title: Sigma A recognition sites in the Bacillus subtilis genome.
abstract: A hidden Markov model of sigma(A) RNA polymerase cofactor recognition sites in Bacillus subtilis, containing either the common or the extended -10 motifs, has been constructed based on experimentally verified sigma(A) recognition sites. This work suggests that more information exists at the initiation site of transcription in both types of promoters than previously thought. When tested on the entire B. subtilis genome, the model predicts that approximately half of the sigma(A) recognition sites are of the extended type. Some of the response-regulator aspartate phosphatases were among the predictions of promoters containing extended sites. The expression of rapA and rapB was confirmed by site-directed mutagenesis to depend on the extended -10 region.
authors.affiliation: Center for Biological Sequence Analysis, Building 2081, and Section for Molecular Microbiology, Building 3012, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark.
authors.forename: Hanne
authors.initials: H
authors.lastname: Jarmer
authors.affiliation: Center for Biological Sequence Analysis, Building 2081, and Section for Molecular Microbiology, Building 3012, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark.
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Larsen
authors.affiliation: Center for Biological Sequence Analysis, Building 2081, and Section for Molecular Microbiology, Building 3012, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark.
authors.forename: Anders
authors.initials: A
authors.lastname: Krogh
authors.affiliation: Center for Biological Sequence Analysis, Building 2081, and Section for Molecular Microbiology, Building 3012, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark.
authors.forename: Hans Henrik
authors.initials: HH
authors.lastname: Saxild
authors.affiliation: Center for Biological Sequence Analysis, Building 2081, and Section for Molecular Microbiology, Building 3012, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark.
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
authors.affiliation: Center for Biological Sequence Analysis, Building 2081, and Section for Molecular Microbiology, Building 3012, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark.
authors.forename: Steen
authors.initials: S
authors.lastname: Knudsen
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics* / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D016680:Genome, Bacterial; D008390:Markov Chains; D008957:Models, Genetic; D016297:Mutagenesis, Site-Directed; D010749:Phosphoprotein Phosphatases / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012808:Sigma Factor / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; C074434:RapA protein, E coli; D012808:Sigma Factor; C091155:rapB protein, Bacillus subtilis; D010749:Phosphoprotein Phosphatases