Bacillus subtilis subsp. subtilis str. AG1839 Targeted Locus (Loci)

DnaA, the replication initiation protein in bacteria, is a AAA+ ATPase that binds and hydrolyzes ATP, and exists in a heterogeneous population of ATP-DnaA and ADP-DnaA. DnaA binds cooperatively to the origin of replication and several other chromosomal regions, and functions as a transcription factor at some of these regions. We determined the binding properties of Bacillus subtilis DnaA to genomic DNA in vitro at single nucleotide resolution using in vitro DNA affinity purification and deep sequencing (IDAP-Seq). We measured binding over a range of DnaA concentrations, and with ATP and ADP bound. Our in vitro characterization of the inherent ability of DnaA to bind the genome at single nucleotide resolution provides a backdrop for interpreting data on in vivo binding and regulation of DnaA, and is an approach that should be readily adaptable to many other DNA binding proteins.