title: Finding and analyzing plant metabolic gene clusters.
abstract: Plants produce an array of diverse secondary metabolites with important ecological functions, providing protection against pests, diseases, and abiotic stresses. Secondary metabolites are also a rich source of bioactive compounds for drug and agrochemical development. Despite the importance of these compounds, the metabolic diversity of plants remains largely unexploited, primarily due to the problems associated with mining large and complex genomes. It has recently emerged that genes for the synthesis of multiple major classes of plant-derived secondary metabolites (benzoxinones, diterpenes, triterpenes, and cyanogenic glycosides) are organized in clusters reminiscent of the metabolic gene clusters found in microbes. Many more secondary metabolic clusters are likely to emerge as the body of sequence information available for plants continues to grow, accelerated by high-throughput sequencing. Here, we describe approaches for the identification of secondary metabolic gene clusters in plants through forward and reverse genetics, map-based cloning, and genome mining and give examples of methods used for the analysis and functional confirmation of new clusters.
authors.affiliation: Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom. anne.osbourn@jic.ac.uk
authors.forename: Anne
authors.initials: A
authors.lastname: Osbourn
authors.forename: Kalliopi K
authors.initials: KK
authors.lastname: Papadopoulou
authors.forename: Xiaoquan
authors.initials: X
authors.lastname: Qi
authors.forename: Ben
authors.initials: B
authors.lastname: Field
authors.forename: Eva
authors.initials: E
authors.lastname: Wegel
mesh_terms: D018554:Avena / Q000235:genetics; D003001:Cloning, Molecular / Q000379:methods; D019295:Computational Biology; D055786:Gene Knockout Techniques; D017343:Genes, Plant; D008040:Genetic Linkage; D056426:Genetic Loci; D005822:Genetic Vectors / Q000235:genetics / Q000378:metabolism; D019751:Intramolecular Transferases / Q000235:genetics / Q000378:metabolism; D055442:Metabolome / Q000235:genetics*; D055432:Metabolomics / Q000379:methods; D005810:Multigene Family; D009154:Mutation; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D059386:Reverse Genetics / Q000379:methods; D012503:Saponins / Q000032:analysis* / Q000235:genetics / Q000378:metabolism; D013729:Terpenes / Q000032:analysis / Q000378:metabolism*; D015003:Yeasts / Q000235:genetics / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D012503:Saponins; D013729:Terpenes; D019751:Intramolecular Transferases; C039924:2,3-oxidosqualene-beta-amyrin-cyclase