Compilation and analysus ofBacillus SubtilisσA-dependent promoter sequences: evidence for extended contact between RNA polymerse and upstream promoter DNA

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Abstract
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 DNA helix: A(n) tracts are common near -43, -54 and -65; T-2 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 alpha subunits of the polymerase core bind DNA and that the promoter may wrap around RNA polymerase.