Systems Biotechnology: Combined in Silico and Omics Analyses for the Improvement of Microorganisms for Industrial Applications - Systems Biology: Networks, Models, and Applications - page 219

Figure 7.12 Procedures for strain improvement combined with in silico
prediction. Step 1: Comparative analysis of two bacterial genomes, E. coli and
M. succiniciproducens, was conducted to select knockout gene candidates for the
subsequent in silico perturbation. Step 2: In silico experiments were then
carried out by means of constraints-based flux analysis, suggesting target genes
for the overproduction of succinic acids. Step 3: Combinatorial gene knockout
experiments were carried out within the suggested candidate genes, and
experimental data were obtained by actual cultivation. Finally, an engineered
strain for the enhanced succinic acid production could be successfully
designed.
Step 1: Comparative genomics for specifying candidate genes. Recently,
the full genome sequence of M. succiniciproducens MBEL55E, and the
genome-scale metabolic characteristics leading to high-level succinic acid
productions, were published [38]. In this step, comparative genome
analysis of this succinic acid-producing strain, M. succiniciproducens , and
E. coli was conducted to select gene candidates for strain improvement.