Bacillus subtilis subsp. subtilis strain:JH642 (AG174) Targeted Locus (Loci)

We identified interactions between the conserved bacterial replication initiator and transcription factor DnaA and the nucleoid-associated protein Rok of Bacillus subtilis. DnaA is a AAA+ ATPase that binds to several chromosomal regions, including the origin of replication, is required for replication initiation, and also functions as a transcription factor. DnaA binds directly to DnaA boxes at the origin of replication and at the promoters of several DnaA-regulated genes. Rok binds A+T-rich sequences throughout the genome and is analogous to H-NS from gamma-proteobacteria and Lsr2 from Mycobacteria. Rok represses many genes and, like H-NS, may play a role in chromosome architecture. Using crosslinking and immunoprecipitation followed by deep sequencing (ChIP-seq), we found that DnaA was associated with many of the same chromosomal regions as Rok. Association of DnaA with these Rok-bound regions appeared to be indirect as it was dependent on Rok and independent of the DNA binding domain of DnaA. In contrast, the binding of DnaA to chromosomal regions with clusters of DnaA boxes was independent of Rok and required the DNA binding domain of DnaA. Gene expression and mutant analyses support a model in which several genes are indirectly repressed by DnaA through its interaction with Rok. The interaction between DnaA and Rok may represent a regulatory connection between DNA replication and chromosome architecture. Based on the presence of Rok (H-NS)-like proteins in many bacteria and the conservation of DnaA, we speculate that these interactions might be widespread.