A YoeB toxin cleaves both RNA and DNA

Area of Science:

• Biochemistry
• Molecular Biology
• Microbiology

Background:

• Type II toxin-antitoxin systems utilize toxin proteins with diverse catalytic functions.
• These toxins possess conserved tertiary folds relevant to biotechnology.
• Understanding toxin mechanisms can reveal novel enzymatic activities.

Purpose of the Study:

• To investigate the catalytic activity of a YoeB family toxin from Agrobacterium tumefaciens.
• To characterize the ribosome-independent nuclease activity of the AtYoeB toxin.
• To compare the RNA and DNA cleavage capabilities of AtYoeB.

Main Methods:

• Quantification of RNA and DNA cleavage activity.
• Analysis of divalent cation and pH dependencies.
• Determination of DNA binding affinity.
• Comparison of ribosome-dependent and -independent reactions.

Main Results:

• AtYoeB displays conserved ribosome-independent non-specific nuclease activity.
• RNA and DNA cleavage show similar dose-dependence but differ in cation and pH requirements.
• AtYoeB acts as a nickase on double-stranded DNA and cleaves single-stranded DNA.
• The toxin binds double-stranded DNA with mid-micromolar affinity.

Conclusions:

• YoeB toxins function as non-specific nucleases, capable of cleaving both RNA and DNA outside the ribosome.
• Ribosome binding enhances AtYoeB's catalytic efficiency by approximately tenfold.
• The identified nuclease activity expands the known functions of toxin-antitoxin systems.