New Research Breakthrough Opens Door to More Effective Infection Treatments
A novel approach to constructing bacteriophage DNA lays the groundwork for improved therapeutic options against bacterial infections, researchers report.
The study describes a method to build phages with entirely synthetic genetic material, enabling scientists to add or remove genes at will. This capability promises deeper insights into how these bacteria-killing viruses function and may lead to new therapies to combat the growing problem of antibacterial resistance.
Phages vary enormously, yet the roles of many individual genes remain poorly understood, notes Graham Hatfull, a biotechnology professor at the University of Pittsburgh and one of the study’s lead researchers. “How are the genes regulated? What happens if this gene is removed or that one is altered? We don’t yet have those answers, but now we can pose—and test—nearly any question about phages,” he explains. “This will accelerate discovery.”
The researchers focused on synthetic DNA modeled after two naturally occurring phages that target Mycobacterium, the genus that includes the bacteria responsible for tuberculosis and leprosy, among others. They successfully edited the synthetic genomes by adding and removing genes in both cases, demonstrating precise genome engineering.
The team’s findings appear in the Proceedings of the National Academy of Sciences.
While biologists routinely create synthetic DNA, phages that infect Mycobacterium pose particular challenges due to their high GC content. DNA consists of base pairs: A with T, and C with G. The Mycobacterium-targeting phages are roughly 65% GC, making standard DNA synthesis difficult compared with bacteria like E. coli, which have more balanced base-pair ratios.
“Conventional DNA synthesis encounters significant hurdles with high-GC DNA,” asserts Hatfull, contrasting these phages with easier-to-edit genomes. To overcome these obstacles, Hatfull collaborated with Greg Lohman of New England Biolabs, a leader in synthetic DNA design and assembly, and Ansa Biotech, which has developed methods to synthesize high-GC DNA. The paper’s first author, Ching-Chung Ko, is a research associate in Hatfull’s lab.
The researchers chemically synthesized DNA identical to two natural phages: BPs, a 40,000-base-pair phage used clinically to combat infections in cystic fibrosis patients, and Bxb1, with 50,000 base pairs. They divided the DNA into 12 segments, inserted them into a host cell, and observed that the cell followed the new genetic instructions to produce phages.
Interest in phages as a potential countermeasure to antibiotic-resistant infections has grown among scientists and clinicians. Phages and bacteria have co-evolved for billions of years, creating highly specialized relationships—some phages attack only specific bacterial strains, much like a precise key fits a single lock. The exact ways phage genomes encode these relationships, however, remain largely a mystery.
Hatfull’s laboratory maintains a vast library of about 28,000 phages collected from soil, ponds, and even decaying fruit. Finding a phage that targets a particular bacterial strain is a process of directed trial and error. When a clinician provides a patient sample, researchers draw on this experience, roughly 5,500 phage genomes, and numerous petri dishes to identify a tailored phage match for the patient.
Precisely editing phage genomes and observing the resulting changes could revolutionize both basic understanding and practical applications. In the future, it may enable the engineering of phages with broader therapeutic uses.
“We’ve faced questions we couldn’t easily answer because the tools weren’t available,” Hatfull notes. “This technological advance makes it feasible to address many questions about phages more straightforwardly.”
Beyond research benefits, the ability to create fully synthetic genomes could reduce the need to maintain vast phage collections in freezers, along with the associated storage and backup requirements. Hatfull envisions a future where phages exist primarily as information rather than as physical samples.
“The possibilities become truly limitless,” Hatfull concludes. “With this capability, any genome can be created. The only real limit is imagination.”
