title: Bioinformatics Tools for the Discovery of New Nonribosomal Peptides.
abstract: This chapter helps in the use of bioinformatics tools relevant to the discovery of new nonribosomal peptides (NRPs) produced by microorganisms. The strategy described can be applied to draft or fully assembled genome sequences. It relies on the identification of the synthetase genes and the deciphering of the domain architecture of the nonribosomal peptide synthetases (NRPSs). In the next step, candidate peptides synthesized by these NRPSs are predicted in silico, considering the specificity of incorporated monomers together with their isomery. To assess their novelty, the two-dimensional structure of the peptides can be compared with the structural patterns of all known NRPs. The presented workflow leads to an efficient and rapid screening of genomic data generated by high throughput technologies. The exploration of such sequenced genomes may lead to the discovery of new drugs (i.e., antibiotics against multi-resistant pathogens or anti-tumors).
authors.affiliation: ProBioGEM, Institut Charles Viollette, Polytech'Lille, University of Lille 1, 59650, Villeneuve d'Ascq, France.|CRIStAL, UMR 9189, Univ Lille, 59650, Villeneuve d'Ascq, France.|Inria Lille Nord-Europe, 59650, Villeneuve d'Ascq, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Leclère
authors.affiliation: The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark.
authors.forename: Tilmann
authors.initials: T
authors.lastname: Weber
authors.affiliation: ProBioGEM, Institut Charles Viollette, Polytech'Lille, University of Lille 1, 59650, Villeneuve d'Ascq, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Jacques
authors.affiliation: CRIStAL, UMR 9189, Univ Lille, 59650, Villeneuve d'Ascq, France. maude.pupin@univ-lille1.fr.|Inria Lille Nord-Europe, 59650, Villeneuve d'Ascq, France. maude.pupin@univ-lille1.fr.
authors.forename: Maude
authors.initials: M
authors.lastname: Pupin
mesh_terms: D001419:Bacteria / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D016680:Genome, Bacterial; D005810:Multigene Family; D046908:Peptide Biosynthesis, Nucleic Acid-Independent; D010453:Peptide Synthases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D010455:Peptides / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012984:Software
chemical_list: D001426:Bacterial Proteins; D010455:Peptides; D010453:Peptide Synthases; C104385:non-ribosomal peptide synthase
keywords: Antibiotic; Bioinformatics tools; Drug discovery; Genome mining; Nonribosomal; Peptide