Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models
Fig 2
Building a parasite knowledgebase.
Genetic data (from EuPathDB), orthology information (from EuPathDB’s OrthoMCL), and biochemical data from metabolomics studies (acquired from a literature review) were used to build our reconstructions in a multistep process; gene essentiality data was used to evaluate resultant models. (A): Reconstruction pipeline. First, de novo reconstructions are built from annotated genomes and supplemented with KEGG reaction-associated genes on the database (see Additional Information: Online Methods). Next, we curated an existing manually curated reconstruction for P. falciparum 3D7. Third, we mapped orthologous genes so that (fourth) we could add all metabolic functions from our curated iPfal22 into the de novo reconstruction by transforming each gene-protein-reaction rule via orthology. Lastly, we performed automated curation by gapfilling reconstructions to known metabolic capabilities and to generate biomass. With the resulting reconstruction, we can compare simulations to experimental data such as gene essentiality screens. (B): Considering compartmentalization. Our approach moves a large proportion of the reconstruction’s reactions from compartments in a biochemical database to biologically-relevant compartments (e.g. periplasm to extracellular). Thus, our de novo reconstruction approach accounts for compartmentalization, unlike many previous metabolic network reconstruction pipelines. Each model is represented by a point. Boxplots for each database denote the interquartile range with the median value at center; whiskers extend to 1.5 times the inter-quartile range (i.e. distance between the first and third quartiles) above or below the median. (C): Orthology adds information. Orthology-based curation improves reconstruction scope regarding total number of genes and reactions. These semi-curated reconstructions (each labeled dark point) are larger in scope due to the addition of reactions associated with genes added via orthologous-transformation. Semi-curated reconstructions are connected via a line to the draft uncurated reconstruction for that genome. Reconstructions are named by the associated species; Plasmodium species are labeled with species name. Light colored dots represent previously published Plasmodium reconstructions (iPfal22, from [57] and [47], iPfa2017 from [49], iPbe-blood and iPbe-liver from [58], all others from [48]). (D): Prediction accuracy. Semi-curated reconstructions (diamonds) recapitulate the biology of experimentally-facile parasites as well as published, manually-curated reconstructions (circles). We tested accuracy of model predictions from the de novo reconstruction (triangle) and the final orthology-translated and semi-curated reconstruction (diamond) for P. berghei and compared these summary statistics to the prediction accuracy generated by our well-curated iPfal22 and other previously published reconstructions [48–50,58,59]. This comparison was used to motivate our approach over de novo reconstruction building as our pipeline generates a reconstruction with greater predictive accuracy than de novo reconstruction and comparable to a well-curated reconstruction.