Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptidesReport as inadecuate

Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 14:658

Eukaryote microbial genomics


BackgroundVarious 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.

ResultsWe performed in silico analyses of NRPS genes present in all published genome sequences of Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv.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.

ConclusionsThis 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.

AbbreviationsA-domainAdenylation domain

ACP-domainAcyl carrier protein domain

C-domainCondensation domain

Cy-domainHeterocyclization domain

Dab2,4-diamino butyric acid


E-domainEpimerization domain

C-E domainCondensation-epimerization domain

NMRNuclear magnetic resonance

NRPSNon-ribosomal peptide synthesis

NRPSsNon-ribosomal peptide synthetases

MLSAMulti locus sequence analyses

MSMass spectrometry

PCP-domainPeptidyl carrier protein domain


PPTase4-phosphopantetheinyl transferase

TALTranscription activator-like

TE-domainThioesterase domain.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-14-658 contains supplementary material, which is available to authorized users.

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Author: Monique Royer - Ralf Koebnik - Mélanie Marguerettaz - Valérie Barbe - Guillaume P Robin - Chrystelle Brin - Sébastien C


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