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Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas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
nonribosomally 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.
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