REORGANIZATION OF TERMINATOR DNA UPON BINDING REPLICATION TERMINATOR PROTEIN - IMPLICATIONS FOR THE FUNCTIONAL REPLICATION FORK ARREST COMPLEX

Termination of DNA replication in Bacillus subtilis involves the polar arrest of replication forks by a specific complex formed between the replication terminator protein (RTP) and DNA terminator sites. While d etermination of the crystal structure of RTP has facilitated our under standing of how a single RTP dimer interacts with terminator DNA, addi tional information is required in order to understand the assembly of a functional fork arrest complex, which requires an interaction betwee n two RTP dimers and the terminator site. In this study, we show that the conformation of the major B. subtilis DNA terminator, Terl, become s considerably distorted upon binding RTP. Binding of the first dimer of RTP to the B site of Terl causes the DNA to become slightly unwound and bent by similar to 40 degrees. Binding of a second dimer of RTP t o the A site causes the bend angle to increase to similar to 60 degree s. We have used this new data to construct two plausible models that m ight explain how the ternary terminator complex can block DNA replicat ion in a polar manner, in the first model, polarity of action is a con sequence of the two RTP-DNA half-sites having different conformations. These different conformations result from different RTP-DNA contacts at each half-site (due to the intrinsic asymmetry at the terminator DN A), as well as interactions (direct or indirect) between the RTP dimer s on the DNA. In the second model, polar fork arrest activity is a con sequence of the different affinities of RTP for the A and B sites of t he terminator DNA, modulated significantly by direct or indirect inter actions between the RTP dimers.