Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products
12 páginas, 4 figuras
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| Language: | English |
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Microbiology Society
2022
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| Subjects: | BGCs, BiG-SCAPE / CORASON, EvoMining, Comparative genomics, Pan-genome, Secondary metabolites, |
| Online Access: | http://hdl.handle.net/10261/263119 http://dx.doi.org/10.13039/501100014180 https://api.elsevier.com/content/abstract/scopus_id/85125157541 |
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dig-irnasa-es-10261-2631192024-05-22T20:36:01Z Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products Saati-Santamaría, Zaki Selem-Mojica, Nelly Peral Aranega, Ezequiel Rivas, Raúl García-Fraile, Paula Junta de Castilla y León Rivas, Raúl [0000-0003-2202-1470] BGCs BiG-SCAPE / CORASON EvoMining Comparative genomics Pan-genome Secondary metabolites 12 páginas, 4 figuras Microbes 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 reviewed 2022-03-07T12:03:50Z 2022-03-07T12:03:50Z 2022 artículo http://purl.org/coar/resource_type/c_6501 Microbial Genomics 8(2): 000758 (2022) http://hdl.handle.net/10261/263119 10.1099/mgen.0.000758 2057-5858 http://dx.doi.org/10.13039/501100014180 35195510 2-s2.0-85125157541 https://api.elsevier.com/content/abstract/scopus_id/85125157541 en Microbial genomics Publisher's version http://dx.doi.org/10.1099/mgen.0.000758 Sí open Microbiology Society |
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BGCs BiG-SCAPE / CORASON EvoMining Comparative genomics Pan-genome Secondary metabolites BGCs BiG-SCAPE / CORASON EvoMining Comparative genomics Pan-genome Secondary metabolites |
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BGCs BiG-SCAPE / CORASON EvoMining Comparative genomics Pan-genome Secondary metabolites BGCs BiG-SCAPE / CORASON EvoMining Comparative genomics Pan-genome Secondary metabolites Saati-Santamaría, Zaki Selem-Mojica, Nelly Peral Aranega, Ezequiel Rivas, Raúl García-Fraile, Paula Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products |
| description |
12 páginas, 4 figuras |
| author2 |
Junta de Castilla y León |
| author_facet |
Junta de Castilla y León Saati-Santamaría, Zaki Selem-Mojica, Nelly Peral Aranega, Ezequiel Rivas, Raúl García-Fraile, Paula |
| format |
artículo |
| topic_facet |
BGCs BiG-SCAPE / CORASON EvoMining Comparative genomics Pan-genome Secondary metabolites |
| author |
Saati-Santamaría, Zaki Selem-Mojica, Nelly Peral Aranega, Ezequiel Rivas, Raúl García-Fraile, Paula |
| author_sort |
Saati-Santamaría, Zaki |
| title |
Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products |
| 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 |
| publisher |
Microbiology Society |
| publishDate |
2022 |
| url |
http://hdl.handle.net/10261/263119 http://dx.doi.org/10.13039/501100014180 https://api.elsevier.com/content/abstract/scopus_id/85125157541 |
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