Plant Reactome Knowledgebase: A Resource for Plant Synthetic Biology

In-silico systems-level pathway knowledgebases are key reference resources that provide conceptual frameworks for plant biologists aiming to design, model, and test synthetic metabolic pathways in plants. Plant Reactome (https://plantreactome.gramene.org) is an open-source, free-of-cost pathway portal of the Gramene project (www.gramene.org). Plant Reactome features plant metabolic, signaling, transport, genetic, regulatory, developmental, and stress-response pathways for 106 plant species, from unicellular photoautotrophs to higher plants. We utilize a combinatorial approach involving manual curation of reference pathways and automated gene orthology-based projection to rapidly scale up pathway knowledge from reference species rice (Oryza sativa) to all other species. Pathway clustering across the broad phylogenetic spectrum of photosynthetic organisms shows distinct gene-pathway association patterns reflecting evolutionary history and ploidy levels. When combined with gene homology, gene family, gene expression data, researchers can compare reference rice pathways with the projected pathways from any hosted plant species to discover species-specific pathway enrichment, regulatory events, and loss/gain of reactions. In addition, they can query how paralogs and orthologs diversity in function, phenotype and gene expression thereby providing necessary clues and hypotheses for building potential pathway engineering and synthetic biology strategies for the improvement the structure, function and physiology of plants. The tools developed by us allow users to upload their data for pathway analysis, visualization, and integration of gene-gene interactions. The Plant Reactome pathway data is provided by us in various standardized formats via an embeddable widget, web services, and other download mechanisms for integration in external resources. The Plant Reactome is funded by the NSF (IOS-1127112), the NIH (U41 HG003751), ENFIN (LSHG-CT-2005-518254), the Ontario Research Fund, the EBI Industry Programme and the USDA-ARS.