ArticleMethods in enzymology2012
Phylogenetic approaches to natural product structure prediction.
Article in Methods in enzymology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Analyzing the Challenges and Opportunities Associated With Harnessing New Antibiotics From the Fungal Microbiome.MicrobiologyOpen · 2025Review
- getphylo: rapid and automatic generation of multi-locus phylogenetic trees.BMC bioinformatics · 2025Article
- Genomic features of lichen-associated black fungi.IUBMB life · 2025Article
- Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products.Natural product reports · 2024Review
- Article
- Article
- Biosynthetic gene cluster synteny: Orthologous polyketide synthases in Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata.MicrobiologyOpen · 2023Article
- Mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2023Article
- Cloning and Functional Characterization of the Polyketide Synthases Based on Genome Mining ofFrontiers in microbiology · 2022Article
- Genome Mining ofMolecules (Basel, Switzerland) · 2021Article
- Diversity of Polyketide Synthases and Nonribosomal Peptide Synthetases Revealed Through Metagenomic Analysis of a Deep Oligotrophic Cave.Microbial ecology · 2021Article
- Biosynthesis of Polyhydroxyalkanoates (PHAs) by the Valorization of Biomass and Synthetic Waste.Molecules (Basel, Switzerland) · 2020Article
- Biosynthesis and Antimicrobial Activity of Pseudodesmin and Viscosinamide Cyclic Lipopeptides Produced by Pseudomonads Associated with the Cocoyam Rhizosphere.Microorganisms · 2020Article
- Biosynthetic Gene Content of the 'Perfume Lichens'Molecules (Basel, Switzerland) · 2019Article
- Informatics and Computational Methods in Natural Product Drug Discovery: A Review and Perspectives.Frontiers in genetics · 2019Review
- A comprehensive catalogue of polyketide synthase gene clusters in lichenizing fungi.Journal of industrial microbiology & biotechnology · 2018Review
- Coronafacoyl Phytotoxin Biosynthesis and Evolution in the Common Scab Pathogen Streptomyces scabiei.Applied and environmental microbiology · 2017Article
- Engineering microbial hosts for production of bacterial natural products.Natural product reports · 2016Review
- Activation and identification of five clusters for secondary metabolites in Streptomyces albus J1074.Microbial biotechnology · 2014Article
- Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
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Abstract
Phylogenetics is the study of the evolutionary relatedness among groups of organisms. Molecular phylogenetics uses sequence data to infer these relationships for both organisms and the genes they maintain. With the large amount of publicly available sequence data, phylogenetic inference has become increasingly important in all fields of biology. In the case of natural product research, phylogenetic relationships are proving to be highly informative in terms of delineating the architecture and function of the genes involved in secondary metabolite biosynthesis. Polyketide synthases and nonribosomal peptide synthetases provide model examples in which individual domain phylogenies display different predictive capacities, resolving features ranging from substrate specificity to structural motifs associated with the final metabolic product. This chapter provides examples in which phylogeny has proven effective in terms of predicting functional or structural aspects of secondary metabolism. The basics of how to build a reliable phylogenetic tree are explained along with information about programs and tools that can be used for this purpose. Furthermore, it introduces the Natural Product Domain Seeker, a recently developed Web tool that employs phylogenetic logic to classify ketosynthase and condensation domains based on established enzyme architecture and biochemical function.
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