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EMBnet

Volume 14 Nr. 3

Abstract 5 - NORINE: A PUBLIC RESOURCE FOR NONRIBOSOMAL PEPTIDES Caboche Ségolène*[1], Pupin Maude[1], Leclère Valérie[2], Jacques Philippe[2], Kucherov Gregory[1] - [1]LIFL (UMR USTL/CNRS 8022) - INRIA ~ Villeneuve d'Ascq ~ France - [2]ProBioGEM (UPRES EA 1026), Lille1 University ~ Villeneuve d'Ascq ~ France # 1J) Biobanks (databases and knowledgebases)

Motivation: In micro-organisms, nonribosomal peptide synthesis is an alternative pathway that allows the production of small bioactive peptides from multienzymatic assembly lines called NonRibosomal Peptide Synthetases (NRPSs). The products, called NonRibosomal Peptides (NRPs), show a great diversity in composition, structure and function. They are short (two to about fifty amino acids), but can potentially contain more than 300 different amino acids (instead of twenty amino acids composing regular proteins). The NRP primary structure can be linear like in classical ribosomal peptides, but it is often more complex (totally or partially cyclic, branched or even poly-cyclic). The NRPs harbour a large spectrum of biological activities (e.g. antibiotics, antitumors, immunosuppressors). In spite of a great interest in NRPs due to their particularities and their important bioactivities, few computational resources and dedicated tools are currently available. Methods: We have developed Norine, a public resource for NRPs. It contains more than 700 peptides and is still growing. Each peptide is annotated with various data collected from scientific publications. Those include the peptide name, its molecular weight, producer organisms, bibliographical references and links to other databases (UniProt and PubChem). The most original information stored in Norine is the NRP structure. We chose to represent the NRP structures at the amino acid level that reflects their biosynthesis, rather than to use the classical chemical representation. Indeed, the NRPSs successively incorporate complete amino acids rather than atoms. A friendly web interface was developed to search for NRPs according to various search criteria. In addition, users can search for a complete structure or a structural pattern (part of a structure possibly with jokers). Results: Norine is the first resource entirely devoted to NRPs and is available at http://bioinfo.lifl.fr/norine/. We believe that Norine can have various usages in a wide range of related biological studies and can be useful in different applications of NRPs including very important applications in pharmacology. Indeed, we hope that Norine can contribute to biosynthetic engineering efforts to reprogram the NRP assembly lines, in particular because it makes possible systematic studies of the function-structure relationship of NRPs.

EMBnet.news 14.3  

Special 20th anniversary issue of the quarterly newsletter published by the EMBnet organisation.

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