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Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity

Specialized metabolites are of great interest due to their possible industrial and clinical applications. The increasing number of antimicrobial resistant infectious agents is a major health threat and therefore, the discovery of chemical diversity and new antimicrobials is crucial. Extensive genomi...

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Autores principales: Vicente, Cláudia M., Thibessard, Annabelle, Lorenzi, Jean-Noël, Benhadj, Mabrouka, Hôtel, Laurence, Gacemi-Kirane, Djamila, Lespinet, Olivier, Leblond, Pierre, Aigle, Bertrand
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6315706/
https://www.ncbi.nlm.nih.gov/pubmed/30279346
http://dx.doi.org/10.3390/antibiotics7040086
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author Vicente, Cláudia M.
Thibessard, Annabelle
Lorenzi, Jean-Noël
Benhadj, Mabrouka
Hôtel, Laurence
Gacemi-Kirane, Djamila
Lespinet, Olivier
Leblond, Pierre
Aigle, Bertrand
author_facet Vicente, Cláudia M.
Thibessard, Annabelle
Lorenzi, Jean-Noël
Benhadj, Mabrouka
Hôtel, Laurence
Gacemi-Kirane, Djamila
Lespinet, Olivier
Leblond, Pierre
Aigle, Bertrand
author_sort Vicente, Cláudia M.
collection PubMed
description Specialized metabolites are of great interest due to their possible industrial and clinical applications. The increasing number of antimicrobial resistant infectious agents is a major health threat and therefore, the discovery of chemical diversity and new antimicrobials is crucial. Extensive genomic data from Streptomyces spp. confirm their production potential and great importance. Genome sequencing of the same species strains indicates that specialized metabolite biosynthetic gene cluster (SMBGC) diversity is not exhausted, and instead, a pool of novel specialized metabolites still exists. Here, we analyze the genome sequence data from six phylogenetically close Streptomyces strains. The results reveal that the closer strains are phylogenetically, the number of shared gene clusters is higher. Eight specialized metabolites comprise the core metabolome, although some strains have only six core gene clusters. The number of conserved gene clusters common between the isolated strains and their closest phylogenetic counterparts varies from nine to 23 SMBGCs. However, the analysis of these phylogenetic relationships is not affected by the acquisition of gene clusters, probably by horizontal gene transfer events, as each strain also harbors strain-specific SMBGCs. Between one and 15 strain-specific gene clusters were identified, of which up to six gene clusters in a single strain are unknown and have no identifiable orthologs in other species, attesting to the existing SMBGC novelty at the strain level.
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spelling pubmed-63157062019-01-11 Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity Vicente, Cláudia M. Thibessard, Annabelle Lorenzi, Jean-Noël Benhadj, Mabrouka Hôtel, Laurence Gacemi-Kirane, Djamila Lespinet, Olivier Leblond, Pierre Aigle, Bertrand Antibiotics (Basel) Communication Specialized metabolites are of great interest due to their possible industrial and clinical applications. The increasing number of antimicrobial resistant infectious agents is a major health threat and therefore, the discovery of chemical diversity and new antimicrobials is crucial. Extensive genomic data from Streptomyces spp. confirm their production potential and great importance. Genome sequencing of the same species strains indicates that specialized metabolite biosynthetic gene cluster (SMBGC) diversity is not exhausted, and instead, a pool of novel specialized metabolites still exists. Here, we analyze the genome sequence data from six phylogenetically close Streptomyces strains. The results reveal that the closer strains are phylogenetically, the number of shared gene clusters is higher. Eight specialized metabolites comprise the core metabolome, although some strains have only six core gene clusters. The number of conserved gene clusters common between the isolated strains and their closest phylogenetic counterparts varies from nine to 23 SMBGCs. However, the analysis of these phylogenetic relationships is not affected by the acquisition of gene clusters, probably by horizontal gene transfer events, as each strain also harbors strain-specific SMBGCs. Between one and 15 strain-specific gene clusters were identified, of which up to six gene clusters in a single strain are unknown and have no identifiable orthologs in other species, attesting to the existing SMBGC novelty at the strain level. MDPI 2018-10-02 /pmc/articles/PMC6315706/ /pubmed/30279346 http://dx.doi.org/10.3390/antibiotics7040086 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Communication
Vicente, Cláudia M.
Thibessard, Annabelle
Lorenzi, Jean-Noël
Benhadj, Mabrouka
Hôtel, Laurence
Gacemi-Kirane, Djamila
Lespinet, Olivier
Leblond, Pierre
Aigle, Bertrand
Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity
title Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity
title_full Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity
title_fullStr Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity
title_full_unstemmed Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity
title_short Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity
title_sort comparative genomics among closely related streptomyces strains revealed specialized metabolite biosynthetic gene cluster diversity
topic Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6315706/
https://www.ncbi.nlm.nih.gov/pubmed/30279346
http://dx.doi.org/10.3390/antibiotics7040086
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