Determination of common structural features in Escherichia coli promoters by computer analysis

Escherichia coli promoters show a large degree of sequence variation. However, they are all recognized specifically by RNA polymerase as the sites for transcription initiation, suggesting that they share common basic structural features distinguishing them from the rest of the sequence. Our hypothesis is that the promoter is determined not only by the two consensus sequences at -10 and -35, but also by the surrounding nucleotides, and that it is not only the identity of the nucleotides that is important for promoter function but the presence of specific physical-chemical and structural characteristics that are sequence dependent. This approach is supported by accumulating evidence indicating the role that the DNA conformation may play in modulating protein-DNA interaction. In this study, four intrinsic sequence-dependent characteristics are examined in E. coli promoter regions: helix stability, helix flexibility, and two conformational parameters represented by the DNA tendencies for B-->Z and B-->A transition. The promoter is defined by the consensus sequences and their vicinity and the examined properties are compared between promoter and random sequences. It is demonstrated that both the consensus and flanking regions are less stable, more flexible and show a higher tendency for the B conformation in comparison to random sequences. Discriminant analysis is used to evaluate the relative contributions of the various characteristics.