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      Norine: A powerful resource for novel nonribosomal peptide discovery

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          Abstract

          Since 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.

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          Most cited references 17

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          A widely distributed bacterial pathway for siderophore biosynthesis independent of nonribosomal peptide synthetases.

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            Vancomycin assembly: nature's way.

            Antibiotics are precious resources in the fight to combat bacterial infections caused by pathogenic organisms. Vancomycin is one of the antibiotics of last resort in the treatment of life-threatening infections by gram-positive bacteria. The rules by which nature assembles the glycopeptide (vancomycin) and lipoglycopeptide (teicoplanin) antibiotics are becoming elucidated and verified: first amino acids are synthesized, then joined together and cross-linked. This knowledge opens up approaches for reprogramming strategies at the level of altered monomers, swapped assembly lines, and different post-assembly tailoring enzymes.
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              Diversity of monomers in nonribosomal peptides: towards the prediction of origin and biological activity.

              Nonribosomal peptides (NRPs) are molecules produced by microorganisms that have a broad spectrum of biological activities and pharmaceutical applications (e.g., antibiotic, immunomodulating, and antitumor activities). One particularity of the NRPs is the biodiversity of their monomers, extending far beyond the 20 proteogenic amino acid residues. Norine, a comprehensive database of NRPs, allowed us to review for the first time the main characteristics of the NRPs and especially their monomer biodiversity. Our analysis highlighted a significant similarity relationship between NRPs synthesized by bacteria and those isolated from metazoa, especially from sponges, supporting the hypothesis that some NRPs isolated from sponges are actually synthesized by symbiotic bacteria rather than by the sponges themselves. A comparison of peptide monomeric compositions as a function of biological activity showed that some monomers are specific to a class of activities. An analysis of the monomer compositions of peptide products predicted from genomic information (metagenomics and high-throughput genome sequencing) or of new peptides detected by mass spectrometry analysis applied to a culture supernatant can provide indications of the origin of a peptide and/or its biological activity.
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                Author and article information

                Contributors
                Journal
                Synth Syst Biotechnol
                Synth Syst Biotechnol
                Synthetic and Systems Biotechnology
                KeAi Publishing
                2405-805X
                2405-805X
                08 December 2015
                June 2016
                08 December 2015
                : 1
                : 2
                : 89-94
                Affiliations
                [a ]Univ Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France
                [b ]Inria-Lille Nord Europe, Villeneuve d'Ascq Cedex F-59655, France
                [c ]Univ Lille, INRA, ISA, Univ Artois, Univ Littoral Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France
                [d ]Bioindustry Unit, Gembloux Agro-Bio Tech-University of Liege, Passage des Déportés, 2, Gembloux 5030, Belgium
                Author notes
                [* ]Corresponding author. Univ Lille, ICV, Charles Viollette Institute, PrBioGEM team, Polytech'Lille, Avenue Langevin, Villeneuve d'Ascq Cedex F-59655, France. Tel.: +33 320 43 46 68.Univ LilleICVCharles Viollette InstitutePrBioGEM teamPolytech'LilleAvenue LangevinVilleneuve d'Ascq CedexF-59655France valerie.leclere@ 123456univ-lille1.fr
                Article
                S2405-805X(15)30014-4
                10.1016/j.synbio.2015.11.001
                5640699
                © 2016 The Authors

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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