Reorganization of terminator DNA upon binding replication terminator protein: implications for the functional...

Area of Science:

• Molecular Biology
• Structural Biology
• Genetics

Background:

• DNA replication termination in Bacillus subtilis relies on the polar arrest of replication forks.
• This arrest is mediated by a complex of replication terminator protein (RTP) and specific DNA terminator sites.
• Previous structural studies elucidated single RTP dimer-DNA interactions, but the assembly of the functional fork arrest complex remained unclear.

Purpose of the Study:

• To investigate the structural changes in the Bacillus subtilis TerI DNA terminator upon binding of RTP.
• To understand the assembly and mechanism of the functional fork arrest complex involving two RTP dimers.
• To propose models explaining the polar manner of DNA replication fork arrest.

Main Methods:

• Structural analysis of the Bacillus subtilis TerI DNA terminator.
• Investigation of DNA conformation changes upon binding of one and two RTP dimers.
• Development of models for polar replication fork arrest based on structural data.

Main Results:

• Binding of the first RTP dimer to the TerI B site induces DNA unwinding and bending (~40 degrees).
• Binding of a second RTP dimer to the A site further increases DNA bending (~60 degrees).
• Two models are proposed: one based on differential RTP-DNA half-site conformations, the other on differential RTP-DNA binding affinities.

Conclusions:

• RTP binding significantly distorts the TerI DNA structure, creating distinct conformations.
• The observed DNA distortions and differential binding affinities likely contribute to the polar arrest of replication forks.
• These findings provide mechanistic insights into how the ternary terminator complex achieves polar fork arrest.