Transcription Factor Profiling of Escherichia coli

      Prediction of regulation targets of the sigma factors and the transcription factors (TFs) was performed using the improved method of Genomic SELEX (ref 1). Both sigma factors and TFs used in this SELEX screening were expressed and purified on the basis of the genome sequence of E. coli K-12 W3110. For mapping of their binding sites, a DNA tilling array was used, which was constructed using the genome DNA from E. coli K-12 MG1655. The complete genome sequence was determined for MG1655 by US group (ref 2) and W3110 by Japan group (ref 3). Both MG1655 and W3110 are descendants of K-12 W1485 and the whole set of genes on the genome is highly conserved between two strains except for one big-size inversion in W3110 (refs 3 and 4). The prediction of regulation targets determined by the Genomic SELEX screening can be applied for both W3110 and MG1655, and thus depending on the research purpose, both strains can be used for detailed analysis of regulation for each regulatory protein.