Compilation and analysus of Bacillus Subtilis σA-dependent promoter sequences: evidence for extended contact between RNA polymerse and upstream promoter DNA

摘要

Sequence analysis of 236 promoters recognized by the Bacillus subtilis σARNA polymerase reveals an extended promoter structure. The most highly conserved bases include the ?35 and ?10 hexanucleotide core elements and a TG dlnucleotide at position ?15,?14. In addition, several weakly conserved A and T residues are present upstream of the ?35 region. Analysis of dinucleotide composition reveals A ₂and T₂-rich sequences in the upstream promoter region (?36 to ?70) which are phased with the DNA helix: A,, tracts are common near ?43, ?54 and ?65; T_n tracts predominate at the intervening positions. When compared with larger regions of the genome, upstream promoter regions have an excess of A_n and T_n sequences for n 4. These data indicate that an RNA polymerase binding site affects DNA sequence as far upstream as ?70. This sequence conservation is discussed in light of recent evidence that the a subunits of the polymerase core bind DNA and that the promoter may wrap around RNA polymerase.