New Methods Shed Light on Gyrase-DNA Interactions

A team led by researchers at Baylor College of Medicine has devised new analytical methods to deepen insights into bacterial DNA management. These approaches uncovered how DNA's sequence, shape, and flexibility steer DNA gyrase, the enzyme once solely credited with controlling DNA topology. DNA characteristics play pivotal roles in this process, with findings relevant to antibiotic development. Published in Nature Communications, the work advances prior demonstrations of gyrase nested in supercoiled DNA loops, the starting point for supercoiling regulation.

Supercoiled DNA, comparable to a coiled landline phone cord, underpins essential activities like reading, copying DNA, and cell division. Improper supercoiling disrupts these in bacteria, where DNA gyrase intervenes, though many specifics of its operation stayed elusive.

The group examined two high-resolution cryoEM structures of gyrase bound to small circular DNA molecules. One featured DNA wrapped tightly around enzyme sections; the other lacked wrapping. Earlier evidence showed sequence recognition insufficient to explain gyrase function fully. “We focused on understanding how the shape of different DNA segments that bend or twist depending on their sequence, influence gyrase function,” said corresponding author Lynn Zechiedrich.

CryoEM details offered atomic-level views of DNA-protein assemblies but lacked sequence clarity. Co-author Haley R. Johnson engineered a computational method to identify bound sequences. Notably, gyrase approached the same DNA region from both sides: wrapped on one, unwrapped on the other. Flexible adjacent DNA facilitated tight wrapping for activity, resembling an elbow bending to wrap around a ball.

“We were surprised to find that gyrase bound the same region of DNA from two different directions. In one structure, gyrase bound one side of the DNA and was wrapped. In the other structure, gyrase bound the other side of the DNA and was not wrapped,” Johnson observed.

Silvia L. Summers, another co-author, analyzed DNA deformability from decades of structural data, pinpointing the most flexible segments. Findings suggest gyrase detects DNA shapes and bending capacity rather than sequences alone, preferring bent binding sites next to wrappable regions.

“3D reconstructions from cryoEM can provide atomic level detail of how large molecular complexes formed by DNA and proteins are organized and interact,” said first author Matthew Baker, now at University of Texas Health Science Center at Houston.

“Gyrase is an important antibiotic target,” Zechiedrich noted. “Understanding how gyrase selects DNA sites could help guide the design of antibiotics that disrupt gyrase’s activity more precisely. Our work shows that, to gyrase, shapes and flexibility of DNA are as important as its genetic code.”