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

Abstract

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in silico analyses of NRPS genes present in all published genome sequences of Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv.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

Burkholderia genome mining for nonribosomal peptide synthetases reveals a great potential for novel siderophores and lipopeptides synthesis

“…These dual C/E domains were described for the first time in the NRPS responsible for arthrofactin production in Pseudomonas (Balibar et al 2005). Since then, they have been detected in many NRPSs catalyzing the synthesis of CLPs in Pseudomonas (Roongsawang et al 2011) and more recently in Xanthomonas (Royer et al 2013). In all these cases, two types of NRPS clusters coexist in the same strain.…”

Genomic Insights into the Evolutionary Origin of Xanthomonas axonopodis pv. citri and Its Ecological Relatives

“…Nonribosomal peptidyl synthase/ polyketide synthases are often involved in the production of bioactive peptides or small molecules. Xanthomonas has been considered a reservoir for the production of bioactive compounds by NRPS pathways (54). Two NRPS pathways identified in Xac have already been explored computationally for their putative functions.…”

“…The second NRPS pathway, in Xac2097, is a pathogenicity island (PAI) proposed to encode a tripeptide related to the phytotoxin syringomycin produced by Pseudomonas syringae (55). Recent reports refer to this NRPS as a pseudogene (54). Third, an NRPS identified in this study that is specific to Xmi is also possibly a PAI, as transposases are found on both sides of the cluster, and there is also a relatively high GC content of the NRPS and PKS genes (see the supplemental material).…”

Biosynthesis of the Peptide Antibiotic Feglymycin by a Linear Nonribosomal Peptide Synthetase Mechanism

“…Homologues of the four gene products are known to be involved in the biosynthesis of Hpg, as has been described for the teicoplanin gene cluster, the balhimycin gene cluster, the complestatin gene cluster, and the A47934 gene cluster in Streptomyces toyocaensis . More recently such gene assemblies have been found in the arylomycin biosynthesis cluster and in the Xanthomonas albilineans genome with as yet unknown biosynthesis products . Accordingly, both l ‐Tyr and prephenate could serve as starting material for Hpg biosynthesis.…”

“…[26] More recently such gene assemblies have been found in the arylomycin biosynthesis cluster [27] and in the Xanthomonas albilineans genome with as yet unknown biosynthesis products. [28] Accordingly,b oth l-Tyr and prephenate could serve as startingm aterialf or Hpg biosynthesis. Prephenate would be converted by FegE into p-hydroxyphenylpyruvate, which is then converted into l-p-hydroxymandelate by FegD, and oxidized by FegC or FegG to yield p-hydroxybenzoylformate.…”