title: Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA.
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 A2- and T2-rich sequences in the upstream promoter region (-36 to -70) which are phased with the DNA helix: An tracts are common near -43, -54 and -65; Tn tracts predominate at the intervening positions. When compared with larger regions of the genome, upstream promoter regions have an excess of An and Tn 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.
authors.affiliation: Section of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA.
authors.forename: J D
authors.initials: JD
authors.lastname: Helmann
mesh_terms: D000225:Adenine / Q000032:analysis; D001412:Bacillus subtilis / Q000235:genetics*; D001483:Base Sequence; D017124:Conserved Sequence; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D006147:Guanine / Q000032:analysis; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D012808:Sigma Factor / Q000378:metabolism*; D013941:Thymine / Q000032:analysis
chemical_list: D004269:DNA, Bacterial; D012808:Sigma Factor; D006147:Guanine; C063505:RNA polymerase sigma A; D012321:DNA-Directed RNA Polymerases; D000225:Adenine; D013941:Thymine