Sigma A recognition sites in the Bacillus subtilis genome

Hanne Østergaard Jarmer, Thomas Schou Larsen, Anders Stærmose Krogh, Hans Henrik Saxild, Søren Brunak, Steen Knudsen

    Research output: Contribution to journalJournal articleResearchpeer-review


    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.
    Original languageEnglish
    Pages (from-to)2417-2424
    Publication statusPublished - 2001

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