A model of DNA unwinding dynamics by the RecBCD complex and its regulation by Chi recognition

The Escherichia coli RecBCD enzyme is a heterotrimeric helicase-nuclease complex responsible for processing of double-stranded DNA breaks for repair by homologous recombination. It is a highly processive, duplex unwinding and degrading motor, with its activities being regulated by the octameric recombination hotspot, Chi, which is read as a single-stranded DNA sequence. Here, a model is presented for DNA unwinding by the RecBCD complex and its regulation by Chi recognition. With the model we study analytically the dynamics of DNA unwinding of both wild-type RecBCD and mutant RecBCDK177Q with the motor function of RecD being inactivated by mutagenesis, giving quantitative explanations of the available single-molecule experimental data. The peculiar features of RecBCD such as large variations of DNA unwinding speed of individual enzymes, sensitivity of unwinding speed of a RecBCD molecule on the change of environment, two translocase or helicase activities of RecBC and RecD, etc., are explained. Furthermore, predicted results are presented.