KBase Metabolic Modeling with Sphagnum

Over the past two decades, progress in the development of in silico metabolic reconstructions of organisms has enabled researchers to explore the complex relationship between genotype and phenotype. PlantSEED was developed as a collaboration between teams at Argonne National Laboratory and the University of Florida utilizing plant-specific databases to create an intensively curated set of primary metabolic pathways that can be used in constructing metabolic models for various plant species. The data used in this work is readily available in the Department of Energy (DOE) Systems Biology Knowledgebase (KBase; http://kbase.us).  KBase is a software and data environment designed to enable researchers to collaboratively generate, test, and share new hypotheses about gene and protein functions; perform large-scale analyses on a scalable computing infrastructure; and model interactions in microbes, plants and their communities.

We show that we can use the data and functions available through KBase to generate a metabolic reconstruction of several transcriptomes of Sphagnum sequenced by the DOE Joint Genome Institute.  We will describe several aspects of the Sphagnum metabolic model, show that it can be merged with a metabolic model of a cyanobacterium that performs nitrogen fixation, and examine the metabolic interactions between the two species.