title: A Workflow for Studying Specialized Metabolism in Nonmodel Eukaryotic Organisms.
abstract: Eukaryotes contain a diverse tapestry of specialized metabolites, many of which are of significant pharmaceutical and industrial importance to humans. Nevertheless, exploration of specialized metabolic pathways underlying specific chemical traits in nonmodel eukaryotic organisms has been technically challenging and historically lagged behind that of the bacterial systems. Recent advances in genomics, metabolomics, phylogenomics, and synthetic biology now enable a new workflow for interrogating unknown specialized metabolic systems in nonmodel eukaryotic hosts with greater efficiency and mechanistic depth. This chapter delineates such workflow by providing a collection of state-of-the-art approaches and tools, ranging from multiomics-guided candidate gene identification to in vitro and in vivo functional and structural characterization of specialized metabolic enzymes. As already demonstrated by several recent studies, this new workflow opens up a gateway into the largely untapped world of natural product biochemistry in eukaryotes.
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA, United States.
authors.forename: M P
authors.initials: MP
authors.lastname: Torrens-Spence
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA, United States; Massachusetts Institute of Technology, Cambridge, MA, United States.
authors.forename: T R
authors.initials: TR
authors.lastname: Fallon
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA, United States; Massachusetts Institute of Technology, Cambridge, MA, United States. Electronic address: wengj@wi.mit.edu.
authors.forename: J K
authors.initials: JK
authors.lastname: Weng
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D006801:Humans; D060847:Metabolic Engineering / Q000379:methods; D053858:Metabolic Networks and Pathways; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D058615:Synthetic Biology; D014026:Nicotiana / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome; D057188:Workflow
keywords: Biosynthesis; Eukaryote; Metabolic engineering; Metabolic evolution; Metabolomics; Natural product; Nonmodel species; Pathway discovery; Specialized metabolism; Transcriptomics