An atlas of bacterial secondary metabolite biosynthesis gene clusters

Summary Bacterial secondary metabolites are rich sources of novel drug leads. The diversity of secondary metabolite biosynthetic gene clusters (BGCs) in genome‐sequenced bacteria, which will provide crucial information for the efficient discovery of novel natural products, has not been systematicall...

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Published in:Environmental microbiology 2021-11, Vol.23 (11), p.6981-6992
Main Authors: Wei, Bin, Du, Ao‐Qi, Zhou, Zhen‐Yi, Lai, Cong, Yu, Wen‐Chao, Yu, Jin‐Biao, Yu, Yan‐Lei, Chen, Jian‐Wei, Zhang, Hua‐Wei, Xu, Xue‐Wei, Wang, Hong
Format: Article
Language:English
Subjects:
Ascomycota - genetics
Bacteria
Biosynthesis
Biosynthetic Pathways - genetics
Comparative analysis
Cyanobacteria - genetics
Gene clusters
Genetic diversity
Genetic variation
Genomes
Metabolism
Metabolites
Microbiological strains
Multigene Family
Natural products
Polyketides
Programming languages
Secondary Metabolism - genetics
Secondary metabolites
Strains (organisms)
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Summary:Summary Bacterial secondary metabolites are rich sources of novel drug leads. The diversity of secondary metabolite biosynthetic gene clusters (BGCs) in genome‐sequenced bacteria, which will provide crucial information for the efficient discovery of novel natural products, has not been systematically investigated. Here, the distribution and genetic diversity of BGCs in 10 121 prokaryotic genomes (across 68 phyla) were obtained from their PRISM4 outputs using a custom python script. A total of 18 043 BGCs are detected from 5743 genomes with non‐ribosomal peptide synthetases (25.4%) and polyketides (15.9%) as the dominant classes of BGCs. Bacterial strains harbouring the largest number of BGCs are revealed and BGC count in strains of some genera vary greatly, suggesting the necessity of individually evaluating the secondary metabolism potential. Additional analysis against 102 strains of discovered bacterial genera with abundant amounts of BGCs confirms that Kutzneria, Kibdelosporangium, Moorea, Saccharothrix, Cystobacter, Archangium, Actinosynnema, Kitasatospora, and Nocardia, may also be important sources of natural products and worthy of priority investigation. Comparative analysis of BGCs within these genera indicates the great diversity and novelty of the BGCs. This study presents an atlas of bacterial secondary metabolite BGCs that provides a lot of key information for the targeted discovery of novel natural products.
ISSN:1462-2912
1462-2920
DOI:10.1111/1462-2920.15761