DNA replication study targets genes for antibiotic resistance

Model of Rep-mediated SaPI DNA initiation of replication.
Model of Rep-mediated SaPI DNA initiation of replication. (A) The ATP-independent flexibility of CTD exposes the residues involved in iteron recognition. The diameter of the barrel in its N and C terminal sides might accommodate dsDNA. In (B), two hexamers have been speculatively depicted embracing dsDNA. Potential hexamer-hexamer interactions might induce opposite rotation movements that favor DNA distortion. Maybe electrostatically wrapping the DNA with the surface of the barrel (not depicted) might be involved in ori melting. (C) The tilting movement of CTD aids the ATPase domain’s staircase mechanism to unwind the DNA and promote replication fork progression. Image: Qiao, Mir-Sanchis, et al.

The discovery of how a certain type of protein moves for DNA to be copied could have implications for understanding how genes for antibiotic resistance spread between bacteria, Swedish researchers say.

Ignacio Mir-Sanchis, lead researcher in the group at Umeå University that published the study, said studying DNA replication was a good starting point for potentially identifying targets for future drug development.

Mir-Sanchi’s lab focuses on infection biology and studies the Staphylococcus aureus bacterium. The researchers are interested in understanding the DNA replication of S. aureus, of viruses that infect S. aureus (called bacteriophages) and viral satellites. Viral satellites are viruses that parasitise on other viruses.

S. aureus infects and kills millions of people worldwide and is considered a significant threat because the bacterium has become resistant to almost all antibiotics. Interestingly, the genes involved in antibiotic resistance are sometimes also present in viral satellites, making the work even more medically relevant. In recent years an increase in the resistance of S. aureus has been noted in horses, with methicillin-resistant Staphylococcus aureus (MRSA) a pathogen of significant concern to veterinary researchers.

All cellular organisms must replicate their genetic material, DNA, to proliferate, so that one copy goes to a daughter cell and the other copy goes to the other daughter cell. The DNA molecule can be likened to a very long string of beads, where the beads are the building blocks or units.

The string of beads has two strands that are intertwined to form a spiral structure, a double helix. To duplicate its genetic material, the cell must go from one to two DNA molecules, a process called DNA replication, and it starts by separating the two strands of DNA. To separate the two strands, cells have specialised proteins called helicases.

The research group at Umeå University’s Department of Medical Biochemistry and Biophysics has found how helicases interact and move on DNA to separate its strands. The discovery was made possible by so-called cryo-electron microscopy, for which Umeå has one of Sweden’s most advanced facilities. This technique allows scientists to take snapshots of a single molecule. They can make a movie by combining millions of snapshots and see how the helicases move.

Cuncun Qiao, a postdoctoral researcher in the team and first author of the paper, said that when the snapshots were analysed, they saw the helicases move different parts, called domains, via two separate motions. “Two domains rotate and tilt towards each other. These movements give us clues about how these helicases move on DNA and separate the two strands.”

The study, supported by the Wallenberg Centre for Molecular Medicine (WCMM) in Umeå, has been published in the scientific journal Nucleic Acids Research.

“The findings broaden our understanding of how antibiotic resistance genes spread, although it is worth noting that the movements we have identified here have also been seen in helicases found in eukaryotic viruses and even in human cells,” Mir-Sanchis said.

“It’s always surprising how important mechanisms are conserved from bacteriophages to humans,” Mir-Sanchis said.

Staphylococcal self-loading helicases couple the staircase mechanism with inter domain high flexibility. Cuncun Qiao, Gianluca Debiasi-Anders, Ignacio Mir-Sanchis. Nucleic Acids Research, 50(14), 8349–8362. doi.org/10.1093/nar/gkac625

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