A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress Public Deposited

http://ir.library.oregonstate.edu/concern/defaults/n009w6157

This is the publisher’s final pdf. The published article is copyrighted by Springer and can be found at:  http://www.springer.com/?SGWID=0-102-0-0-0.

Descriptions

Attribute NameValues
Creator
Abstract or Summary
  • Background: Functional annotations of large plant genome projects mostly provide information on gene function and gene families based on the presence of protein domains and gene homology, but not necessarily in association with gene expression or metabolic and regulatory networks. These additional annotations are necessary to understand the physiology, development and adaptation of a plant and its interaction with the environment. Results: RiceCyc is a metabolic pathway networks database for rice. It is a snapshot of the substrates, metabolites, enzymes, reactions and pathways of primary and intermediary metabolism in rice. RiceCyc version 3.3 features 316 pathways and 6,643 peptide-coding genes mapped to 2,103 enzyme-catalyzed and 87 protein-mediated transport reactions. The initial functional annotations of rice genes with InterPro, Gene Ontology, MetaCyc, and Enzyme Commission (EC) numbers were enriched with annotations provided by KEGG and Gramene databases. The pathway inferences and the network diagrams were first predicted based on MetaCyc reference networks and plant pathways from the Plant Metabolic Network, using the Pathologic module of Pathway Tools. This was enriched by manually adding metabolic pathways and gene functions specifically reported for rice. The RiceCyc database is hierarchically browsable from pathway diagrams to the associated genes, metabolites and chemical structures. Through the integrated tool OMICs Viewer, users can upload transcriptomic, proteomic and metabolomic data to visualize expression patterns in a virtual cell. RiceCyc, along with additional species-specific pathway databases hosted in the Gramene project, facilitates comparative pathway analysis. Conclusions: Here we describe the RiceCyc network development and discuss its contribution to rice genome annotations. As a case study to demonstrate the use of RiceCyc network as a discovery environment we carried out an integrated bioinformatic analysis of rice metabolic genes that are differentially regulated under diurnal photoperiod and biotic stress treatments. The analysis of publicly available rice transcriptome datasets led to the hypothesis that the complete tryptophan biosynthesis and its dependent metabolic pathways including serotonin biosynthesis are induced by taxonomically diverse pathogens while also being under diurnal regulation. The RiceCyc database is available online for free access at http://www.gramene.org/pathway/.
License
Resource Type
DOI
Date Available
Date Issued
Citation
  • Dharmawardhana, P., Ren, L., Amarasinghe, V., Monaco, M., Thomason, J., Ravenscroft, D., . . . Jaiswal, P. (2013). A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. Rice, 6(1), 1-15. doi:10.1186/1939-8433-6-15
Academic Affiliation
Series
Keyword
Rights Statement
Funding Statement (additional comments about funding)
Publisher
Peer Reviewed
Language
Replaces
Additional Information
  • description.provenance : Approved for entry into archive by Deborah Campbell(deborah.campbell@oregonstate.edu) on 2013-08-06T16:06:54Z (GMT) No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) DharmawardhanaPalithaBotanyPlantPathologyGenomeScaleMetabolic.pdf: 3444487 bytes, checksum: f2f43eac804af87645e31bfc323e56c2 (MD5)
  • description.provenance : Made available in DSpace on 2013-08-06T16:06:54Z (GMT). No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) DharmawardhanaPalithaBotanyPlantPathologyGenomeScaleMetabolic.pdf: 3444487 bytes, checksum: f2f43eac804af87645e31bfc323e56c2 (MD5) Previous issue date: 2013
  • description.provenance : Submitted by Deborah Campbell (deborah.campbell@oregonstate.edu) on 2013-08-06T15:44:02Z No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) DharmawardhanaPalithaBotanyPlantPathologyGenomeScaleMetabolic.pdf: 3444487 bytes, checksum: f2f43eac804af87645e31bfc323e56c2 (MD5)

Relationships

Parents:

This work has no parents.

Last modified

Downloadable Content

Download PDF

Items