Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes

Toward the goal of identifying complete sets of transcription factor (TF)-b inding sites in the genomes of several gamma proteobacteria, and hence desc ribing their transcription regulatory networks, we present a phylogenetic f ootprinting method for identifying these sites. Probable transcription regu latory sites upstream of Escherichia coli genes were identified by cross-sp ecies comparison using an extended Gibbs sampling algorithm. Close examinat ion of a study set of 184 genes with documented transcription regulatory si tes revealed that when orthologous data were available from at least two ot her gamma proteobacterial species, 81% of our predictions corresponded with the documented sites, and 67% corresponded when data from only one other s pecies were available, That the remaining predictions included bona fide TF -binding sites was proven by affinity purification of a putative transcript ion factor (YijC) bound to such a site upstream of the fabA gene. Predicted regulatory sites for 2097 E.coli genes are available at http://www.wadswor th.org/resnres/bioinfo/.