Data from: 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 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performed in silico analyses of NRPS genes present in all published genome sequences of Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv.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.Tree of the amino acid sequences of C-domains of strains GPE PC73, XaS3, X11-5A, BAI3, and BLS256 together with C-domains identified by Rausch et al. as starter C-domains or as dual C/E-domains (Additional file 2).The tree was constructed using the maximum likelihood method and GTR as substitution model. Bootstrap percentages retrieved in 100 replications are shown at the main nodes. The scale bar (0.2) indicates the number of amino acid substitutions per site. C-domains belonging to the same clade as dual C/E-domains are in blue. C-domains belonging to the same clade as starter C-domains are in red. Putative starter C-domains of the loci META-A and META-C of strain GPE PC73, the contig G111 of strain XaS3 and the locus of strain BTAi similar to META-A and META-C are in green. C-domains Ax, Bx ad Cx correspond to C-domains of modules of the loci META-A, META-B and META-C of strain GPE PC73, respectively. C-domains Ox correspond to C-domains of modules of the locus META-B of strain BAI3. C-domains USxxx/x correspond to C-domains of modules of contigs of strain X11-5A. C-domains Gxxx/x correspond to C-domains of modules of contigs of strain XaS3. C-domains bradyx correspond to C-domains of the locus of Bradyrhizobium spp. strain BTAi similar to META-A and META-C (genes Bbta_6814, Bbta_6813, Bbta_6812). C-domains XOCx correspond to C-domains of the locus NRPS located in the same region as XaPPTase in strain BLS256. C-domains 0364 and 1145 correspond to C-domains of short NRPS genes XALc_0364 and XALc_1145 of strain GPE PC73, respectively. C-domain 0354XaS3 corresponds to the short NRPS gene of strain XaS3. C-domain Bbta4110 corresponds to the short NRPS gene of strain BTAi. C-domains identified by Rausch et al. [6] as starter C-domains were tagged "Starter1" to "Starter15" as follows: Starter1: Pseusyrin.NP_792633.1.m_1_leu Starter2: Pseusp.Q84BQ6.arfA_1_leu Starter3: Pseufluor.YP_259252.1.m_1_leu Starter4: Baciliche.YP_077640.1.lchAA_1_gln Starter5: Nocafarci.YP_117314.1.m_1_orn_lys_arg Starter6: Nocafarci.YP_119006.1.m_1_tyr Starter7: Nocafarci.YP_119328.1.m_1_ser Starter8: Nocafarci.YP_121279.1.m_1_ser Starter9: Strecoeli.NP_627443.1.m_1_ser Starter10: Strchrys.O68487.acmB_1_thr Starter11: Erwicarot.YP_049593.1.m_1_gln Starter12: Strprist.Q54959.snbC_1_thr Starter13: Bacisubti.NP_388230.1.srfAA_1_glu Starter14: Bacisubti.NP_389716.1.ppsA_1_glu Starter15: Baciliche.YP_090052.1.m_1_gln C-domains identified by Rausch et al. [6] as Dual C/E-domains were tagged "DualC/E1" to "DualC/E18" as follows: DualC/E1:Photlumin.NP_929905.1.m_9_thr_TO_val DualC/E2:Photlumin.NP_930489.1.m_2_val_TO_trp DualC/E3:Photlumin.NP_929905.1.m_6_bht_TO_trp DualC/E4:Bradjapon.NP_768748.1.m_3_ser_TO_phe DualC/E5:Chroviola.NP_902472.1.m_3_val_TO_ile_dual DualC/E6:Chroviola.NP_902472.1.m_1_thr_dual DualC/E7:Burkmalle.YP_106216.1.m_2_glu_TO_gly DualC/E8:Burkpseud.YP_111641.1.m_3_thr_TO_leu DualC/E9:Burkpseud.YP_111641.1.m_1_glu_gln DualC/E10:Pseusyrin.NP_792633.1.m_2_leu_TO_leu DualC/E11:Ralssolan.NP_522203.1.m_3_ser_TO_gly DualC/E12:Ralssolan.NP_522203.1.m_1_val DualC/E13:Pseufluor.YP_259253.1.m_4_leu_TO_ser DualC/E14:Pseufluor.YP_259253.1.m_2_thr_TO_ile DualC/E15:Pseusyrin.NP_792634.1.m_3_thr_TO_val DualC/E16:Pseusyrin.NP_792634.1.m_5_leu_TO_leu DualC/E17:Erwicarot.YP_049592.1.m_4_ser_TO_tyr_bht DualC/E18:Erwicarot.YP_049593.1.m_2_gln_TO_asnCdom_Complete&oryzicola_phyML_v20-07-2012 copie.pd