VitisCyc: A Metabolic Pathway Database for Grapevine

A framework of grape-specific cellular metabolic networks is essential for the analysis of genome-scale expression data sets to develop comprehensive understanding of grape metabolism.  It can help in understanding how development, genetic diversity and changes in the plant’s environment relate to flavor, taste, aroma, and pathogen resistance. We have generated a model of a grape-specific pathway database called VitisCyc (VitisCyc: http://palea.cgrb.oregonstate.edu:1555/jaiswallab/vitiscyc.shtml) based on the sequenced genome of grape cultivar ‘Pinot Noir’ using Pathway tools software (http://bioinformatics.ai.sri.com/ptools/). Conceptually, VitisCyc is a network of predicted biochemical and transport reactions that are likely to occur within a grapevine cell.  VitisCyc harbors 54 super pathways, which include 376 biosynthesis pathways, 34 catabolic pathways, 8 detoxification pathways, 37 energy related and 7 transport pathways, which together represent 10,908 enzymes, 2098 enzymatic reactions, 31 transport reactions and 2035 compounds.  Researchers can search or browse VitisCyc for genes, enzymes, metabolites, and metabolic pathways.  The Omics-viewer tool, built within VitisCyc, allows researchers to upload and analyze high-throughput expression data sets in the context of metabolic pathways and the overall cellular metabolic network.  We look forward to introduce VitisCyc to Grape research community and to build collaborations for curation and further improvement of VitisCyc.