Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes.
Toward the goal of identifying complete sets of transcription factor (TF)-binding sites in the genomes of several gamma proteobacteria, and hence describing their transcription regulatory networks, we present a phylogenetic footprinting method for identifying these sites. Probable transcription regulatory sites upstream of Escherichia coli genes were identified by cross-species comparison using an extended Gibbs sampling algorithm. Close examination of a study set of 184 genes with documented transcription regulatory sites revealed that when orthologous data were available from at least two other gamma proteobacterial species, 81% of our predictions corresponded with the documented sites, and 67% corresponded when data from only one other species were available. That the remaining predictions included bona fide TF-binding sites was proven by affinity purification of a putative transcription 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.wadsworth.org/resnres/bioinfo/.
McCue
L
L
The Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany, NY 12201, USA.
Thompson
W
W
Carmack
C
C
Ryan
M P
MP
Liu
J S
JS
Derbyshire
V
V
Lawrence
C E
CE
D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D016208:Databases, Factual; D004926:Escherichia coli / Q000235:genetics; D020563:Gammaproteobacteria / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D010802:Phylogeny; D011485:Protein Binding; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D014157:Transcription Factors / Q000378:metabolism
D004269:DNA, Bacterial; D014157:Transcription Factors