title: A genomics-guided approach for discovering and expressing cryptic metabolic pathways.
abstract: Genome analysis of actinomycetes has revealed the presence of numerous cryptic gene clusters encoding putative natural products. These loci remain dormant until appropriate chemical or physical signals induce their expression. Here we demonstrate the use of a high-throughput genome scanning method to detect and analyze gene clusters involved in natural-product biosynthesis. This method was applied to uncover biosynthetic pathways encoding enediyne antitumor antibiotics in a variety of actinomycetes. Comparative analysis of five biosynthetic loci representative of the major structural classes of enediynes reveals the presence of a conserved cassette of five genes that includes a novel family of polyketide synthase (PKS). The enediyne PKS (PKSE) is proposed to be involved in the formation of the highly reactive chromophore ring structure (or "warhead") found in all enediynes. Genome scanning analysis indicates that the enediyne warhead cassette is widely dispersed among actinomycetes. We show that selective growth conditions can induce the expression of these loci, suggesting that the range of enediyne natural products may be much greater than previously thought. This technology can be used to increase the scope and diversity of natural-product discovery.
authors.affiliation: Ecopia BioSciences, Inc., 7290 Frederick Banting, Montreal, Quebec H4S 2A1, Canada.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Zazopoulos
authors.forename: Kexue
authors.initials: K
authors.lastname: Huang
authors.forename: Alfredo
authors.initials: A
authors.lastname: Staffa
authors.forename: Wen
authors.initials: W
authors.lastname: Liu
authors.forename: Brian O
authors.initials: BO
authors.lastname: Bachmann
authors.forename: Koichi
authors.initials: K
authors.lastname: Nonaka
authors.forename: Joachim
authors.initials: J
authors.lastname: Ahlert
authors.forename: Jon S
authors.initials: JS
authors.lastname: Thorson
authors.forename: Ben
authors.initials: B
authors.lastname: Shen
authors.forename: Chris M
authors.initials: CM
authors.lastname: Farnet
mesh_terms: D039903:Actinobacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D000475:Alkenes / Q000378:metabolism*; D000480:Alkynes / Q000378:metabolism*; D002478:Cells, Cultured; D004734:Energy Metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D008847:Micromonospora / Q000145:classification / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D009097:Multienzyme Complexes / Q000235:genetics* / Q000378:metabolism*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity; D013302:Streptomyces / Q000145:classification / Q000235:genetics / Q000378:metabolism
chemical_list: D000475:Alkenes; D000480:Alkynes; D009097:Multienzyme Complexes