CathaCyc, a metabolic pathway database built from catharanthus roseus RNA-seq data

A. Van Moerkercke, M. Fabris, J. Pollier, G.J.E. Baart, S. Rombauts, G. Hasnain, Heiko Rischer, J. Memelink, Kirsi-Marja Oksman-Caldentey, A. Goossens (Corresponding Author)

Research output: Contribution to journalArticleScientificpeer-review

74 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)673-685
Number of pages13
JournalPlant and Cell Physiology
Volume54
Issue number5
DOIs
Publication statusPublished - 2013
MoE publication typeA1 Journal article-refereed

Fingerprint

Catharanthus
Catharanthus roseus
Secologanin Tryptamine Alkaloids
Metabolic Networks and Pathways
indole alkaloids
terpenoids
biochemical pathways
Databases
RNA
medicinal plants
Medicinal Plants
triterpenoids
vinblastine
vincristine
metabolism
Genome
genome
Secondary Metabolism
antineoplastic agents
enzymes

Keywords

  • biocyc
  • catharanthus roseus
  • deep sequencing
  • madagascar periwinkle
  • metabolism
  • transcriptome

Cite this

Van Moerkercke, A., Fabris, M., Pollier, J., Baart, G. J. E., Rombauts, S., Hasnain, G., ... Goossens, A. (2013). CathaCyc, a metabolic pathway database built from catharanthus roseus RNA-seq data. Plant and Cell Physiology, 54(5), 673-685. https://doi.org/10.1093/pcp/pct039
Van Moerkercke, A. ; Fabris, M. ; Pollier, J. ; Baart, G.J.E. ; Rombauts, S. ; Hasnain, G. ; Rischer, Heiko ; Memelink, J. ; Oksman-Caldentey, Kirsi-Marja ; Goossens, A. / CathaCyc, a metabolic pathway database built from catharanthus roseus RNA-seq data. In: Plant and Cell Physiology. 2013 ; Vol. 54, No. 5. pp. 673-685.
@article{cb4854cbe0fa449f90dc7c6d7153a49a,
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.",
keywords = "biocyc, catharanthus roseus, deep sequencing, madagascar periwinkle, metabolism, transcriptome",
author = "{Van Moerkercke}, A. and M. Fabris and J. Pollier and G.J.E. Baart and S. Rombauts and G. Hasnain and Heiko Rischer and J. Memelink and Kirsi-Marja Oksman-Caldentey and A. Goossens",
year = "2013",
doi = "10.1093/pcp/pct039",
language = "English",
volume = "54",
pages = "673--685",
journal = "Plant and Cell Physiology",
issn = "0032-0781",
publisher = "Oxford University Press",
number = "5",

}

Van Moerkercke, A, Fabris, M, Pollier, J, Baart, GJE, Rombauts, S, Hasnain, G, Rischer, H, Memelink, J, Oksman-Caldentey, K-M & Goossens, A 2013, 'CathaCyc, a metabolic pathway database built from catharanthus roseus RNA-seq data', Plant and Cell Physiology, vol. 54, no. 5, pp. 673-685. https://doi.org/10.1093/pcp/pct039

CathaCyc, a metabolic pathway database built from catharanthus roseus RNA-seq data. / Van Moerkercke, A.; Fabris, M.; Pollier, J.; Baart, G.J.E.; Rombauts, S.; Hasnain, G.; Rischer, Heiko; Memelink, J.; Oksman-Caldentey, Kirsi-Marja; Goossens, A. (Corresponding Author).

In: Plant and Cell Physiology, Vol. 54, No. 5, 2013, p. 673-685.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - CathaCyc, a metabolic pathway database built from catharanthus roseus RNA-seq data

AU - Van Moerkercke, A.

AU - Fabris, M.

AU - Pollier, J.

AU - Baart, G.J.E.

AU - Rombauts, S.

AU - Hasnain, G.

AU - Rischer, Heiko

AU - Memelink, J.

AU - Oksman-Caldentey, Kirsi-Marja

AU - Goossens, A.

PY - 2013

Y1 - 2013

N2 - 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.

AB - 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.

KW - biocyc

KW - catharanthus roseus

KW - deep sequencing

KW - madagascar periwinkle

KW - metabolism

KW - transcriptome

U2 - 10.1093/pcp/pct039

DO - 10.1093/pcp/pct039

M3 - Article

VL - 54

SP - 673

EP - 685

JO - Plant and Cell Physiology

JF - Plant and Cell Physiology

SN - 0032-0781

IS - 5

ER -

Van Moerkercke A, Fabris M, Pollier J, Baart GJE, Rombauts S, Hasnain G et al. CathaCyc, a metabolic pathway database built from catharanthus roseus RNA-seq data. Plant and Cell Physiology. 2013;54(5):673-685. https://doi.org/10.1093/pcp/pct039