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performed in silico analyses of NRPS genes present in all published genome sequences of Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv.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.
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dig-cirad-fr-570723 |
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CIRAD FR |
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Francia |
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FR |
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Bibliográfico |
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En linea |
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dig-cirad-fr |
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Europa del Oeste |
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Biblioteca del CIRAD Francia |
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eng |
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H20 - Maladies des plantes Xanthomonas Xanthomonas oryzae Xanthomonas albilineans biosynthèse peptide génome séquence nucléotidique PCR relation hôte pathogène Oryza sativa Saccharum officinarum amélioration des plantes résistance aux maladies http://aims.fao.org/aos/agrovoc/c_8455 http://aims.fao.org/aos/agrovoc/c_24383 http://aims.fao.org/aos/agrovoc/c_27422 http://aims.fao.org/aos/agrovoc/c_928 http://aims.fao.org/aos/agrovoc/c_5691 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_34017 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_6727 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_8081 http://aims.fao.org/aos/agrovoc/c_3406 http://aims.fao.org/aos/agrovoc/c_165 http://aims.fao.org/aos/agrovoc/c_3081 H20 - Maladies des plantes Xanthomonas Xanthomonas oryzae Xanthomonas albilineans biosynthèse peptide génome séquence nucléotidique PCR relation hôte pathogène Oryza sativa Saccharum officinarum amélioration des plantes résistance aux maladies http://aims.fao.org/aos/agrovoc/c_8455 http://aims.fao.org/aos/agrovoc/c_24383 http://aims.fao.org/aos/agrovoc/c_27422 http://aims.fao.org/aos/agrovoc/c_928 http://aims.fao.org/aos/agrovoc/c_5691 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_34017 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_6727 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_8081 http://aims.fao.org/aos/agrovoc/c_3406 http://aims.fao.org/aos/agrovoc/c_165 http://aims.fao.org/aos/agrovoc/c_3081 |
spellingShingle |
H20 - Maladies des plantes Xanthomonas Xanthomonas oryzae Xanthomonas albilineans biosynthèse peptide génome séquence nucléotidique PCR relation hôte pathogène Oryza sativa Saccharum officinarum amélioration des plantes résistance aux maladies http://aims.fao.org/aos/agrovoc/c_8455 http://aims.fao.org/aos/agrovoc/c_24383 http://aims.fao.org/aos/agrovoc/c_27422 http://aims.fao.org/aos/agrovoc/c_928 http://aims.fao.org/aos/agrovoc/c_5691 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_34017 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_6727 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_8081 http://aims.fao.org/aos/agrovoc/c_3406 http://aims.fao.org/aos/agrovoc/c_165 http://aims.fao.org/aos/agrovoc/c_3081 H20 - Maladies des plantes Xanthomonas Xanthomonas oryzae Xanthomonas albilineans biosynthèse peptide génome séquence nucléotidique PCR relation hôte pathogène Oryza sativa Saccharum officinarum amélioration des plantes résistance aux maladies http://aims.fao.org/aos/agrovoc/c_8455 http://aims.fao.org/aos/agrovoc/c_24383 http://aims.fao.org/aos/agrovoc/c_27422 http://aims.fao.org/aos/agrovoc/c_928 http://aims.fao.org/aos/agrovoc/c_5691 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_34017 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_6727 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_8081 http://aims.fao.org/aos/agrovoc/c_3406 http://aims.fao.org/aos/agrovoc/c_165 http://aims.fao.org/aos/agrovoc/c_3081 Royer, Monique Koebnik, Ralf Marguerettaz, Mélanie Barbe, Valérie Robin, Guillaume P. Brin, Christelle Carrère, Sébastien Gomez, Camila Hügelland, Manuela Völler, Ginka H. Noëll, Julie Pieretti, Isabelle Rausch, Saskia Verdier, Valérie Poussier, Stéphane Rott, Philippe Süssmuth, Roderich Cociancich, Stéphane 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. |
format |
article |
topic_facet |
H20 - Maladies des plantes Xanthomonas Xanthomonas oryzae Xanthomonas albilineans biosynthèse peptide génome séquence nucléotidique PCR relation hôte pathogène Oryza sativa Saccharum officinarum amélioration des plantes résistance aux maladies http://aims.fao.org/aos/agrovoc/c_8455 http://aims.fao.org/aos/agrovoc/c_24383 http://aims.fao.org/aos/agrovoc/c_27422 http://aims.fao.org/aos/agrovoc/c_928 http://aims.fao.org/aos/agrovoc/c_5691 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_34017 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_6727 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_8081 http://aims.fao.org/aos/agrovoc/c_3406 http://aims.fao.org/aos/agrovoc/c_165 http://aims.fao.org/aos/agrovoc/c_3081 |
author |
Royer, Monique Koebnik, Ralf Marguerettaz, Mélanie Barbe, Valérie Robin, Guillaume P. Brin, Christelle Carrère, Sébastien Gomez, Camila Hügelland, Manuela Völler, Ginka H. Noëll, Julie Pieretti, Isabelle Rausch, Saskia Verdier, Valérie Poussier, Stéphane Rott, Philippe Süssmuth, Roderich Cociancich, Stéphane |
author_facet |
Royer, Monique Koebnik, Ralf Marguerettaz, Mélanie Barbe, Valérie Robin, Guillaume P. Brin, Christelle Carrère, Sébastien Gomez, Camila Hügelland, Manuela Völler, Ginka H. Noëll, Julie Pieretti, Isabelle Rausch, Saskia Verdier, Valérie Poussier, Stéphane Rott, Philippe Süssmuth, Roderich Cociancich, Stéphane |
author_sort |
Royer, Monique |
title |
Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides |
title_short |
Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides |
title_full |
Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides |
title_fullStr |
Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides |
title_full_unstemmed |
Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides |
title_sort |
genome mining reveals the genus xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides |
url |
http://agritrop.cirad.fr/570723/ http://agritrop.cirad.fr/570723/1/document_570723.pdf |
work_keys_str_mv |
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1806036961192837120 |
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dig-cirad-fr-5707232024-07-23T16:02:24Z http://agritrop.cirad.fr/570723/ http://agritrop.cirad.fr/570723/ Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides. Royer Monique, Koebnik Ralf, Marguerettaz Mélanie, Barbe Valérie, Robin Guillaume P., Brin Christelle, Carrère Sébastien, Gomez Camila, Hügelland Manuela, Völler Ginka H., Noëll Julie, Pieretti Isabelle, Rausch Saskia, Verdier Valérie, Poussier Stéphane, Rott Philippe, Süssmuth Roderich, Cociancich Stéphane. 2013. BMC Genomics, 14 (658), 19 p.https://doi.org/10.1186/1471-2164-14-658 <https://doi.org/10.1186/1471-2164-14-658> Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides Royer, Monique Koebnik, Ralf Marguerettaz, Mélanie Barbe, Valérie Robin, Guillaume P. Brin, Christelle Carrère, Sébastien Gomez, Camila Hügelland, Manuela Völler, Ginka H. Noëll, Julie Pieretti, Isabelle Rausch, Saskia Verdier, Valérie Poussier, Stéphane Rott, Philippe Süssmuth, Roderich Cociancich, Stéphane eng 2013 BMC Genomics H20 - Maladies des plantes Xanthomonas Xanthomonas oryzae Xanthomonas albilineans biosynthèse peptide génome séquence nucléotidique PCR relation hôte pathogène Oryza sativa Saccharum officinarum amélioration des plantes résistance aux maladies http://aims.fao.org/aos/agrovoc/c_8455 http://aims.fao.org/aos/agrovoc/c_24383 http://aims.fao.org/aos/agrovoc/c_27422 http://aims.fao.org/aos/agrovoc/c_928 http://aims.fao.org/aos/agrovoc/c_5691 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_34017 http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_6727 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_2328 Burkina Faso Guadeloupe Afrique France http://aims.fao.org/aos/agrovoc/c_8081 http://aims.fao.org/aos/agrovoc/c_3406 http://aims.fao.org/aos/agrovoc/c_165 http://aims.fao.org/aos/agrovoc/c_3081 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/570723/1/document_570723.pdf application/pdf Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1186/1471-2164-14-658 10.1186/1471-2164-14-658 info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2164-14-658 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1186/1471-2164-14-658 info:eu-repo/semantics/dataset/purl/https://doi.org/10.5061/dryad.gh7h8 |