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Updated: May 23, 2025

An Assay for Quantifying Protein-RNA Binding in Bacteria
Published on: June 12, 2019
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.
Abstract:
Protein-primed DNA replication is a unique mechanism, bioorthogonal to other known DNA replication modes. It relies on specialised single-stranded DNA (ssDNA)-binding proteins (SSBs) to stabilise ssDNA intermediates by unknown mechanisms. Here, we present the structural and biochemical characterisation of P12, an SSB from bacteriophage PRD1. High-resolution cryo-electron microscopy reveals that P12 forms a unique, cooperative filament along ssDNA. Each protomer binds the phosphate backbone of 6 nucleotides in a sequence-independent manner, protecting ssDNA from nuclease degradation. Filament formation is driven by an intrinsically disordered C-terminal tail, facilitating cooperative binding. We identify residues essential for ssDNA interaction and link the ssDNA-binding ability of P12 to toxicity in host cells. Bioinformatic analyses place the P12 fold as a distinct branch within the OB-like fold family. This work offers new insights into protein-primed DNA replication and lays a foundation for biotechnological applications.
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