Identification of the sequences recognized by the Bacillus subtilis response regulator YclJ

The Bacillus subtilis yclJ gene encodes an OmpR-type response regulator of a two-component regulatory system with unknown function. A previous DNA microarray experiment suggested that multicopy yclJ greatly enhances the expression of several operons in a cognate kinase (YclK)-deficient strain. To confirm this, lacZ fusion analysis was performed in the yclK background with overexpressed yclJ. As a result, yclHI, ykcBC, and yngABC were indeed positively regulated by YclJ. Gel retardation and DNase I footprint analyses revealed that YclJ binds to the promoter regions of yclHI, ykcBC, and yngABC. Nucleotide sequence analysis of the binding regions suggested that YclJ recognizes a direct repeat of the consensus sequence TTCATANTTT, the upstream half of which has close similarity to the consensus binding sequence of the other OmpR family response regulator PhoP. LacZ fusion analysis of the control region of yngA with deletion or point mutation confirmed that the YclJ-binding sequence is required for the YclJ-mediated activation of yngA. Furthermore, we identified two more YclJ-regulated genes, yycA and yfjR, using bioinformatic analysis of the B. subtilis genome, and it was shown that YclJ binds to those promoters and controls the expression of those genes.