Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs.
BACKGROUND
In bacteria, sigma factors and other transcriptional regulatory proteins recognize DNA patterns upstream of their target genes and interact with RNA polymerase to control transcription. As a consequence of evolution, DNA sequences recognized by transcription factors are thought to be enriched in intergenic regions (IRs) and depleted from coding regions of prokaryotic genomes.


RESULTS
In this work, we report that genomic distribution of transcription factors binding sites is biased towards IRs, and that this bias is conserved amongst bacterial species. We further take advantage of this observation to develop an algorithm that can efficiently identify promoter boxes by a distribution-dependent approach rather than a direct sequence comparison approach. This strategy, which can easily be combined with other methodologies, allowed the identification of promoter sequences in ten species and can be used with any annotated bacterial genome, with results that rival with current methodologies. Experimental validations of predicted promoters also support our approach.


CONCLUSIONS
Considering that complete genomic sequences of over 1000 bacteria will soon be available and that little transcriptional information is available for most of them, our algorithm constitutes a promising tool for the prediction of promoter sequences. Importantly, our methodology could also be adapted to identify DNA sequences recognized by other regulatory proteins.
Jacques
Pierre-Etienne
PE
Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada. Pierre-Etienne.Jacques@USherbrooke.ca
Rodrigue
Sébastien
S
Gaudreau
Luc
L
Goulet
Jean
J
Brzezinski
Ryszard
R
D000465:Algorithms; D001483:Base Sequence; D016680:Genome, Bacterial / Q000235:genetics*; D008969:Molecular Sequence Data; D039662:Prokaryotic Initiation Factors / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017421:Sequence Analysis / Q000379:methods; D014158:Transcription, Genetic / Q000235:genetics
D039662:Prokaryotic Initiation Factors