Figure 5.

The future of the E. coli GEM. The most widely used E. coli reconstruction accounts only for metabolism (the ‘M’ matrix) (Feist et al, 2009). However, efforts are currently underway to integrate the operon structure that determines cellular regulation (the ‘O’ matrix), the transcriptional and translational machinery allowing for the expression of proteins (the ‘E’ matrix; Thiele et al, 2009) and other cellular processes (e.g., DNA replication, posttranslational modifications, etc.) with metabolism. The integration of these cellular processes, supported by high-throughput data types, into a single mathematical model, will allow researchers to more accurately compute complex phenotypes, and will guide the discovery of unknown aspects of cellular functions beyond that of just metabolism.