Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products

12 páginas, 4 figuras

Detalles Bibliográficos
Autores: Saati-Santamaría, Zaki, Selem-Mojica, Nelly, Peral Aranega, Ezequiel, Rivas, Raúl, García-Fraile, Paula
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/263119
Acceso en línea:http://hdl.handle.net/10261/263119
https://api.elsevier.com/content/abstract/scopus_id/85125157541
Access Level:acceso abierto
Palabra clave:BGCs
BiG-SCAPE / CORASON
EvoMining
Comparative genomics
Pan-genome
Secondary metabolites
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spelling Unveiling the genomic potential of Pseudomonas type strains for discovering new natural productsSaati-Santamaría, ZakiSelem-Mojica, NellyPeral Aranega, EzequielRivas, RaúlGarcía-Fraile, PaulaBGCsBiG-SCAPE / CORASONEvoMiningComparative genomicsPan-genomeSecondary metabolites12 páginas, 4 figurasMicrobes host a huge variety of biosynthetic gene clusters that produce an immeasurable array of secondary metabolites with many different biological activities such as antimicrobial, anticarcinogenic and antiviral. Despite the complex task of isolating and characterizing novel natural products, microbial genomic strategies can be useful for carrying out these types of studies. However, although genomic-based research on secondary metabolism is on the increase, there is still a lack of reports focusing specifically on the genus Pseudomonas. In this work, we aimed (i) to unveil the main biosynthetic systems related to secondary metabolism in Pseudomonas type strains, (ii) to study the evolutionary processes that drive the diversification of their coding regions and (iii) to select Pseudomonas strains showing promising results in the search for useful natural products. We performed a comparative genomic study on 194 Pseudomonas species, paying special attention to the evolution and distribution of different classes of biosynthetic gene clusters and the coding features of antimicrobial peptides. Using EvoMining, a bioinformatic approach for studying evolutionary processes related to secondary metabolism, we sought to decipher the protein expansion of enzymes related to the lipid metabolism, which may have evolved toward the biosynthesis of novel secondary metabolites in Pseudomonas. The types of metabolites encoded in Pseudomonas type strains were predominantly non-ribosomal peptide synthetases, bacteriocins, N-acetylglutaminylglutamine amides and ß-lactones. Also, the evolution of genes related to secondary metabolites was found to coincide with Pseudomonas species diversification. Interestingly, only a few Pseudomonas species encode polyketide synthases, which are related to the lipid metabolism broadly distributed among bacteria. Thus, our EvoMining-based search may help to discover new types of secondary metabolite gene clusters in which lipid-related enzymes are involved. This work provides information about uncharacterized metabolites produced by Pseudomonas type strains, whose gene clusters have evolved in a species-specific way. Our results provide novel insight into the secondary metabolism of Pseudomonas and will serve as a basis for the prioritization of the isolated strains. This article contains data hosted by Microreact.Z.S.S. and E.P.A. received grants from the Regional Government of Castile and Leon. Also, this work was supported by the Regional Government of Castile and Leon (Escalera de Excelencia CLU-2018-04) and co-funded by the Operational Program of the European Regional Development Fund for Castile and Leon 2014–2020.Peer reviewedMicrobiology SocietyJunta de Castilla y LeónRivas, Raúl [0000-0003-2202-1470]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202220222022info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/263119https://api.elsevier.com/content/abstract/scopus_id/85125157541reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésMicrobial genomicshttp://dx.doi.org/10.1099/mgen.0.000758Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2631192026-05-22T06:33:51Z
dc.title.none.fl_str_mv Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products
title Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products
spellingShingle Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products
Saati-Santamaría, Zaki
BGCs
BiG-SCAPE / CORASON
EvoMining
Comparative genomics
Pan-genome
Secondary metabolites
title_short Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products
title_full Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products
title_fullStr Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products
title_full_unstemmed Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products
title_sort Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products
dc.creator.none.fl_str_mv Saati-Santamaría, Zaki
Selem-Mojica, Nelly
Peral Aranega, Ezequiel
Rivas, Raúl
García-Fraile, Paula
author Saati-Santamaría, Zaki
author_facet Saati-Santamaría, Zaki
Selem-Mojica, Nelly
Peral Aranega, Ezequiel
Rivas, Raúl
García-Fraile, Paula
author_role author
author2 Selem-Mojica, Nelly
Peral Aranega, Ezequiel
Rivas, Raúl
García-Fraile, Paula
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Junta de Castilla y León
Rivas, Raúl [0000-0003-2202-1470]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv BGCs
BiG-SCAPE / CORASON
EvoMining
Comparative genomics
Pan-genome
Secondary metabolites
topic BGCs
BiG-SCAPE / CORASON
EvoMining
Comparative genomics
Pan-genome
Secondary metabolites
description 12 páginas, 4 figuras
publishDate 2022
dc.date.none.fl_str_mv 2022
2022
2022
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/263119
https://api.elsevier.com/content/abstract/scopus_id/85125157541
url http://hdl.handle.net/10261/263119
https://api.elsevier.com/content/abstract/scopus_id/85125157541
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Microbial genomics
http://dx.doi.org/10.1099/mgen.0.000758
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Microbiology Society
publisher.none.fl_str_mv Microbiology Society
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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