title: CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data.
abstract: The medicinal plant Madagascar periwinkle (Catharanthus roseus) synthesizes numerous terpenoid indole alkaloids (TIAs), such as the anticancer drugs vinblastine and vincristine. The TIA pathway operates in a complex metabolic network that steers plant growth and survival. Pathway databases and metabolic networks reconstructed from 'omics' sequence data can help to discover missing enzymes, study metabolic pathway evolution and, ultimately, engineer metabolic pathways. To date, such databases have mainly been built for model plant species with sequenced genomes. Although genome sequence data are not available for most medicinal plant species, next-generation sequencing is now extensively employed to create comprehensive medicinal plant transcriptome sequence resources. Here we report on the construction of CathaCyc, a detailed metabolic pathway database, from C. roseus RNA-Seq data sets. CathaCyc (version 1.0) contains 390 pathways with 1,347 assigned enzymes and spans primary and secondary metabolism. Curation of the pathways linked with the synthesis of TIAs and triterpenoids, their primary metabolic precursors, and their elicitors, the jasmonate hormones, demonstrated that RNA-Seq resources are suitable for the construction of pathway databases. CathaCyc is accessible online (http://www.cathacyc.org) and offers a range of tools for the visualization and analysis of metabolic networks and 'omics' data. Overlay with expression data from publicly available RNA-Seq resources demonstrated that two well-characterized C. roseus terpenoid pathways, those of TIAs and triterpenoids, are subject to distinct regulation by both developmental and environmental cues. We anticipate that databases such as CathaCyc will become key to the study and exploitation of the metabolism of medicinal plants.
authors.affiliation: Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium.
authors.forename: Alex
authors.initials: A
authors.lastname: Van Moerkercke
authors.forename: Michele
authors.initials: M
authors.lastname: Fabris
authors.forename: Jacob
authors.initials: J
authors.lastname: Pollier
authors.forename: Gino J E
authors.initials: GJ
authors.lastname: Baart
authors.forename: Stephane
authors.initials: S
authors.lastname: Rombauts
authors.forename: Ghulam
authors.initials: G
authors.lastname: Hasnain
authors.forename: Heiko
authors.initials: H
authors.lastname: Rischer
authors.forename: Johan
authors.initials: J
authors.lastname: Memelink
authors.forename: Kirsi-Marja
authors.initials: KM
authors.lastname: Oksman-Caldentey
authors.forename: Alain
authors.initials: A
authors.lastname: Goossens
mesh_terms: D030008:Catharanthus / Q000235:genetics / Q000378:metabolism*; D016000:Cluster Analysis; D003517:Cyclopentanes / Q000378:metabolism; D019992:Databases as Topic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053858:Metabolic Networks and Pathways / Q000235:genetics; D058977:Molecular Sequence Annotation; D054883:Oxylipins / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism*; D046948:Secologanin Tryptamine Alkaloids / Q000737:chemistry / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics
chemical_list: D003517:Cyclopentanes; D054883:Oxylipins; D018749:RNA, Plant; D046948:Secologanin Tryptamine Alkaloids; C011006:jasmonic acid
keywords: BioCyc; Catharanthus roseus; Deep sequencing; Madagascar periwinkle; Metabolism; Transcriptome