Substrate interactions and promiscuity in a viral DNA packaging motor

Area of Science:

• Structural biology
• Molecular motors
• Biochemistry

Background:

• The ASCE superfamily comprises ATPases involved in diverse cellular processes, including DNA transport by ring-shaped motors.
• Understanding how these motors engage DNA substrates is crucial for elucidating their mechanochemical mechanisms.
• Previous research has focused on the ATPase activity but lacked detail on DNA interaction specifics.

Purpose of the Study:

• To investigate the precise nature of DNA-motor interactions during the mechanochemical cycle of a DNA packaging motor.
• To determine whether motor contacts with DNA are specific or distributed and their role in the cycle.
• To utilize the Bacillus subtilis bacteriophage varphi29 motor as a model system.

Main Methods:

• Utilized modified DNA substrates to challenge the bacteriophage varphi29 genome packaging motor.
• Analyzed the motor's mechanochemical cycle, distinguishing between ATP-loading dwell and translocation burst phases.
• Investigated DNA-protein interactions using biochemical and biophysical approaches (implied).

Main Results:

• Identified specific contacts with phosphates every 10 base pairs on the 5'-3' strand during the ATP-loading dwell phase.
• Demonstrated that these phosphate interactions stabilize the motor and regulate its chemical cycle.
• Revealed extensive, non-specific DNA contacts during the translocation burst phase, driving movement against high forces.

Conclusions:

• The study elucidates distinct DNA interaction modes during different phases of the motor's cycle.
• Phosphate interactions are key for substrate engagement and regulation during the dwell phase.
• Non-specific contacts likely facilitate efficient translocation by protein translocases in the ASCE superfamily.