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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doaj-1f1fd61d91264e428d9b63891fe5224f2020-11-24T22:24:01ZengMDPI AGAntibiotics2079-63822018-10-01748610.3390/antibiotics7040086antibiotics7040086Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster DiversityCláudia M. Vicente0Annabelle Thibessard1Jean-Noël Lorenzi2Mabrouka Benhadj3Laurence Hôtel4Djamila Gacemi-Kirane5Olivier Lespinet6Pierre Leblond7Bertrand Aigle8Université de Lorraine, INRA, DynAMic, F-54000 Nancy, FranceUniversité de Lorraine, INRA, DynAMic, F-54000 Nancy, FranceInstitute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Sud, University Paris-Saclay, Gif-sur-Yvette CEDEX, FranceUniversité de Lorraine, INRA, DynAMic, F-54000 Nancy, FranceUniversité de Lorraine, INRA, DynAMic, F-54000 Nancy, FranceDepartment of Biochemistry, Faculty of Science, University Badji Mokhtar Annaba, Annaba 23000, AlgeriaInstitute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Sud, University Paris-Saclay, Gif-sur-Yvette CEDEX, FranceUniversité de Lorraine, INRA, DynAMic, F-54000 Nancy, FranceUniversité de Lorraine, INRA, DynAMic, F-54000 Nancy, FranceSpecialized 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.http://www.mdpi.com/2079-6382/7/4/86Streptomycesstrainspecialized metabolitesbiosynthetic gene cluster |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Cláudia M. Vicente Annabelle Thibessard Jean-Noël Lorenzi Mabrouka Benhadj Laurence Hôtel Djamila Gacemi-Kirane Olivier Lespinet Pierre Leblond Bertrand Aigle |
spellingShingle |
Cláudia M. Vicente Annabelle Thibessard Jean-Noël Lorenzi Mabrouka Benhadj Laurence Hôtel Djamila Gacemi-Kirane Olivier Lespinet Pierre Leblond Bertrand Aigle Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity Antibiotics Streptomyces strain specialized metabolites biosynthetic gene cluster |
author_facet |
Cláudia M. Vicente Annabelle Thibessard Jean-Noël Lorenzi Mabrouka Benhadj Laurence Hôtel Djamila Gacemi-Kirane Olivier Lespinet Pierre Leblond Bertrand Aigle |
author_sort |
Cláudia M. Vicente |
title |
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_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_sort |
comparative genomics among closely related streptomyces strains revealed specialized metabolite biosynthetic gene cluster diversity |
publisher |
MDPI AG |
series |
Antibiotics |
issn |
2079-6382 |
publishDate |
2018-10-01 |
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. |
topic |
Streptomyces strain specialized metabolites biosynthetic gene cluster |
url |
http://www.mdpi.com/2079-6382/7/4/86 |
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