The amount of the rare sugar tagatose on tomato leaves decreases after spray application under greenhouse conditions

Tagatose is a rare sugar that suppresses plant diseases, such as late blight of tomato, caused by Phytophthora infestans. Tagatose can be metabolized by some microorganisms and no information is available on its persistence on tomato leaves. The aim of this study was to assess the persistence of tagatose on tomato leaves under commercial greenhouse conditions. The amount of tagatose on tomato leaves and the inhibitory activity against P. infestans decreased seven days after spray application in the absence of rain wash-off. Potential tagatose-degrading bacteria were isolated from tomato leaves, and they belonged to Acinetobacter sp., Bacillus sp., Comamonas sp., Enterobacter sp., Methylobacterium sp., Microbacterium sp., Pantoea sp., Plantibacter sp., Pseudomonas sp., Ralstonia sp., Rhodococcus sp., Sphingobium sp., and Sphingomonas sp. Thus, indigenous phyllosphere microorganisms could partially metabolize tagatose laid on plant leaves after spray application, reducing the persistence of this fungal inhibitor on tomato leave

Norine: a powerful resource for novel nonribosomal peptide discovery

International audienceSince its first release in 2008, Norine remains the unique resource completely devoted to nonribosomal peptides (NRPs). They are very attractive microbial secondary metabolites, displaying a remarkable diversity of structure and functions. Norine (http://bioinfo.lifl.fr/NRP) includes a database now containing more than 1160 annotated peptides and user-friendly interfaces enabling the querying of the database, through the annotations or the structure of the peptides. Dedicated tools are associated for structural comparison of the compounds and prediction of their biological activities. In this paper, we start by describing the knowledgebase and the dedicated tools. We then present some user cases to show how useful Norine is for the discovery of novel nonribosomal peptides

Norine, Florine, s2m : powerful bioinformatics resource and tools for the discovery of novel nonribosomal peptides, natural metabolites with versatile activities

International audienceNonRibosomal peptides (NRPs) are a huge untapped resource of natural products displaying activities with applications in health (i.e. antibiotics) or in biocontrol (especially siderophores and lipopeptides with antifungal activity). NRPs are microbial secondary metabolites produced by enzymatic complexes, so-called non-ribosomal peptide synthetases (NRPSs). These modular assembly lines work step by step to build the peptides, each module adding one monomer to the peptidic chain. Considering the modular organization of NRPSs, and the structural specific features of the NRPs, dedicated bioinformatics tools have been developed with the aim of accelerating the screening for new active metabolites

Paraburkholderia phytofirmans PsJN-Plants Interaction: From Perception to the Induced Mechanisms

The use of plant-associated bacteria has received many scientific and economic attention as an effective and alternative method to reduce the chemical pesticides use in agriculture. The genus Burkholderia includes at least 90 species including pathogenic strains, plant pathogens, as well as plant beneficial species as those related to Paraburkholderia, which has been reported to be associated with plants and exerts a positive effect on plant growth and fitness. Paraburkholderia phytofirmans PsJN, a beneficial endophyte able to colonize a wide range of plants, is an established model for plant-associated endophytic bacteria. Indeed, in addition to its plant growth promoting ability, it can also induce plant resistance against biotic as well as abiotic stresses. Here, we summarized an inventory of knowledge on PsJN-plant interaction, from the perception to the resistance mechanisms induced in the plant by a way of the atypical colonization mode of this endophyte. We also have carried out an extensive genome analysis to identify all gene clusters which contribute to the adaptive mechanisms under different environments and partly explaining the high ecological competence of P. phytofirmans PsJN

Heterologous production of cyclic lipopeptides using versatile bacterial chassis

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Identification de nouvelles synthétases non ribosomiques et de leurs produits à partir de données de génomique

Les micro-organismes sont considérés comme l'une des sources les plus importantes de métabolites secondaires, y compris les peptides ribosomiques et non ribosomiques. La recherche de nouveaux peptides non ribosomiques a été motivée par leurs larges applications dans diverses industries telles que les secteurs pharmaceutiques et phytosanitaires. Ils sont produits par complexes enzymatiques appelés NRPSs. Plus de 70% des peptides non ribosomiques ont une structure complexe qui comprend un ou plusieurs cycles et des ramifications. Par conséquent, le développement d'outils spécifiques dédiés à la prédiction de ces peptides est nécessaire car ils ne peuvent pas être prédits et analysés comme les peptides classiques. Dans le but d'analyser les voies de biosynthèse et d'identifier de nouveaux peptides actifs, j'ai étudié principalement deux modèles bactériens: Burkholderia et Aeromonas. Le genome-mining est un’ approche très performante pour la découverte de nouveaux NRPs. En effet, pour 48 souches de Burkholderia analysées in silico à l’aide du workflow Florine, 228 clusters de gènes contenant des gènes de NRPS et hybrides NRPS-PKS ont été trouvés. Cette étude a permis de mettre en évidence de nouveaux peptides produits par des Burkholderia, incluant la phymabactin, un nouveau siderophore, et un lipopeptide cyclique que nous avons appelé burkhomycin. La présente étude a d’autre part permis d’éclaircir le mécanisme de fonctionnement des synthétases non ribosomiques, illustrés par la détection des domaines C/E dans des synthétases de lipopeptides cycliques et une utilisation originale des domaines et modules dans les NRPS impliquées dans la biosynthèse des amonabactines chez A.hydrophila.Microorganisms are considered one of the most important sources of secondary metabolites including ribosomal and non ribosomal peptides. The search of new non ribosomal peptides has been motivated by their wide applications exploited by industries in different area including pharmaceutical and phytosanitary sectors. They are produced through complex synthetases called non ribosomal peptides synthetases. More than 70% of NRPs have a complex structure that includes one or more cycles and branches. Therefore, development of specific tools dedicated to the screening of these peptides is necessary as they cannot be predicted and analyzed as classical peptides. With the aim to further analyse biosynthesis pathways and to identify new active peptides, I mainly studied two bacterial models: Burkholderia and Aeromonas. The genome-mining is a very powerful approach for the discovery of new non NRPs. Indeed, among 48 strains of Burkholderia, 228 gene clusters containing NRPSs and hybrid NRPS-PKS were found via in silico analysis following Florine workflow. The current study lead to the discovery of new peptides in Burkholderia including a new siderophore named phymabactin and a cyclic lipopeptide we have called burkhomycin. It also gave new insights on the mechanism of nonribosomal synthetases, exemplified by the detection of dual C/E domains in NRPSs involved in the production of cyclic lipopeptides by Burkholderia and the identification of a unique use of domains and modules in the pathway responsible for synthesis of amonabactins in A. hydrophila

Analyses of Lysin-motif Receptor-like Kinase (<i>LysM-RLK</i>) Gene Family in Allotetraploid <i>Brassica napus</i> L. and Its Progenitor Species: An In Silico Study

The LysM receptor-like kinases (LysM-RLKs) play a crucial role in plant symbiosis and response to environmental stresses. Brassica napus, B. rapa, and B. oleracea are utilized as valuable vegetables. Different biotic and abiotic stressors affect these crops, resulting in yield losses. Therefore, genome-wide analysis of the LysM-RLK gene family was conducted. From the genome of the examined species, 33 LysM-RLK have been found. The conserved domains of Brassica LysM-RLKs were divided into three groups: LYK, LYP, and LysMn. In the BrassicaLysM-RLK gene family, only segmental duplication has occurred. The Ka/Ks ratio for the duplicated pair of genes was less than one indicating that the genes’ function had not changed over time. The BrassicaLysM-RLKs contain 70 cis-elements, indicating that they are involved in stress response. 39 miRNA molecules were responsible for the post-transcriptional regulation of 12 Brassica LysM-RLKs. A total of 22 SSR loci were discovered in 16 Brassica LysM-RLKs. According to RNA-seq data, the highest expression in response to biotic stresses was related to BnLYP6. According to the docking simulations, several residues in the active sites of BnLYP6 are in direct contact with the docked chitin and could be useful in future studies to develop pathogen-resistant B. napus. This research reveals comprehensive information that could lead to the identification of potential genes for Brassica species genetic manipulation

Heterologous production of Cyclic lipopeptides (CLiPs) using versatile bacterial chassis

International audienceCyclic LipoPeptides (CLiPs) constitute a unique major class of microbial secondary metabolites with surfactant and antifungal properties that make it possible to consider their use in biocontrol applications. They can act through direct antagonism mechanisms towards the pathogen (biocides) or indirectly by inducing plant defense responses. CLiPs are non-ribosomally synthesized by modular mega-enzymes so-called Non-Ribosomal Peptide Synthetases (NRPS) that are encoded by large biosynthetic gene clusters (BGCs) spanning over dozens of kilobases (kb) in the genomes. NRPSs work as production chains to catalyse, step by step, the assembly of amino acids leading to the construction of non-ribosomal peptides. For a decade, bioinformatics tools have been developed to facilitate the identification of BGCs within the genomes and to predict the structure of potentially produced CLiPs. Several obstacles to the use of CLiPs in biocontrol have been identified. On one hand, CLiPs are frequently produced in small quantities (at most a few tens of miligrams per liter of culture), and the same strain is often capable of co-producing several lipopeptides in a mixture, which poses difficulties in their extraction/purification. On the other hand, some BGCs are even cryptic, i.e. not expressed under laboratory culture conditions. To overcome these limits, heterologous production consists of using a host strain into which BGCs containing biosynthesis genes are introduced to produce the targeted CLiP. We developed molecular tools in combination with a chassis strain, capable of receiving various BGCs, to control the production of variable CLiPs of various origins and in sufficient quantities to i) analyze their structure, ii) understand their mode of action, and iii) evaluate their activities at different scales (laboratory, greenhouse, field). Here, we present the results of proof of concept with orfamide synthetase genes cluster expressed in the strain Paraburkholderia phytofirmans PsJN

Norine, Florine, s2m : powerful bioinformatics resource and tools for the discovery of novel nonribosomal peptides, natural metabolites with versatile activities

International audienceNonRibosomal peptides (NRPs) are a huge untapped resource of natural products displaying activities with applications in health (i.e. antibiotics) or in biocontrol (especially siderophores and lipopeptides with antifungal activity). NRPs are microbial secondary metabolites produced by enzymatic complexes, so-called non-ribosomal peptide synthetases (NRPSs). These modular assembly lines work step by step to build the peptides, each module adding one monomer to the peptidic chain. Considering the modular organization of NRPSs, and the structural specific features of the NRPs, dedicated bioinformatics tools have been developed with the aim of accelerating the screening for new active metabolites

Plant Beneficial Bacteria as Bioprotectants against Wheat and Barley Diseases

Wheat and barley are the main cereal crops cultivated worldwide and serve as staple food for a third of the world’s population. However, due to enormous biotic stresses, the annual production has significantly reduced by 30–70%. Recently, the accelerated use of beneficial bacteria in the control of wheat and barley pathogens has gained prominence. In this review, we synthesized information about beneficial bacteria with demonstrated protection capacity against major barley and wheat pathogens including Fusarium graminearum, Zymoseptoria tritici and Pyrenophora teres. By summarizing the general insights into molecular factors involved in plant-pathogen interactions, we show to an extent, the means by which beneficial bacteria are implicated in plant defense against wheat and barley diseases. On wheat, many Bacillus strains predominantly reduced the disease incidence of F. graminearum and Z. tritici. In contrast, on barley, the efficacy of a few Pseudomonas, Bacillus and Paraburkholderia spp. has been established against P. teres. Although several modes of action were described for these strains, we have highlighted the role of Bacillus and Pseudomonas secondary metabolites in mediating direct antagonism and induced resistance against these pathogens. Furthermore, we advance a need to ascertain the mode of action of beneficial bacteria/molecules to enhance a solution-based crop protection strategy. Moreover, an apparent disjoint exists between numerous experiments that have demonstrated disease-suppressive effects and the translation of these successes to commercial products and applications. Clearly, the field of cereal disease protection leaves a lot to be explored and uncovered