Prediction of Monomer Isomery in Florine: A Workflow Dedicated to Nonribosomal Peptide DiscoveryReportar como inadecuado

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1 PROBIOGEM - Laboratoire des Procédés Biologiques Génie Enzymatique et Microbien 2 LIFL - Laboratoire d-Informatique Fondamentale de Lille 3 BONSAI - Bioinformatics and Sequence Analysis LIFL - Laboratoire d-Informatique Fondamentale de Lille, Inria Lille - Nord Europe 4 ORPAILLEUR - Knowledge representation, reasonning Inria Nancy - Grand Est, LORIA - NLPKD - Department of Natural Language Processing & Knowledge Discovery

Abstract : Nonribosomal peptides represent a large variety of natural active compounds produced by microorganisms. Due to their specific biosynthesis pathway through large assembly lines called NonRibosomal Peptide Synthetases NRPSs, they often display complex structures with cycles and branches. Moreover they often contain non proteogenic or modified monomers, such as the D-monomers produced by epimerization. We investigate here some sequence specificities of the condensation C and epimerization E domains of NRPS that can be used to predict the possible isomeric state D or L of each monomer in a putative peptide. We show that C-and E-domains can be divided into 2 sub-regions called Up-Seq and Down-Seq. The Up-Seq region corresponds to an InterPro domain IPR001242 and is shared by C-and E-domains. The Down-Seq region is specific to the enzymatic activity of the domain. Amino-acid signatures represented as sequence logos previously described for complete C-and E-domains have been restricted to the Down-Seq region and amplified thanks to additional sequences. Moreover a new Down-Seq signature has been found for Ct-domains found in fungi and responsible for terminal cyclization of the peptides. The identification of these signatures has been included in a workflow named Florine, aimed to predict nonribosomal peptides from NRPS sequence analyses. In some cases, the prediction of isomery is guided by genus-specific rules. Florine was used on a Pseudomonas genome to allow the determination of the type of pyoverdin produced, the update of syringafactin structure and the identification of novel putative products. Citation: Caradec T, Pupin M, Vanvlassenbroeck A, Devignes M-D, Smal-Tabbone M, et al. 2014 Prediction of Monomer Isomery in Florine: A Workflow Dedicated to Nonribosomal Peptide Discovery. PLoS ONE 91: e85667.

Autor: Thibault Caradec - Maude Pupin - Aurélien Vanvlassenbroeck - Marie-Dominique Devignes - Malika Smaïl-Tabbone - Philippe Jacques



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