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Background  Studies on bacterial signal transduction systems have revealed complex networks of functional interactions, where the response regulators play a pivotal role. The AtoSC system of  E. coli  activates the expression of  atoDAEB  operon genes, and the subsequent catabolism of short-chain fatty acids, upon acetoacetate induction. Transcriptome and phenotypic analyses suggested that  atoSC  is also involved in several other cellular activities, although we have recently reported a palindromic repeat within the  atoDAEB  promoter as the single,  cis -regulatory binding site of the AtoC response regulator. In this work, we used a computational approach to explore the presence of yet unidentified AtoC binding sites within other parts of the  E. coli  genome.    Results  Through the implementation of a computational  de novo  motif detection workflow, a set of candidate motifs was generated, representing putative AtoC binding targets within the  E. coli  genome. In order to assess the biological relevance of the motifs and to select for experimental validation of those sequences related robustly with distinct cellular functions, we implemented a novel approach that applies Gene Ontology Term Analysis to the motif hits and selected those that were qualified through this procedure. The computational results were validated using Chromatin Immunoprecipitation assays to assess the  in vivo  binding of AtoC to the predicted sites. This process verified twenty-two additional AtoC binding sites, located not only within intergenic regions, but also within gene-encoding sequences.    Conclusions  This study, by tracing a number of putative AtoC binding sites, has indicated an AtoC-related cross-regulatory function. This highlights the significance of computational genome-wide approaches in elucidating complex patterns of bacterial cell regulation.

Escherichia coli genome-wide promoter analysis: Identification of additional AtoC binding target elements