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 se quence. Our hypothesis is that the promoter is determined not only by the two consensus sequences at -10 and -35, but also by the surroundin g 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 dep endent. 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 charact eristics are examined in E. coli promoter regions: helix stability, he lix 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 proper ties are compared between promoter and random sequences. It is demonst rated that both the consensus and flanking regions are less stable, mo re flexible and show a higher tendency for the B conformation in compa rison to random sequences. Discriminant analysis is used to evaluate t he relative contributions of the various characteristics.