title: A roadmap for natural product discovery based on large-scale genomics and metabolomics.
abstract: Actinobacteria encode a wealth of natural product biosynthetic gene clusters, whose systematic study is complicated by numerous repetitive motifs. By combining several metrics, we developed a method for the global classification of these gene clusters into families (GCFs) and analyzed the biosynthetic capacity of Actinobacteria in 830 genome sequences, including 344 obtained for this project. The GCF network, comprising 11,422 gene clusters grouped into 4,122 GCFs, was validated in hundreds of strains by correlating confident mass spectrometric detection of known small molecules with the presence or absence of their established biosynthetic gene clusters. The method also linked previously unassigned GCFs to known natural products, an approach that will enable de novo, bioassay-free discovery of new natural products using large data sets. Extrapolation from the 830-genome data set reveals that Actinobacteria encode hundreds of thousands of future drug leads, and the strong correlation between phylogeny and GCFs frames a roadmap to efficiently access them.
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: James R
authors.initials: JR
authors.lastname: Doroghazi
authors.affiliation: 1] Department of Chemistry, Northwestern University, Evanston, Illinois, USA. [2] Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA. [3] Feinberg School of Medicine, Northwestern University, Evanston, Illinois, USA.
authors.forename: Jessica C
authors.identifier: 0000000163681331
authors.initials: JC
authors.lastname: Albright
authors.affiliation: 1] Department of Chemistry, Northwestern University, Evanston, Illinois, USA. [2] Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA. [3] Feinberg School of Medicine, Northwestern University, Evanston, Illinois, USA.
authors.forename: Anthony W
authors.initials: AW
authors.lastname: Goering
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Kou-San
authors.initials: KS
authors.lastname: Ju
authors.affiliation: Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Robert R
authors.initials: RR
authors.lastname: Haines
authors.affiliation: Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Konstantin A
authors.initials: KA
authors.lastname: Tchalukov
authors.affiliation: Bacterial Foodborne Pathogens and Mycology Research, US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, Illinois, USA.
authors.forename: David P
authors.initials: DP
authors.lastname: Labeda
authors.affiliation: 1] Department of Chemistry, Northwestern University, Evanston, Illinois, USA. [2] Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA. [3] Feinberg School of Medicine, Northwestern University, Evanston, Illinois, USA.
authors.forename: Neil L
authors.initials: NL
authors.lastname: Kelleher
authors.affiliation: 1] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: William W
authors.identifier: 0000000201820671
authors.initials: WW
authors.lastname: Metcalf
mesh_terms: D039903:Actinobacteria / Q000235:genetics* / Q000378:metabolism*; D001688:Biological Products / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism*; D055808:Drug Discovery / Q000379:methods*; D023281:Genomics; D055432:Metabolomics; D015394:Molecular Structure; D005810:Multigene Family / Q000235:genetics; D064210:Secondary Metabolism
chemical_list: D001688:Biological Products