Molecular Biology and Evolution 23(5) , 997-1010 (May 2006)
The selective mechanisms operating in regulatory regions of bacterial genomes are poorly understood. We have previously shown that, in most bacterial genomes, regulatory regions contain high densities of sigma(70) promoter-like signals that are significantly above the densities detected in nonregulatory genomic regions. In order to investigate the molecular evolutionary forces that operate in bacterial regulatory regions and how they affect the observed redundancy of promoter-like signals, we have undertaken a comparative analysis across the completely sequenced genomes of enteric gamma-proteobacteria. This analysis detects significant positional conservation of promoter-like signal clusters across enterics, some times in spite of strong primary sequence divergence. This suggests that the conservation of the nature and exact position of specific nucleotides is not necessarily the priority of selection for maintaining the transcriptional function in these bacteria. We have further characterized the structural conservation of the regulatory regions of dnaQ and crp across all enterics. These two regions differ in essentiality and mode of regulation, the regulation of crp being more complex and involving interactions with several transcription factors. This results in substantially different modes of evolution, with the dnaQ region appearing to evolve under stronger purifying selection and the crp region showing the likely effects of stabilizing selection for a complex pattern of gene expression. The higher flexibility of the crp region is consistent with the observed less conservation of global regulators in evolution. Patterns of regulatory evolution are also found to be markedly different in endosymbiotic bacteria, in a manner consistent with regulatory regions suffering some level of degradation, as has been observed for many other characters in these genomes. Therefore, the mode of evolution of bacterial regulatory regions appears to be highly dependent on both the lifestyle of the bacterium and the specific regulatory requirements of different genes. In fact, in many bacteria, the mode of evolution of genes requiring significant physiological adaptability in expression levels may follow patterns similar to those operating in the more complex regulatory regions of eukaryotic genomes.