Quantitative analysis of the mechanism of DNA binding by Bacillus DnaA protein.

Abstract DnaA protein has the sole responsibility of initiating a new round of DNA replication in prokaryotic organisms. It recognizes the origin of DNA replication, and initiates chromosomal DNA replication in the bacterial genome. In Gram-negative Escherichia coli , a large number of DnaA molecules bind to specific DNA sequences (known as DnaA boxes) in the origin of DNA replication, ori C, leading to the activation of the origin. We have cloned, expressed, and purified full-length DnaA protein in large quantity from Gram-positive pathogen Bacillus anthracis (DnaA BA ). DnaA BA was a highly soluble monomeric protein making it amenable to quantitative analysis of its origin recognition mechanisms. DnaA BA bound DnaA boxes with widely divergent affinities in sequence and ATP-dependent manner. In the presence of ATP, the K D ranged from 3.8 × 10 −8  M for a specific DnaA box sequence to 4.1 × 10 −7  M for a non-specific DNA sequence and decreased significantly in the presence of ADP. Thermodynamic analyses of temperature and salt dependence of DNA binding indicated that hydrophobic (entropic) and ionic bonds contributed to the DnaA BA ·DNA complex formation. DnaA BA had a DNA-dependent ATPase activity. DNA sequences acted as positive effectors and modulated the rate ( V max ) of ATP hydrolysis without any significant change in ATP binding affinity.