PMN, A Unified Resource For Plant Metabolism

Plant metabolism is responsible for the majority of food, feed, and medicine production. However, despite the significant role that plant metabolism plays we still know very little about it. To better understand plant metabolism and facilitate enzyme/pathway discovery and metabolic engineering, we developed a comprehensive infrastructure through which known information about plant metabolism can be easily accessed and a sequenced genome can be annotated into enzymes, reactions and pathways with high quality. The infrastructure includes a machine-learning-based enzyme function prediction pipeline (E2P2), a pathway inference software (Pathway Tools, developed by SRI International), and a semi-automated pipeline for validating inferred pathways (SAVI). Using this infrastructure, we predicted the metabolic networks of 22 sequenced genomes in the green lineage (10 monocots, 9 eudicots, 2 lower plants and 1 green algal species). We have also developed an extensively curated pan-plant biochemical pathway database called PlantCyc that catalogs a comprehensive set of known plant biochemical pathways involved in primary and specialized metabolism. Major data types in all databases include pathway diagrams and summaries, reaction equations, compound chemical structures, and enzyme properties. Evidence codes along with references are attached to pathways and enzymes for quality assurance. The databases we generated are available online at the Plant Metabolic Network (PMN) website (www.plantcyc.org). Tools provided at our web site allow users to display and examine large scale “omics” data in a metabolic context, to compare pathways between species, and to BLAST against specific enzyme datasets.