Compilation and analysis of Bacillus subtilis sigma~A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA

摘要

Sequence analysis of 236 promoters recognized by the Bacillus subtilis sigma~A-RNA polymerase reveals an extended promoter structure. The most highly conserved bases include the -35 and -10 hexanucleotide core elements and a TG dinucleotide 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_2- and T_2-rich sequences in the upstream promoter region (-36 to -70) which are phased with the DNAhelix: A_n 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.