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

Abstract

BackgroundStudies 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.ResultsThrough 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.ConclusionsThis 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.

Involvement of AtoSC two-component system in Escherichia coli flagellar regulon

“…A recent genome-wide analysis has revealed additional putative AtoC-binding sites except its established atoDAEB promoter within E. coli genome, including amongst others the fliA promoter (Pilalis et al 2011). The in vivo AtoC-binding was verified for 22 of those targets, located not only within intergenic promoters regions, but also within gene-encoding sequences, including the fliA promoter (Pilalis et al 2011). Recent studies have revealed that the flhDC operon can be expressed either by the established r 70 -dependent transcription or by a newly identified r 54 -dependent transcription (Zhao et al 2010).…”

“…AtoC RR belongs in the r 54 -RNA polymerase activators family . A recent genome-wide analysis has revealed additional putative AtoC-binding sites except its established atoDAEB promoter within E. coli genome, including amongst others the fliA promoter (Pilalis et al 2011). The in vivo AtoC-binding was verified for 22 of those targets, located not only within intergenic promoters regions, but also within gene-encoding sequences, including the fliA promoter (Pilalis et al 2011).…”

“…-mediated manner (Theodorou et al 2009). The emergent complexity of possible AtoSC-related regulatory networks are underlined by a recent E. coli genome-wide promoter analysis revealing new AtoC binding sites in additional potential downstream targets of AtoSC TCS (Pilalis et al 2011). The expression of AtoSC in some pathogenic E. coli strains as well as other pathogenic bacteria, led very recently to identification of three inhibitors of the AtoSC signalling, belonging to different chemical classes, i.e.…”

Genome-wide motif predictions of BCARR-box in the amino-acid repressed genes of Lactobacillus helveticus CM4

“…Various approaches have been introduced in various bacterial gene expressions to study global regulatory genes. Specific DNA sequences for regulatory protein biding have been searched for genome-wide in Escherichia coli [ 15 ], Sulfolobus acidophilus [ 16 ], Bacillus anthracis [ 17 ], Bacillus subtilis [ 19 , 21 , 31 – 34 ], Clostridium difficile [ 35 ], L. lactis [ 18 , 36 , 37 ] and Streptococcus thermophilus [ 38 ]. Homologous sequences to the Cre-box sequence were searched for in the whole Bacillus genome and mapped on the genome, and the consensus sequence was newly deduced [ 33 ].…”

“…Genome-wide search is a powerful tool to understand the contribution of the regulatory system in specific gene expressions in response to some metabolites [ 15 – 19 ]. In the present study, we searched the BCARR-box previously predicted from six kinds of proteolytic genes which were down-regulated in response to amino acids in CM4 [ 10 ].…”