Elementary Conversion Modes Unveil All Capabilities of Metabolic Networks

Abstract

The metabolic capabilities of cells determine their biotechnological potential, niches in multicellular host-organisms, fitness in ecosystems, and threat levels as a pathogen. Their comprehensive experimental characterisation is generally not feasible, in particular for unculturable and extremophile microorganisms. In principle, the full range of metabolic capabilities can be computed from an organism's annotated genome sequence using a metabolic network reconstruction. However, current computational methods cannot deal with genome-scale metabolic networks. Part of the problem is that these methods generally aim to enumerate all feasible metabolic pathways, while computation of all possible (elementally balanced) conversions between nutrients and products (elementary conversion modes, ECMs) would suffice. All the ECMs of a metabolic network capture its full metabolic capability. We have implemented ECM enumeration in ecmtool and illustrate its usage in several examples. This work contributes to the elucidation of the full metabolic footprint of any cell and provides an exhaustive list of its metabolic capabilities.