researchers revealed a new inhibitory mechanism against bacterial DNA replication

During the process of bacterial DNA replication, DNA Polymerase, which catalyze the synthesis of DNA, plays an indispensable role. In order to keep DNA Polymerase III sliding along, a protein complex namely β-clamp forms a ring-like structure around DNA, serving as a processivity-promoting factor. Due to the critical function of β-clamp in the replication of bacteria and the formation of tumors, various β-clamp inhibitors have been investigated to a great extent for antibacterial studies.

Recently, a research team led by Prof. ZHANG Kaiming from University of Science and Technology of China (USTC) of the Chinese Academy of Sciences found the Gp168 protein of bacteriophage Twort inhibited β-clamp function by occupying the DNA sliding channel. The study was published in Nucleic Acids Research.

The research team reported a cryo-EM structure of the clamp-Gp168 complex at 3.2-˚A resolution. Researchers revealed that the Gp168 dimer occupied the DNA sliding channel of β-clamp and blocked its loading onto DNA.

In previous studies, most of the published β-clamp inhibitors and binding proteins engaged the β-clamp via hydrophobic protein-binding pocket. Meanwhile, since Gp168 could form complex with the β-clamp of Staphylococcus aureus and Bacillus subtilis, it is potentially a cross-species β-clamp inhibitor.

To understand the formation of the Gp168-clamp complex, the researchers identified that Gp168 existed as a hexameric complex in solution. The pulled-down experiment involving Gp168 and the β-clamp of Staphylococcus aureus showed that Gp168 could form a stable complex with the β-clamp of Staphylococcus aureus. The researchers subsequently performed the cryo-EM single-particle analysis mentioned above to further understand the detailed structure of the Gp168-clamp complex.

Based on the results, they concluded that Gp168 likely represented a new class of proteins with other members yet to be discovered.

The study not only reveals an alternative mechanism for bacteriophages to inhibit β-clamp but also provides inspiration for the development of new antimicrobial reagents.