Structural basis for the concerted antiphage activity in the SIR2-HerA system

Area of Science:

• Bacteriology
• Structural Biology
• Molecular Mechanisms

Background:

• A novel two-gene bacterial defense system against phages, involving SIR2 NADase and HerA ATPase/helicase, has been identified.
• The precise molecular mechanism of this bacterial SIR2-HerA immune system is not fully understood.

Purpose of the Study:

• To elucidate the molecular mechanism of the bacterial SIR2-HerA immune system.
• To determine the cryo-electron microscopy (cryo-EM) structures of SIR2, HerA, and their complex from Paenibacillus sp. 453MF in various functional states.

Main Methods:

• Cryo-electron microscopy (cryo-EM) to determine high-resolution structures.
• Structural analysis of individual SIR2 and HerA proteins and their assembled complex.
• Biochemical assays to assess enzymatic activities (NADase, nuclease, ATPase, helicase).

Main Results:

• The SIR2 protein forms a dodecameric ring structure in an auto-inhibited state.
• HerA adopts a unique split spiral hexameric arrangement, stabilized by a C-terminal extension.
• The SIR2-HerA complex forms a ∼1.1 MDa torch-shaped structure, crucial for antiphage activity.
• Complex formation activates SIR2's NADase/nuclease and HerA's ATPase/helicase activities.
• SIR2 shifts from a dodecamer to a tetradecamer upon binding HerA.

Conclusions:

• The study provides a structural basis for the functional communication between SIR2 and HerA.
• A novel concerted antiviral mechanism involving NAD+ degradation, ATP hydrolysis, and DNA cleavage is revealed.
• Disruption of SIR2-HerA interactions significantly impairs antiphage activity.