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

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 silicoanalyses of NRPS genes offers an attractive opportunity to uncover new bioactive non-ribosomally synthesized peptides. Xanthomonasis 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 Xanthomonasspp. by in silicoanalyses of NRPS genes with unknown function recently identified in the sequenced genomes of X. albilineans and related species of Xanthomonas. Results: We performed in silicoanalyses of NRPS genes present in all published genome sequences of Xanthomonasspp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv. oryzaestrain BAI3 and Xanthomonasspp. strain XaS3. These two latter strains, together with X. albilineans strain GPE PC73 and X. oryzaepv. oryzaestrains X8-1A and X11-5A, possess novel NRPS gene clustersand share related NRPS-associated genes such as those required for the biosynthesis of non-proteinogenic amino acidsor the secretion of peptides. In silicoprediction 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 clusteror related to known compounds from natural product databases. PCR screening of a collection of 94 plant pathogenic bacteria indicates that these novel NRPS gene clustersare specific to the genus Xanthomonasand are also present in Xanthomonas translucensand X. oryzaepv. oryzicola. Further genome mining revealed other novel NRPS genes specific to X. oryzaepv. oryzicola or Xanthomonas sacchari. Conclusions: This study revealed the significant potential of the genus Xanthomonasto produce new non-ribosomally synthesized peptides. Interestingly, this biosynthetic potential seems to be specific to strains of Xanthomonasassociated with monocotyledonousplants, suggesting a putative involvement of non-ribosomally synthesized peptides in plant-bacteria interactions.