyrénées, Unité MIA-T, Chemin de Borde Rouge, Castanet-Tolosan, France
| | - Claudine Médigue
- CEA, Genoscope & CNRS, UMR 8030, Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Evry, France
| | - Zoé Rouy
- CEA, Genoscope & CNRS, UMR 8030, Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Evry, France
| | - Corinne Teyssier
- Université Montpellier 1, UFR des Sciences Pharmaceutiques et Biologiques/UMR95 Qualisud, CIRAD-Persyst, France
| | - Stéphanie Vincent
- CEA, Genoscope & CNRS, UMR 8030, Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Evry, France
| | - Patrick Tailliez
- INRA, UMR Diversité, Génomes et Interactions Microorganismes-Insectes (DGIMI), Montpellier, FranceUniversité Montpellier 2, UMR Diversité, Génomes et Interactions Microorganismes-Insectes (DGIMI), France
| | - Alain Givaudan
- INRA, UMR Diversité, Génomes et Interactions Microorganismes-Insectes (DGIMI), Montpellier, FranceUniversité Montpellier 2, UMR Diversité, Génomes et Interactions Microorganismes-Insectes (DGIMI), France
| | - Sophie Gaudriault
- INRA, UMR Diversité, Génomes et Interactions Microorganismes-Insectes (DGIMI), Montpellier, FranceUniversité Montpellier 2, UMR Diversité, Génomes et Interactions Microorganismes-Insectes (DGIMI), France
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47
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Fuchs SW, Grundmann F, Kurz M, Kaiser M, Bode HB. Fabclavines: bioactive peptide-polyketide-polyamino hybrids from Xenorhabdus. Chembiochem 2014; 15:512-6. [PMID: 24532262 DOI: 10.1002/cbic.201300802] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Indexed: 11/12/2022]
Abstract
The structure of the fabclavines-unique mixtures of nonribosomally derived peptide-polyketide hybrids connected to an unusual polyamino moiety-has been solved by detailed NMR and MS methods. These compounds have been identified in two different entomopathogenic Xenorhabdus strains, thereby leading also to the identification of the fabclavine biosynthesis gene cluster. Detailed analysis of these clusters and initial mutagenesis experiments allowed the prediction of a biosynthesis pathway in which the polyamino moiety is derived from an unusual type of fatty acid synthase that is normally involved in formation of polyunsaturated fatty acids. As fabclavines show broad-spectrum activity against bacteria, fungi, and other eukaryotic cells, they might act as "protection factors" against all kinds of food competitors during the complex life cycle of Xenorhabdus, its nematode host, and their insect prey.
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Affiliation(s)
- Sebastian W Fuchs
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany)
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48
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Vizcaino MI, Guo X, Crawford JM. Merging chemical ecology with bacterial genome mining for secondary metabolite discovery. J Ind Microbiol Biotechnol 2014; 41:285-99. [PMID: 24127069 PMCID: PMC3946945 DOI: 10.1007/s10295-013-1356-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/23/2013] [Indexed: 12/24/2022]
Abstract
The integration of chemical ecology and bacterial genome mining can enhance the discovery of structurally diverse natural products in functional contexts. By examining bacterial secondary metabolism in the framework of its ecological niche, insights into the upregulation of orphan biosynthetic pathways and the enhancement of the enzyme substrate supply can be obtained, leading to the discovery of new secondary metabolic pathways that would otherwise be silent or undetected under typical laboratory cultivation conditions. Access to these new natural products (i.e., the chemotypes) facilitates experimental genotype-to-phenotype linkages. Here, we describe certain functional natural products produced by Xenorhabdus and Photorhabdus bacteria with experimentally linked biosynthetic gene clusters as illustrative examples of the synergy between chemical ecology and bacterial genome mining in connecting genotypes to phenotypes through chemotype characterization. These Gammaproteobacteria share a mutualistic relationship with nematodes and a pathogenic relationship with insects and, in select cases, humans. The natural products encoded by these bacteria distinguish their interactions with their animal hosts and other microorganisms in their multipartite symbiotic lifestyles. Though both genera have similar lifestyles, their genetic, chemical, and physiological attributes are distinct. Both undergo phenotypic variation and produce a profuse number of bioactive secondary metabolites. We provide further detail in the context of regulation, production, processing, and function for these genetically encoded small molecules with respect to their roles in mutualism and pathogenicity. These collective insights more widely promote the discovery of atypical orphan biosynthetic pathways encoding novel small molecules in symbiotic systems, which could open up new avenues for investigating and exploiting microbial chemical signaling in host-bacteria interactions.
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Affiliation(s)
- Maria I. Vizcaino
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Xun Guo
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, 06510, USA
- Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
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Zhou Q, Grundmann F, Kaiser M, Schiell M, Gaudriault S, Batzer A, Kurz M, Bode HB. Structure and biosynthesis of xenoamicins from entomopathogenic Xenorhabdus. Chemistry 2013; 19:16772-9. [PMID: 24203528 DOI: 10.1002/chem.201302481] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Indexed: 01/07/2023]
Abstract
During the search for novel natural products from entomopathogenic Xenorhabdus doucetiae DSM17909 and X. mauleonii DSM17908 novel peptides named xenoamicins were identified in addition to the already known antibiotics xenocoumacin and xenorhabdin. Xenoamicins are acylated tridecadepsipeptides consisting of mainly hydrophobic amino acids. The main derivative xenoamicin A (1) was isolated from X. mauleonii DSM17908, and its structure elucidated by detailed 1D and 2D NMR experiments. Detailed MS experiments, also in combination with labeling experiments, confirmed the determined structure and allowed structure elucidation of additional derivatives. Moreover, the xenoamicin biosynthesis gene cluster was identified and analyzed in X. doucetiae DSM17909, and its participation in xenoamicin biosynthesis was confirmed by mutagenesis. Advanced Marfey's analysis of 1 showed that the absolute configuration of the amino acids is in agreement with the predicted stereochemistry deduced from the nonribosomal peptide synthetase XabABCD. Biological testing revealed activity of 1 against Plasmodium falciparum and other neglected tropical diseases but no antibacterial activity.
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Affiliation(s)
- Qiuqin Zhou
- Goethe-Universität Frankfurt, Department of Molecular Biotechnology, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main (Germany)
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Jubelin G, Lanois A, Severac D, Rialle S, Longin C, Gaudriault S, Givaudan A. FliZ is a global regulatory protein affecting the expression of flagellar and virulence genes in individual Xenorhabdus nematophila bacterial cells. PLoS Genet 2013; 9:e1003915. [PMID: 24204316 PMCID: PMC3814329 DOI: 10.1371/journal.pgen.1003915] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 09/11/2013] [Indexed: 12/17/2022] Open
Abstract
Heterogeneity in the expression of various bacterial genes has been shown to result in the presence of individuals with different phenotypes within clonal bacterial populations. The genes specifying motility and flagellar functions are coordinately regulated and form a complex regulon, the flagellar regulon. Complex interplay has recently been demonstrated in the regulation of flagellar and virulence gene expression in many bacterial pathogens. We show here that FliZ, a DNA-binding protein, plays a key role in the insect pathogen, Xenorhabdus nematophila, affecting not only hemolysin production and virulence in insects, but efficient swimming motility. RNA-Seq analysis identified FliZ as a global regulatory protein controlling the expression of 278 Xenorhabdus genes either directly or indirectly. FliZ is required for the efficient expression of all flagellar genes, probably through its positive feedback loop, which controls expression of the flhDC operon, the master regulator of the flagellar circuit. FliZ also up- or downregulates the expression of numerous genes encoding non-flagellar proteins potentially involved in key steps of the Xenorhabdus lifecycle. Single-cell analysis revealed the bimodal expression of six identified markers of the FliZ regulon during exponential growth of the bacterial population. In addition, a combination of fluorescence-activated cell sorting and RT-qPCR quantification showed that this bimodality generated a mixed population of cells either expressing (“ON state”) or not expressing (“OFF state”) FliZ-dependent genes. Moreover, studies of a bacterial population exposed to a graded series of FliZ concentrations showed that FliZ functioned as a rheostat, controlling the rate of transition between the “OFF” and “ON” states in individuals. FliZ thus plays a key role in cell fate decisions, by transiently creating individuals with different potentials for motility and host interactions. Heterogeneity in the expression of bacterial genes may result in the presence of cells with different phenotypes in an isogenic population. The existence of such “non-genetic individuality” was the first described many years ago for the flagellum-driven swimming behavior of bacteria. In this study, we identified a new bimodal switch controlling the expression of genes involved in flagellum biosynthesis and host interactions in the insect pathogen Xenorhabdus nematophila. This switch is modulated by a transcriptional regulator called FliZ. In addition to identifying all the specific genes up- and downregulated by FliZ, we showed that the concentration of FliZ fine-tuned the expression of FliZ target genes, resulting in individuals with different potentials for bacterial locomotion, host colonization and virulence.
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Affiliation(s)
- Grégory Jubelin
- INRA, UMR 1333 Laboratoire DGIMI, Montpellier, France
- Université Montpellier 2, UMR 1333 Laboratoire DGIMI, Montpellier, France
| | - Anne Lanois
- INRA, UMR 1333 Laboratoire DGIMI, Montpellier, France
- Université Montpellier 2, UMR 1333 Laboratoire DGIMI, Montpellier, France
| | - Dany Severac
- MGX-Montpellier GenomiX, c/o IGF-Institut de Génomique Fonctionnelle, Montpellier, France
| | - Stéphanie Rialle
- MGX-Montpellier GenomiX, c/o IGF-Institut de Génomique Fonctionnelle, Montpellier, France
| | - Cyrille Longin
- CEA, Genoscope & CNRS-UMR 8030, Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, Evry, France
| | - Sophie Gaudriault
- INRA, UMR 1333 Laboratoire DGIMI, Montpellier, France
- Université Montpellier 2, UMR 1333 Laboratoire DGIMI, Montpellier, France
| | - Alain Givaudan
- INRA, UMR 1333 Laboratoire DGIMI, Montpellier, France
- Université Montpellier 2, UMR 1333 Laboratoire DGIMI, Montpellier, France
- * E-mail:
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