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Volume 8, Issue 2

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

Abstract

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 . In this work, we aimed (i) to unveil the main biosynthetic systems related to secondary metabolism in type strains (ii) to study the evolutionary processes that drive the diversification of their coding regions and (iii) to select strains showing promising results in the search for useful natural products. We performed a comparative genomic study on 194 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 . The types of metabolites encoded in 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 species diversification. Interestingly, only a few 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 type strains, whose gene clusters have evolved in a species-specific way. Our results provide novel insight into the secondary metabolism of and will serve as a basis for the prioritization of the isolated strains. This article contains data hosted by Microreact.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): BGCs , BiG-SCAPE / CORASON , comparative genomics , EvoMining , pan-genome and secondary metabolites
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2022-02-23
2024-04-27
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Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products
M Gen 8, 000758 (2022); https://doi.org/10.1099/mgen.0.000758
/content/journal/mgen/10.1099/mgen.0.000758
/content/journal/mgen/10.1099/mgen.0.000758
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