The Spo0A-box of C. difficile In B. subtilis, the binding site of Spo0A on target DNA has been well-characterized, through a combination of in vitro binding assays, determination of in vivo binding profiles and mutagenesis of regulated promoter sequences. This work has led to the identification of a conserved core motif, TGTCGAA, or Spo0A box [5, 10, 11, 45] . Depending on the analysis, this motif is flanked by one or more adenine or thymine residues [10, 11] . Interestingly, many target genes do not harbor a perfect match to this consensus sequence, but rather contain one or more degenerate motifs. The differences in these motifs may reflect different promoter architectures (e.g. AT content), modes of action (e.g. activation or repression) or levels of regulation. Spo0A genes in B. subtilis can be divided in different classes that respond to different levels of phosphorylated Spo0A [43, 57] .