title: Automated identification of depsipeptide natural products by an informatic search algorithm.
abstract: Nonribosomal depsipeptides are a class of potent microbial natural products, which include several clinically approved pharmaceutical agents. Genome sequencing has revealed a large number of uninvestigated natural-product biosynthetic gene clusters. However, while novel informatic search methods to access these gene clusters have been developed to identify peptide natural products, depsipeptide detection has proven challenging. Herein, we present an improved version of our informatic search algorithm for natural products (iSNAP), which facilitates the detection of known and genetically predicted depsipeptides in complex microbial culture extracts. We validated this technology by identifying several depsipeptides from novel producers, and located a large number of novel depsipeptide gene clusters for future study. This approach highlights the value of chemoinformatic search methods for the discovery of genetically encoded metabolites by targeting specific areas of chemical space.
authors.affiliation: Department of Chemistry and Chemical Biology, Department of Biochemistry and Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8N 3Z5 (Canada).
authors.forename: Michael A
authors.initials: MA
authors.lastname: Skinnider
authors.forename: Chad W
authors.initials: CW
authors.lastname: Johnston
authors.forename: Rostyslav
authors.initials: R
authors.lastname: Zvanych
authors.forename: Nathan A
authors.initials: NA
authors.lastname: Magarvey
mesh_terms: D000465:Algorithms; D001688:Biological Products; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D047630:Depsipeptides / Q000235:genetics; D016680:Genome, Bacterial; D008390:Markov Chains; D005810:Multigene Family; D013302:Streptomyces / Q000235:genetics* / Q000378:metabolism*; D053719:Tandem Mass Spectrometry; D014634:Valinomycin / Q000378:metabolism
chemical_list: D001688:Biological Products; D047630:Depsipeptides; D014634:Valinomycin
keywords: bioinformatics; chemoinformatics; depsipeptides; mass spectrometry; natural products