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CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data

Van Moerkercke, Alex LU ; Fabris, Michele; Pollier, Jacob; Baart, Gino J E; Rombauts, Stephane; Hasnain, Ghulam; Rischer, Heiko; Memelink, Johan; Oksman-Caldentey, Kirsi-Marja and Goossens, Alain (2013) In Plant and Cell Physiology 54(5). p.673-685
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... (More)

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.

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keywords
Catharanthus, Cluster Analysis, Cyclopentanes, Databases as Topic, Gene Expression Profiling, Gene Expression Regulation, Plant, Metabolic Networks and Pathways, Molecular Sequence Annotation, Oxylipins, RNA, Plant, Secologanin Tryptamine Alkaloids, Sequence Analysis, RNA, Transcriptome, Journal Article, Research Support, Non-U.S. Gov't
in
Plant and Cell Physiology
volume
54
issue
5
pages
13 pages
publisher
Oxford University Press
external identifiers
  • scopus:84877978998
ISSN
1471-9053
DOI
10.1093/pcp/pct039
language
English
LU publication?
no
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8501c616-d43d-411d-9805-bf772c16b38f
date added to LUP
2017-11-06 11:31:02
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2019-09-26 03:58:52
@article{8501c616-d43d-411d-9805-bf772c16b38f,
  abstract     = {<p>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.</p>},
  author       = {Van Moerkercke, Alex and Fabris, Michele and Pollier, Jacob and Baart, Gino J E and Rombauts, Stephane and Hasnain, Ghulam and Rischer, Heiko and Memelink, Johan and Oksman-Caldentey, Kirsi-Marja and Goossens, Alain},
  issn         = {1471-9053},
  keyword      = {Catharanthus,Cluster Analysis,Cyclopentanes,Databases as Topic,Gene Expression Profiling,Gene Expression Regulation, Plant,Metabolic Networks and Pathways,Molecular Sequence Annotation,Oxylipins,RNA, Plant,Secologanin Tryptamine Alkaloids,Sequence Analysis, RNA,Transcriptome,Journal Article,Research Support, Non-U.S. Gov't},
  language     = {eng},
  number       = {5},
  pages        = {673--685},
  publisher    = {Oxford University Press},
  series       = {Plant and Cell Physiology},
  title        = {CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data},
  url          = {http://dx.doi.org/10.1093/pcp/pct039},
  volume       = {54},
  year         = {2013},
}