Comprehensive analysis for the recognition sequences of DNA-binding transcription factors within the E. coli genome using the newly developed "Promoter Chip"

Escherichia coli adapts to changes in external environment by selective transcription of a total of about 4,400 genes on its genome. In each case of the adaptation, the expression of a specific set of stress-response genes is controlled mainly at the step of transcription initiation by selective recognition of the promoters by the RNA polymerase. The RNA polymerase core enzyme binds to one of seven sigma factors to form the holoezyme, which recognizes a specific promoter. Furthermore, the promoter recognition of RNA polymerase is modulated by DNA-binding transcription factors. From E. coli K-12 genome sequence, a total of about 300 species of transcription factor are predicted. In order to understand the global regulation of E. coli genome, it is essential to identify the set of promoter recognized by each of all these transcription factors. We have developed a Promoter Array system using a novel DNA microarray, "Promoter Chip", on which 1,000 species of E. coli promoter fragments amplified by PCR were spotted. This system was found to be a powerful technology to identify the target promoters recognized by DNA-binding transcription factors.