Lawrence Berkeley National Laboratory

The selective mechanisms operating in regulatory regions of bacterial genomes are poorly understood. In Escherichia coli, we have found that regulatory regions contain high densities of overlapping and probably competing promoter-like signals, in contrast to coding regions and regions located between convergently-transcribed genes. Functional promoter sites identified experimentally are often found in the subregions of highest density of signals, even when individual sites with higher binding affinity for RNA polymerase exist elsewhere within the region [Huerta & Collado-Vides 2003]. In order to explore whether this trend discovered in E. coli promoter regions is common in other bacterial species, we conducted similar analyses for a representative set containing 40 additional genomes belonging to different genera across all major bacterial phyla. This comparison is validated by the fact that RNAPs are evolutionarily conserved across all bacteria.