The Deinococcus protease PprI senses DNA damage by directly interacting with single-stranded DNA

Area of Science:

• Microbiology
• Molecular Biology
• Biochemistry

Background:

• Bacteria possess stress response systems for adaptation.
• A DNA damage response in Deinococcus involves metallopeptidase PprI cleaving repressor DdrO.
• The upstream signal activating this PprI-DdrO system was previously unknown.

Purpose of the Study:

• To identify the upstream regulatory signal activating the PprI-DdrO protease-based DNA damage response system.
• To elucidate the mechanism by which this signal activates the system.
• To explore the implications for bacterial survival and drug resistance.

Main Methods:

• In vivo and in vitro biochemical assays to study protein interactions and cleavage.
• Structural analysis of PprI in apo and single-stranded DNA-bound states.
• Investigation of PprI monomer-dimer equilibrium and its effect on activity.

Main Results:

• Single-stranded DNA physically interacts with PprI protease.
• This interaction enhances PprI-DdrO interaction and DdrO cleavage in a length-dependent manner.
• Structural data reveal DNA-binding interfaces on PprI that shape the cleavage site.
• PprI's dynamic monomer-dimer equilibrium is crucial for its cleavage activity.

Conclusions:

• Single-stranded DNA acts as the upstream signal for DNA damage sensing in the bacterial metalloprotease/repressor system.
• This discovery provides insights into a novel SOS-independent pathway for bacterial survival under stress.
• The findings may explain bacterial survival and acquired drug resistance mechanisms.