Genome-Scale Metabolic Reconstructions for Phylogeny?

Constraint-based modeling is a widely used and powerful methodology to assess the metabolic phenotypes and capabilities of an organism. Genome-scale metabolic models, based on the genome and including all reactions of the organism, are mostly created for that purpose. However, that does not cover their full potential.

Since all reactions are included in the models, it is possible to compare these models and thereby the species directly by creating a consolidated reconstruction of several organisms. This consolidated reconstruction including every reaction occurring at least once allows for identifying cross-organism wide conserved reactions, linked to a gene of the source-organism.

AutoKEGGRec is an automated tool that creates first draft reconstructions of single organisms, community and a consolidated reconstruction for a list of organisms or strains. AutoKEGGRec is developed in Matlab and works seamlessly with the COBRA Toolbox v3, and it is based on only using the KEGG database as external input. The first draft reconstructions consist of all reactions for a KEGG organism ID and corresponding linked genes. This provides a comprehensive starting point for further refinement and curation using the host of COBRA toolbox functions or other preferred tools. Furthermore, additional functionalities are provided, like the organisms-reaction-genes matrix allowing for advanced cross-organism reaction engineering.

Here, a consolidated model for organisms across Domains was created using the innovative capabilities of AutoKEGGRec. The metabolic reconstructions were used to create a phylogenetic tree of life based on the basis of the reaction networks. Both the direct gene sequence as well as the underlying protein sequence were used.

This tree of “metabolic networks” can be used to compare organisms focusing on the whole metabolome instead of using small parts of the DNA. Furthermore, it enlightens the metabolic engineering possibilities in between species throughout their maybe similar reactions for similar living environments in distinct points.