ArticleGenome biology and evolution2016
Phylogenomic Analysis of Natural Products Biosynthetic Gene Clusters Allows Discovery of Arseno-Organic Metabolites in Model Streptomycetes.
Article in Genome biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- γ-Butyrolactone-induced coelimycin synthesis inhibits AtrA-dependent actinorhodin overproduction inmBio · 2026Article
- Multi-Omic Assessment of Microbial Communities and Their Polyketide Biosynthetic Potential Across Abyssal Sediments.Environmental microbiology · 2026Article
- Functional shifts of the dual-substrate phosphoribosyl isomerase PriA from primary to specialized metabolism in rare Actinomycetota.Microbial genomics · 2026Article
- Advances in natural product discovery: strategies, technologies, and insights.Natural products and bioprospecting · 2026Review
- The Role of Nucleotide Sequencing in Natural Product Drug Discovery.Journal of natural products · 2025Review
- Evolutionary Tree in Chemical Space of Natural Products.bioRxiv : the preprint server for biology · 2025Article
- Identification of widely conserved biosynthetic gene cluster involved in pigment production ofmSystems · 2025Article
- Exploring new natural products by utilizing untapped secondary metabolic pathways in actinomycetes.Journal of natural medicines · 2025Review
- Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.mSystems · 2025Review
- Pangenome mining of the Streptomyces genus redefines species' biosynthetic potential.Genome biology · 2025Article
- Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products.Natural product reports · 2024Review
- Mining microbial and metabolic dark matter in extreme environments: a roadmap for harnessing the power of multi-omics data.Advanced biotechnology · 2024Review
- Synteruptor: mining genomic islands for non-classical specialized metabolite gene clusters.NAR genomics and bioinformatics · 2024Article
- Lipophilic arsenic compounds in the cultured green alga Chlamydomonas reinhardtii.Analytical and bioanalytical chemistry · 2024Article
- Genomic mining and diversity of assembly line polyketide synthases.Open biology · 2023Article
- The Cytotoxic Properties of Extreme Fungi's Bioactive Components-An Updated Metabolic and Omics Overview.Life (Basel, Switzerland) · 2023Review
- Crosstalk between primary and secondary metabolism: Interconnected fatty acid and polyketide biosynthesis in prokaryotes.Bioorganic & medicinal chemistry letters · 2023Review
- Genome Analysis of a Variant ofMicroorganisms · 2023Article
- Streptomyces lividans 66 produces a protease inhibitor via a tRNA-utilizing enzyme interacting with a C-minus NRPS.Journal of industrial microbiology & biotechnology · 2023Article
- Integrated Metabolomic-Genomic Workflows Accelerate Microbial Natural Product Discovery.Analytical chemistry · 2022Review
6 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Natural products from microbes have provided humans with beneficial antibiotics for millennia. However, a decline in the pace of antibiotic discovery exerts pressure on human health as antibiotic resistance spreads, a challenge that may better faced by unveiling chemical diversity produced by microbes. Current microbial genome mining approaches have revitalized research into antibiotics, but the empirical nature of these methods limits the chemical space that is explored.Here, we address the problem of finding novel pathways by incorporating evolutionary principles into genome mining. We recapitulated the evolutionary history of twenty-three enzyme families previously uninvestigated in the context of natural product biosynthesis in Actinobacteria, the most proficient producers of natural products. Our genome evolutionary analyses where based on the assumption that expanded-repurposed enzyme families-from central metabolism, occur frequently and thus have the potential to catalyze new conversions in the context of natural products biosynthesis. Our analyses led to the discovery of biosynthetic gene clusters coding for hidden chemical diversity, as validated by comparing our predictions with those from state-of-the-art genome mining tools; as well as experimentally demonstrating the existence of a biosynthetic pathway for arseno-organic metabolites in Streptomyces coelicolor and Streptomyces lividans, Using a gene knockout and metabolite profile combined strategy.As our approach does not rely solely on sequence similarity searches of previously identified biosynthetic enzymes, these results establish the basis for the development of an evolutionary-driven genome mining tool termed EvoMining that complements current platforms. We anticipate that by doing so real 'chemical dark matter' will be unveiled.
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