Every day, the DNA of living organisms is exposed to damage from normal cellular processes, environmental toxins, and even some medicines. Among the most dangerous forms of damage are interstrand DNA crosslinks (ICLs), chemical bonds that effectively staple the two strands of DNA together and prevent cells from reading, copying, or repairing their genetic information.
While scientists have long known that bacteria possess mechanisms to repair these lesions, exactly how they recognize and remove them has remained unclear.
In a new study, the Eichman lab and the Skaar lab provide the first detailed structural view of AlkX, a DNA repair enzyme found in several disease-causing bacteria, revealing how it detects and repairs these potentially lethal DNA crosslinks.
Using X-ray crystallography, the researchers captured AlkX bound to damaged DNA, allowing them to visualize the molecular interactions that occur during repair. The structure revealed specialized regions of the enzyme that grip DNA and identify the damaged site. Through a combination of structural biology, biochemical experiments, and bacterial growth studies, the researchers demonstrated that these regions are essential for repair. When key components of AlkX were altered, the enzyme lost much of its ability to recognize and remove DNA crosslinks, leaving bacteria significantly more vulnerable to DNA-damaging chemicals.
The findings are particularly relevant because AlkX-like enzymes are widespread among important human pathogens, including Acinetobacter baumannii, Salmonella enterica, Listeria monocytogenes, and Pseudomonas aeruginosa. A. baumannii is considered one of the world’s most concerning antibiotic-resistant pathogens and is a major cause of hospital-acquired infections. Previous work showed that AlkX helps this bacterium survive stressful conditions encountered during infection, but the new study explains the molecular basis for that protective effect.
The researchers also identified a naturally occurring genetic variant in an antibiotic-resistant strain of Salmonella that disrupts AlkX function, demonstrating how structural insights can help explain the consequences of genetic mutations in pathogenic bacteria.
Beyond revealing the workings of a single enzyme, the study advances our understanding of how microbes maintain the integrity of their genomes under extreme stress. It also highlights DNA repair pathways as potential targets for future antimicrobial therapies.
By disabling enzymes such as AlkX, researchers may one day be able to weaken bacterial defenses, making dangerous pathogens more susceptible to DNA damage and less capable of causing infection. As antibiotic resistance continues to rise worldwide, uncovering vulnerabilities in bacterial survival mechanisms represents an important step toward developing new strategies to combat hard-to-treat infections.
Together, these findings provide a molecular blueprint for how bacteria repair some of the most toxic forms of DNA damage and open new avenues for understanding pathogen survival and developing next-generation antibacterial treatments.