Consensus symmetry pattern in E. coli promoter sequences.

Abstract

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.