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Understanding the regulation and control of the expression of genes encoding metabolic enzymes is crucial for production using microbes. To overcome technical difficulties involved in identifying regulatory network systems, we designed a DNA motif finding procedure combining transcriptome and genome sequence data. Here, we used the ArcAB two-component system of Escherichia coli, which controls genes involved in the TCA cycle and energy metabolism, as a model to identify DNA motifs involved in gene-expression regulation. DNA-array data were used to extract up-regulated genes from ΔarcA and ΔarcB E. coli strains, and the upstream sequences were subjected to DNA-motif finding.
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