Cryo-EM Snapshots Capture Multi-Stage Structural Transitions During DNA Recombination

Bacteriophages, or viruses that infect bacteria, have a fiendishly simple purpose in life: attach to a bacterial cell, inject their DNA, and then use the host's genetic machinery to reproduce. In doing so, they may have evolved some of the most efficient gene editing tools ever seen in nature.

New research by scientists at the University of Chicago shows how bacteriophages ("phages" for short) use a special class of enzymes to recognize specific DNA sequences in their host and insert large stretches of their own DNA with remarkable precision. The study also shows how these enzymes can switch directions and remove the phage DNA without a trace, offering new insights that could help scientists develop more precise tools for genome engineering and synthetic biology.

"I've always found these enzymes fascinating, because they are really such clever little molecular machines," said Phoebe Rice, PhD, Professor of Biochemistry and Molecular Biology and senior author of the study, which was published in Molecular Cell.

One of the nice advantages of these enzymes for genome editing is that they leave no DNA damage. When they work like they're supposed to, they don't even leave a single nicked bond in the host DNA."

Phoebe Rice, PhD, Professor of Biochemistry and Molecular Biology, The University of Chicago

The study focuses on large serine integrases, enzymes that phages use to insert their DNA without relying on the host cell's own DNA repair machinery. A longstanding mystery has been how these enzymes control directionality, or whether DNA is being inserted or removed from the host.

In nature, an integrase first inserts viral DNA into a bacterial chromosome in one direction. To reverse the process and remove the DNA, the enzyme requires help from a partner protein known as a recombination directionality factor (RDF). Scientists have known about this behavior for years but lacked detailed structural information explaining how the molecular switch works. 

To solve the problem, Rice and her colleagues used cryo-electron microscopy (cryo-EM), a technique that allows scientists to visualize biological molecules at near-atomic resolution by rapidly freezing them and taking a snapshot of them with an electron microscope. This helped them see three-dimensional structures of the enzyme system, capturing multiple stages of both DNA insertion and removal. 

The structures showed that part of the integrase acts like a movable arm that helps lock the newly inserted phage DNA into place. When it's time to remove the phage DNA, the RDF changes the enzyme into a different shape. In other words, the enzyme uses two distinct processes depending on whether it's inserting DNA or removing it. 

"The protein can assume a different shape when it's bound to the product, which traps it that way," Rice said. "But these phages can also pop back out of the host. So, they make a second protein that binds to the integrase protein, changes its shape again, and then the reverse reaction happens."

Beyond answering a fascinating biological question, the work could have practical implications. Large serine integrases are already being explored as tools for genome editing and programmable genetic switches. For example, Rice and her lab have been collaborating with Weixin Tang, PhD, Associate Professor of Chemistry at UChicago, on using these enzymes for genome editing in mammalian cells. By revealing which parts of the proteins control activity and directionality, the study offers a roadmap for engineering improved versions tailored for biotechnology and medicine.