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Updated: May 23, 2025
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An Assay for Quantifying Protein-RNA Binding in Bacteria
Published on: June 12, 2019
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Structural basis for cooperative ssDNA binding by bacteriophage protein filament P12
Lena K Träger1, Morris Degen2,3, Joana Pereira2,4
1Department of Biosystems Science and Engineering, ETH Zurich, Schanzenstrasse 44, 4056 Basel, Switzerland.
Nucleic Acids Research
|March 7, 2025
Summary
Researchers characterized P12, a single-stranded DNA-binding protein (SSB) from bacteriophage PRD1. P12 forms a unique filament on ssDNA, crucial for protein-primed DNA replication and host cell toxicity.
Area of Science:
- Molecular Biology
- Structural Biology
- Virology
Background:
- Protein-primed DNA replication is a distinct mechanism requiring specialized single-stranded DNA-binding proteins (SSBs).
- The stabilization mechanisms of ssDNA intermediates by SSBs are not fully understood.
Purpose of the Study:
- To structurally and biochemically characterize P12, an SSB from bacteriophage PRD1.
- To elucidate the ssDNA binding mechanism and structural features of P12.
Main Methods:
- High-resolution cryo-electron microscopy (cryo-EM) for structural determination.
- Biochemical assays to assess ssDNA binding and filament formation.
- Bioinformatic analyses to classify the P12 fold.
Main Results:
- P12 forms a unique, cooperative filament along single-stranded DNA (ssDNA).
- Each P12 protomer binds six nucleotides of the ssDNA phosphate backbone independently of sequence.
- An intrinsically disordered C-terminal tail drives cooperative filament formation.
- Specific residues essential for ssDNA interaction were identified.
- P12's ssDNA-binding capability correlates with host cell toxicity.
Conclusions:
- P12 exhibits a novel ssDNA binding mode, forming a cooperative filament essential for protein-primed DNA replication.
- The P12 fold represents a distinct lineage within the OB-like fold superfamily.
- This study provides fundamental insights into protein-primed DNA replication and potential biotechnological applications.
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