DOI: 10.5061/dryad.gh7h8
title: Data from: Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides

description: 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 well as in unpublished draft genome sequences of Xanthomonas oryzae pv.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.
description: 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.pdf