Bioinformatics tools for the discovery of new lipopeptides with biocontrol applications

As conventional or chemical pesticides have negative impact on environment and health of both farmer and consumers, it becomes relevant to develop alternative solutions to limit their use. In this context, innovative strategies to accelerate the development of biocontrol agents are welcome. For a decade of years, it has been demonstrated that lipopeptides are very efficient weapons against fungi responsible for crop diseases. Lipopeptides are secondary metabolites, produced by many microorganisms including beneficial rhizobacteria. The lipopeptide biosynthetic pathways include nonribosomal peptide synthetases. These modular enzymatic complexes work as assembly lines to build the peptides step by step, leading to the production of original peptide compounds with specific features as the presence of non proteinogenic monomers and cyclic and branched structures. In this paper, Florine and Norine bioinformatics tools, especially dedicated to non-ribosomal synthetases and their products are presented. Their use is mainly focused on the discovery of lipopeptides produced by Bacillus or Pseudomonas because they seem to represent a versatile reservoir of active secondary metabolites with promising activities for applications in phytosanitary area. © 2018, Koninklijke Nederlandse Planteziektenkundige Vereniging.Peer reviewe

Norine, the knowledgebase dedicated to nonribosomal peptides, is now open to crowdsourcing

International audienceSince its creation in 2006, Norine remains the unique knowledgebase dedicated to non-ribosomal pep-tides (NRPs). These secondary metabolites, produced by bacteria and fungi, harbor diverse interesting biological activities (such as antibiotic, anti-tumor, siderophore or surfactant) directly related to the diversity of their structures. The Norine team goal is to collect the NRPs and provide tools to analyze them efficiently. We have developed a user-friendly interface and dedicated tools to provide a complete bioinformatics platform. The knowledgebase gathers abundant and valuable annotations on more than 1100 NRPs. To increase the quantity of described NRPs and improve the quality of associated annotations , we are now opening Norine to crowdsourc-ing. We believe that contributors from the scientific community are the best experts to annotate the NRPs they work on. We have developed MyNorine to facilitate the submission of new NRPs or modifications of stored ones. This article presents MyNorine and other novelties of Norine interface released since the first publication. Norine is freely accessible from the following URL: http://bioinfo.lifl.fr/NRP

Identification of a conserved N-terminal domain in the first module of ACV synthetases

Abstract The l‐δ‐(α‐aminoadipoyl)‐l‐cysteinyl‐d‐valine synthetase (ACVS) is a trimodular nonribosomal peptide synthetase (NRPS) that provides the peptide precursor for the synthesis of β‐lactams. The enzyme has been extensively characterized in terms of tripeptide formation and substrate specificity. The first module is highly specific and is the only NRPS unit known to recruit and activate the substrate l‐α‐aminoadipic acid, which is coupled to the α‐amino group of l‐cysteine through an unusual peptide bond, involving its δ‐carboxyl group. Here we carried out an in‐depth investigation on the architecture of the first module of the ACVS enzymes from the fungus Penicillium rubens and the bacterium Nocardia lactamdurans. Bioinformatic analyses revealed the presence of a previously unidentified domain at the N‐terminus which is structurally related to condensation domains, but smaller in size. Deletion variants of both enzymes were generated to investigate the potential impact on penicillin biosynthesis in vivo and in vitro. The data indicate that the N‐terminal domain is important for catalysis

Deployment of a hierarchical middleware

International audienceAccessing the power of distributed resources can nowadays easily be done using a middleware based on a client/server approach. Several architectures exist for those middleware. The most scalable ones rely on a hierarchical design. Determining the best shape for the hierarchy, the one giving the best throughput of services, is not an easy task. We first propose a computation and communication model for such hierarchical middleware. Our model takes into account the deployment of several services in the hierarchy. Then, based on this model, we propose an algorithm for automatically constructing a hierarchy. This algorithm aims at offering the users the best obtained to requested throughput ratio, while providing fairness on this ratio for the different kind of services, and using as few resources as possible. Finally, we compare our model with experimental results on a real middleware called Diet