1. Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides
- Author
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Valérie Verdier, Manuela Hügelland, Ralf Koebnik, Guillaume P. Robin, Monique Royer, Ginka H. Völler, Camila Gomez, Stéphane Poussier, Isabelle Pieretti, Mélanie Marguerettaz, Chrystelle Brin, Julie Noëll, Valérie Barbe, Philippe Rott, Saskia Rausch, Sébastien Carrère, Roderich D. Süssmuth, Stéphane Cociancich, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Résistance des plantes aux bio-agresseurs (UMR RPB), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 2 - Sciences et Techniques (UM2), Ctr Natl Sequencage, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Inst Chem, Technische Universität Berlin (TUB), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Agence Nationale de la Recherche, France [ANR-09-BLAN-0413-01], Region Languedoc-Roussillon, PhD fellowship awarded by the Region Languedoc-Roussillon, Centre National de la Recherche Scientifique, France [07-845], European Commission, Agence Nationale de la Recherche [ANR-09-BLAN-0413-01], Deutsche Forschungsgemeinschaft [DFG SU239/11-1], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Technische Universität Berlin (TU), and Technical University of Berlin / Technische Universität Berlin (TU)
- Subjects
ORYZAE PATHOVAR ORYZAE ,ADENYLATION DOMAINS ,PHOSPHOPANTETHEINYL TRANSFERASE ,ALBICIDIN BIOSYNTHESIS ,FUNCTIONAL-ANALYSIS ,ESCHERICHIA-COLI ,ALBILINEANS ,SYNTHETASES ,GENES ,SUGARCANE ,[SDV]Life Sciences [q-bio] ,Biosynthèse ,Xanthomonas albilineans ,Xanthomonas oryzae ,Polymerase Chain Reaction ,Genome ,Xanthomonas sacchari ,Gene cluster ,Genetics ,0303 health sciences ,Saccharum officinarum ,biology ,Fatty Acids ,Plants ,Physical Chromosome Mapping ,PCR ,Multigene Family ,Peptide ,Peptide Biosynthesis, Nucleic Acid-Independent ,Research Article ,Biotechnology ,Xanthomonas ,Séquence nucléotidique ,Oryza sativa ,Bacterial genome size ,Relation hôte pathogène ,03 medical and health sciences ,Computer Simulation ,Amino Acid Sequence ,030304 developmental biology ,H20 - Maladies des plantes ,Génome ,Sequence Homology, Amino Acid ,030306 microbiology ,Computational Biology ,biology.organism_classification ,Résistance aux maladies ,Xanthomonas translucens ,Amélioration des plantes ,Genes, Bacterial ,Genetic Loci ,Peptides ,Genome, Bacterial - Abstract
Background Various bacteria can use non-ribosomal peptide synthesis (NRPS) to produce peptides or other small molecules. Conserved features within the NRPS machinery allow the type, and sometimes even the structure, of the synthesized polypeptide to be predicted. Thus, bacterial genome mining via in silico analyses of NRPS genes offers an attractive opportunity to uncover new bioactive non-ribosomally synthesized peptides. Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant species. To date, the only known small molecule synthesized by NRPS in this genus is albicidin produced by Xanthomonas albilineans. This study aims to estimate the biosynthetic potential of Xanthomonas spp. by in silico analyses of NRPS genes with unknown function recently identified in the sequenced genomes of X. albilineans and related species of Xanthomonas. Results We performed in silico analyses of NRPS genes present in all published genome sequences of Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv. oryzae strain BAI3 and Xanthomonas spp. strain XaS3. These two latter strains, together with X. albilineans strain GPE PC73 and X. oryzae pv. oryzae strains X8-1A and X11-5A, possess novel NRPS gene clusters and share related NRPS-associated genes such as those required for the biosynthesis of non-proteinogenic amino acids or the secretion of peptides. In silico prediction of peptide structures according to NRPS architecture suggests eight different peptides, each specific to its producing strain. Interestingly, these eight peptides cannot be assigned to any known gene cluster or related to known compounds from natural product databases. PCR screening of a collection of 94 plant pathogenic bacteria indicates that these novel NRPS gene clusters are specific to the genus Xanthomonas and are also present in Xanthomonas translucens and X. oryzae pv. oryzicola. Further genome mining revealed other novel NRPS genes specific to X. oryzae pv. oryzicola or Xanthomonas sacchari. Conclusions This study revealed the significant potential of the genus Xanthomonas to produce new non-ribosomally synthesized peptides. Interestingly, this biosynthetic potential seems to be specific to strains of Xanthomonas associated with monocotyledonous plants, suggesting a putative involvement of non-ribosomally synthesized peptides in plant-bacteria interactions.
- Published
- 2013
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