1
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Getzke F, Wang L, Chesneau G, Böhringer N, Mesny F, Denissen N, Wesseler H, Adisa PT, Marner M, Schulze-Lefert P, Schäberle TF, Hacquard S. Physiochemical interaction between osmotic stress and a bacterial exometabolite promotes plant disease. Nat Commun 2024; 15:4438. [PMID: 38806462 PMCID: PMC11133316 DOI: 10.1038/s41467-024-48517-5] [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: 09/08/2023] [Accepted: 05/01/2024] [Indexed: 05/30/2024] Open
Abstract
Various microbes isolated from healthy plants are detrimental under laboratory conditions, indicating the existence of molecular mechanisms preventing disease in nature. Here, we demonstrated that application of sodium chloride (NaCl) in natural and gnotobiotic soil systems is sufficient to induce plant disease caused by an otherwise non-pathogenic root-derived Pseudomonas brassicacearum isolate (R401). Disease caused by combinatorial treatment of NaCl and R401 triggered extensive, root-specific transcriptional reprogramming that did not involve down-regulation of host innate immune genes, nor dampening of ROS-mediated immunity. Instead, we identified and structurally characterized the R401 lipopeptide brassicapeptin A as necessary and sufficient to promote disease on salt-treated plants. Brassicapeptin A production is salt-inducible, promotes root colonization and transitions R401 from being beneficial to being detrimental on salt-treated plants by disturbing host ion homeostasis, thereby bolstering susceptibility to osmolytes. We conclude that the interaction between a global change stressor and a single exometabolite from a member of the root microbiome promotes plant disease in complex soil systems.
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Affiliation(s)
- Felix Getzke
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Lei Wang
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392, Giessen, Germany
| | - Guillaume Chesneau
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Nils Böhringer
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392, Giessen, Germany
| | - Fantin Mesny
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Institute for Plant Sciences, University of Cologne, 50674, Cologne, Germany
| | - Nienke Denissen
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Hidde Wesseler
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Priscilla Tijesuni Adisa
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Michael Marner
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392, Giessen, Germany
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, 35392, Giessen, Germany.
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392, Giessen, Germany.
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392, Giessen, Germany.
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
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2
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Zhou L, Höfte M, Hennessy RC. Does regulation hold the key to optimizing lipopeptide production in Pseudomonas for biotechnology? Front Bioeng Biotechnol 2024; 12:1363183. [PMID: 38476965 PMCID: PMC10928948 DOI: 10.3389/fbioe.2024.1363183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Lipopeptides (LPs) produced by Pseudomonas spp. are specialized metabolites with diverse structures and functions, including powerful biosurfactant and antimicrobial properties. Despite their enormous potential in environmental and industrial biotechnology, low yield and high production cost limit their practical use. While genome mining and functional genomics have identified a multitude of LP biosynthetic gene clusters, the regulatory mechanisms underlying their biosynthesis remain poorly understood. We propose that regulation holds the key to unlocking LP production in Pseudomonas for biotechnology. In this review, we summarize the structure and function of Pseudomonas-derived LPs and describe the molecular basis for their biosynthesis and regulation. We examine the global and specific regulator-driven mechanisms controlling LP synthesis including the influence of environmental signals. Understanding LP regulation is key to modulating production of these valuable compounds, both quantitatively and qualitatively, for industrial and environmental biotechnology.
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Affiliation(s)
- Lu Zhou
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Rosanna C. Hennessy
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
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3
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Zboralski A, Biessy A, Ciotola M, Cadieux M, Albert D, Blom J, Filion M. Harnessing the genomic diversity of Pseudomonas strains against lettuce bacterial pathogens. Front Microbiol 2022; 13:1038888. [PMID: 36620043 PMCID: PMC9814014 DOI: 10.3389/fmicb.2022.1038888] [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: 09/07/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Lettuce is a major vegetable crop worldwide that is affected by numerous bacterial pathogens, including Xanthomonas hortorum pv. vitians, Pseudomonas cichorii, and Pectobacterium carotovorum. Control methods are scarce and not always effective. To develop new and sustainable approaches to contain these pathogens, we screened more than 1,200 plant-associated Pseudomonas strains retrieved from agricultural soils for their in vitro antagonistic capabilities against the three bacterial pathogens under study. Thirty-five Pseudomonas strains significantly inhibited some or all three pathogens. Their genomes were fully sequenced and annotated. These strains belong to the P. fluorescens and P. putida phylogenomic groups and are distributed in at least 27 species, including 15 validly described species. They harbor numerous genes and clusters of genes known to be involved in plant-bacteria interactions, microbial competition, and biocontrol. Strains in the P. putida group displayed on average better inhibition abilities than strains in the P. fluorescens group. They carry genes and biosynthetic clusters mostly absent in the latter strains that are involved in the production of secondary metabolites such as 7-hydroxytropolone, putisolvins, pyochelin, and xantholysin-like and pseudomonine-like compounds. The presence of genes involved in the biosynthesis of type VI secretion systems, tailocins, and hydrogen cyanide also positively correlated with the strains' overall inhibition abilities observed against the three pathogens. These results show promise for the development of biocontrol products against lettuce bacterial pathogens, provide insights on some of the potential biocontrol mechanisms involved, and contribute to public Pseudomonas genome databases, including quality genome sequences on some poorly represented species.
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Affiliation(s)
- Antoine Zboralski
- Centre de Recherche et de Développement de Saint-Jean-sur-Richelieu, Agriculture et Agroalimentaire Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Adrien Biessy
- Centre de Recherche et de Développement de Saint-Jean-sur-Richelieu, Agriculture et Agroalimentaire Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Marie Ciotola
- Centre de Recherche et de Développement de Saint-Jean-sur-Richelieu, Agriculture et Agroalimentaire Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Mélanie Cadieux
- Centre de Recherche et de Développement de Saint-Jean-sur-Richelieu, Agriculture et Agroalimentaire Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Daphné Albert
- Centre de Recherche et de Développement de Saint-Jean-sur-Richelieu, Agriculture et Agroalimentaire Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Martin Filion
- Centre de Recherche et de Développement de Saint-Jean-sur-Richelieu, Agriculture et Agroalimentaire Canada, Saint-Jean-sur-Richelieu, QC, Canada,*Correspondence: Martin Filion,
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4
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Bricout A, Morris CE, Chandeysson C, Duban M, Boistel C, Chataigné G, Lecouturier D, Jacques P, Leclère V, Rochex A. The Diversity of Lipopeptides in the Pseudomonas syringae Complex Parallels Phylogeny and Sheds Light on Structural Diversification during Evolutionary History. Microbiol Spectr 2022; 10:e0145622. [PMID: 36287007 PMCID: PMC9769872 DOI: 10.1128/spectrum.01456-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/12/2022] [Indexed: 01/05/2023] Open
Abstract
Pseudomonas spp. colonize diverse aquatic and terrestrial habitats and produce a wide variety of secondary metabolites, including lipopeptides. However, previous studies have often examined a limited number of lipopeptide-producing strains. In this study, we performed a systematic analysis of lipopeptide production across a wide data set of strains of the Pseudomonas syringae complex (724) by using a combined bioinformatics, mass spectrometry, and phylogenetics approach. The large P. syringae complex, which is composed of 13 phylogroups, is known to produce factins (including syringafactin-like lipopeptides), mycins (including syringomycin-like lipopeptides), and peptins (such as syringopeptins). We found that 80.8% of P. syringae strains produced lipopeptides and that factins were the most frequently produced (by 96% of the producing strains). P. syringae strains were either factin monoproducers or factin, mycin, and peptin coproducers or lipopeptide nonproducers in relation to their phylogenetic group. Our analyses led to the discovery of 42 new lipopeptides, bringing the number of lipopeptides identified in the P. syringae complex to 75. We also highlighted that factins have high structural resemblance and are widely distributed among the P. syringae complex, while mycins and peptins are highly structurally diverse and patchily distributed. IMPORTANCE This study provides an insight into the P. syringae metabolome that emphasizes the high diversity of lipopeptides produced within the P. syringae complex. The production profiles of strains are closely related to their phylogenetic classification, indicating that structural diversification of lipopeptides parallels the phylogeny of this bacterial complex, thereby further illustrating the inherent importance of lipopeptides in the ecology of this group of bacteria throughout its evolutionary history. Furthermore, this overview of P. syringae lipopeptides led us to propose a refined classification that could be extended to the lipopeptides produced by other bacterial groups.
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Affiliation(s)
- Alexandre Bricout
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
- Agence de la transition écologique (ADEME), Angers, France
| | | | | | - Matthieu Duban
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
| | - Corinne Boistel
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
| | - Gabrielle Chataigné
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
| | - Didier Lecouturier
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
| | - Philippe Jacques
- Université de Liège, Université de Lille, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Valérie Leclère
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
| | - Alice Rochex
- Université de Lille, Université de Liège, UMRt BioEcoAgro 1158-INRAE, Métabolites Secondaires d’Origine Microbienne, Charles Viollette Institute, Lille, France
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5
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Zhao M, Tyson C, Gitaitis R, Kvitko B, Dutta B. Rouxiella badensis, a new bacterial pathogen of onion causing bulb rot. Front Microbiol 2022; 13:1054813. [DOI: 10.3389/fmicb.2022.1054813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
Onion bulb rot can be caused by multiple plant pathogens including bacterial pathogens. During our routine survey of commercial onion farms in 2014, 2020, and 2021, seven putative Rouxiella spp. strains were isolated from symptomatic onion samples in Georgia, United States. Upon fulfilling Koch’s postulates on onion, a genome analysis was conducted. Whole-genome indices (ANI and dDDH) showed that the strains belonged to Rouxiella badensis. Although the seven R. badensis strains were not pathogenic on onion foliage, the strains were able to cause bulb rot and could also produce necrotic lesions in a red onion scale assay. R. badensis populations increased significantly and to a level comparable to P. ananatis PNA 97-1R in a red onion scale infection assay. The core-genome analysis grouped all onion R. badensis strains from Georgia together, and distinct from R. badensis strains isolated from other sources and locations. Based on the genome analysis of strains (from the current study and available genomes in the repository), type I, III (Ssa-Esc and Inv-Mxi-Spa types), and V secretion systems are present in R. badensis genomes, while type II, IV, and VI secretion systems are absent. However, various secondary metabolite gene clusters were identified from R. badensis genomes, and a thiol/redox-associated enzyme gene cluster similar to the Pantoea alt cluster mediating thiosulfinate tolerance was also present in onion strains of R. badensis. This is the first report of R. badensis as a plant pathogen.
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6
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Bioactive Lipodepsipeptides Produced by Bacteria and Fungi. Int J Mol Sci 2022; 23:ijms232012342. [DOI: 10.3390/ijms232012342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Natural products are a vital source for agriculture, medicine, cosmetics and other fields. Lipodepsipeptides (LPDs) are a wide group of natural products distributed among living organisms such as bacteria, fungi, yeasts, virus, insects, plants and marine organisms. They are a group of compounds consisting of a lipid connected to a peptide, which are able to self-assemble into several different structures. They have shown different biological activities such as phytotoxic, antibiotic, antiviral, antiparasitic, antifungal, antibacterial, immunosuppressive, herbicidal, cytotoxic and hemolytic activities. Their biological activities seem to be due to their interactions with the plasma membrane (MP) because they are able to mimic the architecture of the native membranes interacting with their hydrophobic segment. LPDs also have surfactant properties. The review has been focused on the lipodepsipeptides isolated from fungal and bacterial sources, on their biological activity, on the structure–activity relationships of some selected LPD subgroups and on their potential application in agriculture and medicine. The chemical and biological characterization of lipodepsipeptides isolated in the last three decades and findings that resulted from SCI-FINDER research are reported. A critical evaluation of the most recent reviews dealing with the same argument has also been described.
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7
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Castaldi S, Cimmino A, Masi M, Evidente A. Bacterial Lipodepsipeptides and Some of Their Derivatives and Cyclic Dipeptides as Potential Agents for Biocontrol of Pathogenic Bacteria and Fungi of Agrarian Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4591-4598. [PMID: 35395154 PMCID: PMC9026286 DOI: 10.1021/acs.jafc.1c08139] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/01/2022] [Accepted: 03/23/2022] [Indexed: 06/02/2023]
Abstract
Biotic stresses (fungi, bacteria, insects, weeds, etc.) are some of the most important causes of the decrease in the quality and quantity of crops that could become an emergency due to a noteworthy increase in the world population. Thus, to overcome these problems, massive use of chemical pesticides has been carried out with heavy consequences for environmental pollution and food safety. An eco-friendly alternative can be using natural compound-based biopesticides with high efficacy and selectivity. Some bacterial lipodepsipeptides (tolaasins I, II, A, D, and E and WLIP together with hexacetyl- and tetrahydro-tolaasin I and WLIP methyl ester) and cyclic dipeptides (cyclo(l-Pro-l-Tyr), cyclo(d-Pro-l-Tyr), cyclo(l-Pro-l-Val), and cyclo(l-Pro-l-Leu)) were assayed against several pathogenic bacteria and fungi of important agrarian plants. Lipodepsipeptides showed strong growth inhibition of all microorganisms tested in the range of 0.1-0.8 μg/mL, while cyclodipeptides, despite preserving this ability, showed a noteworthily reduced antimicrobial activity being active only in the range of 15-900 μg/mL. Among the lipodepsipeptides and cyclic dipeptides assayed, tolaasin d and cyclo(l-Pro-l-Tyr) (also named maculosin-1) appeared to be the most toxic compounds. Some structure-activity relationships of lipodepsipeptides were also discussed along with their practical application as biopesticides in agriculture.
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Affiliation(s)
- Stefany Castaldi
- Department
of Biology, University of Naples Federico
II, Complesso Universitario
Monte S. Angelo, 80126 Napoli, Italy
| | - Alessio Cimmino
- Department
of Chemical Sciences, University of Naples
Federico II, Complesso
Universitario Monte S. Angelo, 80126 Napoli, Italy
| | - Marco Masi
- Department
of Chemical Sciences, University of Naples
Federico II, Complesso
Universitario Monte S. Angelo, 80126 Napoli, Italy
| | - Antonio Evidente
- Department
of Chemical Sciences, University of Naples
Federico II, Complesso
Universitario Monte S. Angelo, 80126 Napoli, Italy
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8
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Transporter Gene-mediated Typing for Detection and Genome Mining of Lipopeptide-producing Pseudomonas. Appl Environ Microbiol 2021; 88:e0186921. [PMID: 34731056 PMCID: PMC8788793 DOI: 10.1128/aem.01869-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Pseudomonas lipopeptides (LPs) are involved in diverse ecological functions and have biotechnological application potential associated with their antimicrobial and/or antiproliferative activities. They are synthesized by multimodular nonribosomal peptide synthetases which, together with transport and regulatory proteins, are encoded by large biosynthetic gene clusters (BGCs). These secondary metabolites are classified in distinct families based on the sequence and length of the oligopeptide and size of the macrocycle, if present. The phylogeny of PleB, the MacB-like transporter that is part of a dedicated ATP-dependent tripartite efflux system driving export of Pseudomonas LPs, revealed a strong correlation with LP chemical diversity. As each LP BGC carries its cognate pleB, PleB is suitable as a diagnostic sequence for genome mining, allowing assignment of the putative metabolite to a particular LP family. In addition, pleB proved to be a suitable target gene for an alternative PCR method for detecting LP-producing Pseudomonas sp. and did not rely on amplification of catalytic domains of the biosynthetic enzymes. Combined with amplicon sequencing, this approach enabled typing of Pseudomonas strains as potential producers of a LP belonging to one of the known LP families, underscoring its value for strain prioritization. This finding was validated by chemical characterization of known LPs from three different families secreted by novel producers isolated from the rice or maize rhizosphere, namely, the type strains of Pseudomonas fulva (putisolvin), Pseudomonas zeae (tensin), and Pseudomonas xantholysinigenes (xantholysin). In addition, a new member of the Bananamide family, prosekin, was discovered in the type strain of Pseudomonas prosekii, which is an Antarctic isolate. IMPORTANCEPseudomonas spp. are ubiquitous bacteria able to thrive in a wide range of ecological niches, and lipopeptides often support their lifestyle but also their interaction with other micro- and macro-organisms. Therefore, the production of lipopeptides is widespread among Pseudomonas strains. Consequently, Pseudomonas lipopeptide research not only affects chemists and microbiologists but also touches a much broader audience, including biochemists, ecologists, and plant biologists. In this study, we present a reliable transporter gene-guided approach for the detection and/or typing of Pseudomonas lipopeptide producers. Indeed, it allows us to readily assess the lipopeptide diversity among sets of Pseudomonas isolates and differentiate strains likely to produce known lipopeptides from producers of potentially novel lipopeptides. This work provides a valuable tool that can also be integrated in a genome mining strategy and adapted for the typing of other specialized metabolites.
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9
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Zhu Z, Zhang B, Cai Q, Cao Y, Ling J, Lee K, Chen B. A critical review on the environmental application of lipopeptide micelles. BIORESOURCE TECHNOLOGY 2021; 339:125602. [PMID: 34311406 DOI: 10.1016/j.biortech.2021.125602] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
The importance of lipopeptide micelles in environmental applications has been highlighted. These vessels exhibit various sizes, shapes, and surface properties under different environmental conditions. An in-depth understanding of the tunable assembling behavior of biosurfactant micelles is of great importance for their applications. However, a systematic review of such behaviors with assorted micro/nano micellar structures under given environmental conditions, particularly under low temperature and high salinity, remains untapped. Such impacts on their environmental applications have yet to be summarized. This review tried to fill the knowledge gaps by providing a comprehensive summary of the recent knowledge advancement in genetically regulated lipopeptides production, micelles associated decontamination mechanisms in low temperature and high salinity environments, and up-to-date environmental applications. This work is expected to deliver valuable insights to guide lipopeptide design and discovery. The mechanisms concluded in this study could inspire the forthcoming research efforts in the advanced environmental application of lipopeptide micelles.
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Affiliation(s)
- Zhiwen Zhu
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, Canada
| | - Baiyu Zhang
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, Canada.
| | - Qinhong Cai
- Biotechnology Research Institute of the National Research Council of Canada, Montreal, QC, Canada
| | - Yiqi Cao
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, Canada
| | - Jingjing Ling
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, Canada
| | - Kenneth Lee
- Ecosystem Science, Fisheries and Oceans Canada, Ottawa, ON, Canada
| | - Bing Chen
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, Canada
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10
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Girard L, Höfte M, De Mot R. Lipopeptide families at the interface between pathogenic and beneficial Pseudomonas-plant interactions. Crit Rev Microbiol 2020; 46:397-419. [PMID: 32885723 DOI: 10.1080/1040841x.2020.1794790] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Lipopeptides (LPs) are a prominent class of molecules among the steadily growing spectrum of specialized metabolites retrieved from Pseudomonas, in particular soil-dwelling and plant-associated isolates. Among the multiple LP families, pioneering research focussed on phytotoxic and antimicrobial cyclic lipopeptides (CLPs) of the ubiquitous plant pathogen Pseudomonas syringae (syringomycin and syringopeptin). Their non-ribosomal peptide synthetases (NRPSs) are embedded in biosynthetic gene clusters (BGCs) that are tightly co-clustered on a pathogenicity island. Other members of the P. syringae group (Pseudomonas cichorii) and some species of the Pseudomonas asplenii group and Pseudomonas fluorescens complex have adopted these biosynthetic strategies to co-produce their own mycin and peptin variants, in some strains supplemented with an analogue of the P. syringae linear LP (LLP), syringafactin. This capacity is not confined to phytopathogens but also occurs in some biocontrol strains, which indicates that these LP families not solely function as general virulence factors. We address this issue by scrutinizing the structural diversity and bioactivities of LPs from the mycin, peptin, and factin families in a phylogenetic and evolutionary perspective. BGC functional organization (including associated regulatory and transport genes) and NRPS modular architectures in known and candidate LP producers were assessed by genome mining.
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Affiliation(s)
- Léa Girard
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Heverlee-Leuven, Belgium
| | - Monica Höfte
- Department of Plants and Crops, Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Heverlee-Leuven, Belgium
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11
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Friend or foe? Exploring the fine line between Pseudomonas brassicacearum and phytopathogens. J Med Microbiol 2020; 69:347-360. [DOI: 10.1099/jmm.0.001145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pseudomonas brassicacearum
is one of over fifty species of bacteria classified into the
P. fluorescens
group. Generally considered a harmless commensal, these bacteria are studied for their plant-growth promotion (PGP) and biocontrol characteristics. Intriguingly,
P. brassicacearum
is closely related to
P. corrugata
, which is classified as an opportunistic phytopathogen. Twenty-one
P. brassicacearum
genomes have been sequenced to date. In the current review, genomes of
P. brassicacearum
and strains from the
P. corrugata
clade were mined for regions associated with PGP, biocontrol and pathogenicity. We discovered that ‘beneficial’ bacteria and those classified as plant pathogens have many genes in common; thus, only a fine line separates beneficial/harmless commensals from those capable of causing disease in plants. The genotype and physiological state of the plant, the presence of biotic/abiotic stressors, and the ability of bacteria to manipulate the plant immune system collectively contribute to how the bacterial-plant interaction plays out. Because production of extracellular metabolites is energetically costly, these compounds are expected to impart a fitness advantage to the producer.
P. brassicacearum
is able to reduce the threat of nematode predation through release of metabolites involved in biocontrol. Moreover this bacterium has the unique ability to form biofilms on the head of Caenorhabditis elegans, as a second mechanism of predator avoidance. Rhizobacteria, plants, fungi, and microfaunal predators have occupied a shared niche for millions of years and, in many ways, they function as a single organism. Accordingly, it is essential that we appreciate the dynamic interplay among these members of the community.
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12
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Rego A, Sousa AGG, Santos JP, Pascoal F, Canário J, Leão PN, Magalhães C. Diversity of Bacterial Biosynthetic Genes in Maritime Antarctica. Microorganisms 2020; 8:microorganisms8020279. [PMID: 32085500 PMCID: PMC7074882 DOI: 10.3390/microorganisms8020279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial natural products (NPs) are still a major source of new drug leads. Polyketides (PKs) and non-ribosomal peptides (NRP) are two pharmaceutically important families of NPs and recent studies have revealed Antarctica to harbor endemic polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes, likely to be involved in the production of novel metabolites. Despite this, the diversity of secondary metabolites genes in Antarctica is still poorly explored. In this study, a computational bioprospection approach was employed to study the diversity and identity of PKS and NRPS genes to one of the most biodiverse areas in maritime Antarctica—Maxwell Bay. Amplicon sequencing of soil samples targeting ketosynthase (KS) and adenylation (AD) domains of PKS and NRPS genes, respectively, revealed abundant and unexplored chemical diversity in this peninsula. About 20% of AD domain sequences were only distantly related to characterized biosynthetic genes. Several PKS and NRPS genes were found to be closely associated to recently described metabolites including those from uncultured and candidate phyla. The combination of new approaches in computational biology and new culture-dependent and -independent strategies is thus critical for the recovery of the potential novel chemistry encoded in Antarctica microorganisms.
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Affiliation(s)
- Adriana Rego
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - António G. G. Sousa
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
| | - João P. Santos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
- Institute F.-A. Forel, Earth and Environmental Sciences, Faculty of Sciences, University of Geneva, 66, Boulevard Carl-Vogt, 1211 Genève 4, Switzerland
| | - Francisco Pascoal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
| | - João Canário
- Centro de Química Estrutural at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
| | - Pedro N. Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
- Correspondence: (P.N.L); (C.M.)
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
- Faculty of Sciences, University of Porto, 4150-179 Porto, Portugal
- School of Science, University of Waikato, Hamilton 3216, New Zealand
- Correspondence: (P.N.L); (C.M.)
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13
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Götze S, Stallforth P. Structure, properties, and biological functions of nonribosomal lipopeptides from pseudomonads. Nat Prod Rep 2020; 37:29-54. [DOI: 10.1039/c9np00022d] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacteria of the genusPseudomonasdisplay a fascinating metabolic diversity. In this review, we focus our attention on the natural product class of nonribosomal lipopeptides, which help pseudomonads to colonize a wide range of ecological niches.
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Affiliation(s)
- Sebastian Götze
- Faculty 7: Natural and Environmental Sciences
- Institute for Environmental Sciences
- University Koblenz Landau
- 76829 Landau
- Germany
| | - Pierre Stallforth
- Junior Research Group Chemistry of Microbial Communication
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
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14
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Stringlis IA, Zhang H, Pieterse CMJ, Bolton MD, de Jonge R. Microbial small molecules - weapons of plant subversion. Nat Prod Rep 2019; 35:410-433. [PMID: 29756135 DOI: 10.1039/c7np00062f] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Covering: up to 2018 Plants live in close association with a myriad of microbes that are generally harmless. However, the minority of microbes that are pathogens can severely impact crop quality and yield, thereby endangering food security. By contrast, beneficial microbes provide plants with important services, such as enhanced nutrient uptake and protection against pests and diseases. Like pathogens, beneficial microbes can modulate host immunity to efficiently colonize the nutrient-rich niches within and around the roots and aerial tissues of a plant, a phenomenon mirroring the establishment of commensal microbes in the human gut. Numerous ingenious mechanisms have been described by which pathogenic and beneficial microbes in the plant microbiome communicate with their host, including the delivery of immune-suppressive effector proteins and the production of phytohormones, toxins and other bioactive molecules. Plants signal to their associated microbes via exudation of photosynthetically fixed carbon sources, quorum-sensing mimicry molecules and selective secondary metabolites such as strigolactones and flavonoids. Molecular communication thus forms an integral part of the establishment of both beneficial and pathogenic plant-microbe relations. Here, we review the current knowledge on microbe-derived small molecules that can act as signalling compounds to stimulate plant growth and health by beneficial microbes on the one hand, but also as weapons for plant invasion by pathogens on the other. As an exemplary case, we used comparative genomics to assess the small molecule biosynthetic capabilities of the Pseudomonas genus; a genus rich in both plant pathogenic and beneficial microbes. We highlight the biosynthetic potential of individual microbial genomes and the population at large, providing evidence for the hypothesis that the distinction between detrimental and beneficial microbes is increasingly fading. Knowledge on the biosynthesis and molecular activity of microbial small molecules will aid in the development of successful biological agents boosting crop resiliency in a sustainable manner and could also provide scientific routes to pathogen inhibition or eradication.
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Affiliation(s)
- Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands.
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15
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Zhao H, Liu YP, Zhang LQ. In silico and Genetic Analyses of Cyclic Lipopeptide Synthetic Gene Clusters in Pseudomonas sp. 11K1. Front Microbiol 2019; 10:544. [PMID: 30941113 PMCID: PMC6433849 DOI: 10.3389/fmicb.2019.00544] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/01/2019] [Indexed: 02/02/2023] Open
Abstract
Pseudomonas sp. 11K1, originally isolated from rhizosphere, possesses inhibitory activity against plant pathogenic fungi and bacteria. Herein, the genome of strain 11K1 was sequenced and subjected to in silico, mutational, and functional analyses. The 11K1 genome is 6,704,877 bp in length, and genome mining identified three potential cyclic lipopeptide (CLP) biosynthetic clusters, subsequently named brasmycin, braspeptin, and brasamide. Insertional and deletion mutants displayed impaired brasmycin and braspeptin production, and lost antifungal activity, but retained antibacterial activity against Xanthomonas oryzae. The structures of these two active CLPs were predicted based on adenylation (A) domains. Brasmycin is composed of nine amino acids and belongs to the syringomycin class, while braspeptin is a 22 amino acid cyclic peptide belonging to the tolaasin group. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) mass spectrometry analysis revealed that brasmycin and braspeptin have different molecular weights compared with known syringomycin and tolaasin members, respectively. Mutation of brasmycin and braspeptin gene clusters affected both biofilm formation and colony morphology. Collectively, these results indicate that Pseudomonas sp. 11K1 produces two novel CLPs that may help bacteria compete for nutrients and niches in the environment.
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Affiliation(s)
- Hui Zhao
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, China
| | - Yan-Ping Liu
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Li-Qun Zhang
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing, China
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16
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Komatsu H, Shirakawa T, Uchiyama T, Hoshino T. Chemical structure of cichorinotoxin, a cyclic lipodepsipeptide that is produced by Pseudomonas cichorii and causes varnish spots on lettuce. Beilstein J Org Chem 2019; 15:299-309. [PMID: 30800180 PMCID: PMC6369977 DOI: 10.3762/bjoc.15.27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/22/2019] [Indexed: 11/23/2022] Open
Abstract
Pseudomonas cichorii, which causes varnish spots on lettuce and seriously damages lettuce production during the summer season in the highland areas of Japan (e.g., Nagano and Iwate prefectures) was isolated. The structure of a toxin produced by this organism was analyzed based on the detailed evaluation of its 2D NMR and FABMS spectra, and this compound has not been reported previously. We propose the name cichorinotoxin for this toxin. In conjunction with the D or L configurations of each amino acid, which were determined by Marfey's method, we propose the structure of cichorinotoxin to be as follows: 3-hydroxydecanoyl-(Z)-dhThr1-D-Pro2-D-Ala3-D-Ala4-D-Ala5-D-Val6-D-Ala7-(Z)-dhThr8-Ala9-Val10-D-Ile11-Ser12-Ala13-Val14-Ala15-Val16-(Z)-dhThr17-D-alloThr18-Ala19-L-Dab20-Ser21-Val22, and an ester linkage is present between D-alloThr18 and Val22 (dhThr: 2-aminobut-2-enoic acid; Dab: 2,4-diaminobutanoic acid). Thus, the toxin is a lipodepsipeptide with 22 amino acids. The mono- and tetraacetate derivatives and two alkaline hydrolysates, compounds A and B, were prepared. We discuss here the structure-activity relationships between the derivatives and their necrotic activities toward lettuce.
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Affiliation(s)
- Hidekazu Komatsu
- Department of Applied Biological Chemistry, Faculty of Agriculture and Graduate School of Science and Technology, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
| | - Takashi Shirakawa
- Department of Planning and General Administration, Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8519, Japan
| | - Takeo Uchiyama
- Department of Applied Biological Chemistry, Faculty of Agriculture and Graduate School of Science and Technology, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
| | - Tsutomu Hoshino
- Department of Applied Biological Chemistry, Faculty of Agriculture and Graduate School of Science and Technology, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
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17
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Adeniji AA, Aremu OS, Babalola OO. Selecting lipopeptide-producing, Fusarium-suppressing Bacillus spp.: Metabolomic and genomic probing of Bacillus velezensis NWUMFkBS10.5. Microbiologyopen 2018; 8:e00742. [PMID: 30358165 PMCID: PMC6562122 DOI: 10.1002/mbo3.742] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/03/2018] [Accepted: 09/10/2018] [Indexed: 12/29/2022] Open
Abstract
The results of this study indicate that the maize rhizosphere remains a reservoir for microbial strains with unique beneficial properties. The study sought to provide an indigenous Bacillus strain with a bioprotective potential to alleviate maize fusariosis in South Africa. We selected seven Bacillus isolates (MORWBS1.1, MARBS2.7, VERBS5.5, MOREBS6.3, MOLBS8.5, MOLBS8.6, and NWUMFkBS10.5) with biosuppressive effects against two maize fungal pathogens (Fusarium graminearum and Fusarium culmorum) based on 16S rDNA gene characterization and lipopeptide gene analysis. The PCR analysis revealed that lipopeptide genes encoding the synthesis of iturin, surfactin, and fengycin might be responsible for their antifungal activities. Few of the isolates also showed possible biosurfactant capability, and their susceptibility to known antibiotics is indicative of their eco‐friendly attributes. In addition, in silico genomic analysis of our best isolate (Bacillus velezensis NWUMFkBS10.5) and characterization of its active metabolite with FTIR, NMR, and ESI‐Micro‐Tof MS confirmed the presence of valuable genes clusters and metabolic pathways. The versatile genomic potential of our Bacillus isolate emphasizes the continued relevance of Bacillus spp. in biological management of plant diseases.
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Affiliation(s)
- Adetomiwa Ayodele Adeniji
- Department of Biological Sciences, Faculty of Natural and Agriculture Science, North-West University, Mmabatho, South Africa.,Food Security and Safety Niche Area, Faculty of Natural and Agriculture Science, North-West University, Mmabatho, South Africa
| | - Oluwole Samuel Aremu
- Department of Chemistry, Faculty of Natural and Agriculture Science, North-West University, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Department of Biological Sciences, Faculty of Natural and Agriculture Science, North-West University, Mmabatho, South Africa.,Food Security and Safety Niche Area, Faculty of Natural and Agriculture Science, North-West University, Mmabatho, South Africa
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18
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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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19
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Janata J, Kamenik Z, Gazak R, Kadlcik S, Najmanova L. Biosynthesis and incorporation of an alkylproline-derivative (APD) precursor into complex natural products. Nat Prod Rep 2018. [DOI: 10.1039/c7np00047b] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review covers the biosynthetic and evolutionary aspects of lincosamide antibiotics, antitumour pyrrolobenzodiazepines (PBDs) and the quorum-sensing molecule hormaomycin.
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Affiliation(s)
- J. Janata
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - Z. Kamenik
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - R. Gazak
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - S. Kadlcik
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - L. Najmanova
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
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20
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Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides. Nat Microbiol 2016; 2:16197. [PMID: 27798598 DOI: 10.1038/nmicrobiol.2016.197] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/09/2016] [Indexed: 12/16/2022]
Abstract
Pseudomonads are cosmopolitan microorganisms able to produce a wide array of specialized metabolites. These molecules allow Pseudomonas to scavenge nutrients, sense population density and enhance or inhibit growth of competing microorganisms. However, these valuable metabolites are typically characterized one-molecule-one-microbe at a time, instead of being inventoried in large numbers. To index and map the diversity of molecules detected from these organisms, 260 strains of ecologically diverse origins were subjected to mass-spectrometry-based molecular networking. Molecular networking not only enables dereplication of molecules, but also sheds light on their structural relationships. Moreover, it accelerates the discovery of new molecules. Here, by indexing the Pseudomonas specialized metabolome, we report the molecular-networking-based discovery of four molecules and their evolutionary relationships: a poaeamide analogue and a molecular subfamily of cyclic lipopeptides, bananamides 1, 2 and 3. Analysis of their biosynthetic gene cluster shows that it constitutes a distinct evolutionary branch of the Pseudomonas cyclic lipopeptides. Through analysis of an additional 370 extracts of wheat-associated Pseudomonas, we demonstrate how the detailed knowledge from our reference index can be efficiently propagated to annotate complex metabolomic data from other studies, akin to the way in which newly generated genomic information can be compared to data from public databases.
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