A novel method for promoter search enhanced by function-specific subgrouping of promoters--developed and tested on E.coli system.

A new method for evaluating some complex characteristics of the primary structure of E.coli promoters is proposed. The method, of nonparametric statistical significance, selects important conserved single-base positions in combination with 2-base coupling relations of identity and complementarity. The extended consensus of promoter characteristics thus obtained was used to scan unknown sequences for similarity with E.coli promoters. In terms of this method, a complete set of 244 E.coli promoters was shown to be structurally inconsistent. The set was then broken down into functionally homogeneous subsets of promoters to enhance the selectivity of the search for E.coli-specific promoter sequences, with a high significance level being attained.

Consensus symmetry pattern in E. coli promoter sequences.

A computer method was used to select two subgroups in 172 Escherichia coli promoter nucleotide sequences characterized by "standard" 17 bp and "non-standard" 17 +/- 2 bp spacing between the Pribnow box and -35 region. The conservation of the two-fold rotational (2f) and true palindrome (tp) symmetry relations was determined between nucleotide doublets in both promoter subgroups which represent consensus symmetry patterns. Statistically significant symmetries were primarily distinguished from those established by the nucleotide sequence conservation. The consensus symmetry pattern of standard promoters involves 45 of the 60 promoter nucleotide positions at which less strongly conserved and non-conserved sequences were mostly occupied (per se). They also show a high level of symmetry centre conservation. The conservation of the statistically significant 2f symmetry centres at positions -4.5 and -31.5 suggests partial conservation of the Pribnow box and -35 pentamer in the codogenic strand in an opposite orientation, respectively. The non-standard promoters differ from the standard ones by the consensus symmetry pattern and by the 2f and tp symmetry centre distribution with an overall lower degree of symmetry conservation in the -35 region. It has been suggested that the conserved symmetry relations provide an additional condition necessary for the specific interaction of RNA polymerase with the promoter sequence to initiate transcription.