Transcription Factor Profiling of Escherichia coli

      The bacterial genome is transcribed by a single species of DNA-dependent RNA polymerase (RNAP). The gene selectivity of RNAP is, however, modulated after interaction with two groups of the regulatory protein, the sigma factor with promoter recognition activity and the transcription factor (TF) that controls the activity and specificity of RNAP holoenzyme (1,2). In order to understand the molecular mechanisms underlying transcription regulation of the genome as a whole, the identification of regulation targets of all sigma factors and all TFs and the regulatory mode of each sigma and each TF are absolutely necessary. Towards this ultimate purpose, we have performed several lines of research using Escherichia coli K-12 as a model organism, including that: 1) Genomic SELEX screening of regulation target promoters, genes and operons under the control of each sigma factor and each TF (3); 2) PS(promoter-specific)-TF screening for identification of the whole set of TFs involved in regulation of each promoter (4); 3) determination of intracellular levels of all sigma factors and all TFs under various growth phases and various culture conditions (5).

     For enhance the research of genome-wide regulation in E. coli, we decided to share all these accumulated data sets with a variety of research communities. For this purpose, we developed a novel database “Transcription Profiling of Escherichia coli” (TEC) and to make it open to the public (6). In this first edition of TEC, we included a set of SELEX-chip screening of regulatory targets of a total of 116 TFs in the absence and presence of effector ligands, altogether a total of 156 SELEX data. The SELEX research was performed by a research group, headed by Akira ISHIHAMA (Hosei University, Tokyo, Japan), including a number of teams as listed in the list of project organization.
     The most important and unique aspect of this genome-wide research is that all experiments were performed using a single E. coli strain, the same experimental protocols with use of the same set of resources, and in the same research group. At present, this care is particularly important because the heterogeneity in genetic, metabolic and regulatory grounds even between the same E. coli strains but from different laboratories is widely accepted, raising a risk alarm of misunderstanding and incorrect prediction with use of experimental data obtained using different laboratories.
     Details of SELEX screening of individual TFs will be described in publications from each team [Note that some of the SELEX results have already been published as listed in the publication list]. TEC could be effectively used in conjunction with PEC (Profile of Escherichia coli) database.

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