Lawrence Berkeley National Laboratory

Background: It has been shown that selection acts to remove the promoter's 10 and 35 consensus sequences in both coding and noncoding regions, implying that it is disadvantageous to maintain misplaced sites that can strongly bind ?70 and interfere with proper gene expression. Here we analyze 56 bacterial genomes and show that the numbers of nonconsensus, potential ?70 binding sites in both regulatory and non-regulatory noncoding regions deviate significantly from the random expectations when compensating for base composition, di- and tri-nucleotide bias in a majority of eubacteria. Not only do we expect that selection is maintaining high densities of potential ?70 binding sites in regulatory DNA, but that there is selection against these sites in non-regulatory DNA. The often overlapping binding sites inregulatory DNA likely confer some subtle survival advantage, even though experimental evidence suggests only one or a few of these sites are actual transcription initiation sites. Remarkably, we find that the degree of selection against potential ?70 binding sites in non-regulatory DNA correlates positively with rate of growth, adaptive codonbias and number of tRNA genes. This is evidence that the efficiency needed for faster growing bacteria can only be achieved by reducing spurious RNA polymerase binding to false sites, and that transcription and translation efficiencies are both optimized at a genome-wide level to permit faster growth.