Scientists take aim at virulent bacteria by decoding machinery of key control enzyme

By deciphering the ingenious mechanism used by a particular enzyme to modify bacterial chromosome chemistry, scientists have come a step closer to designing a new kind of drug that could stop virulent bacterial infections in their tracks. Their research will be published in the May 6 issue of the journal Cell.

Scientists have known for many years that an enzyme called Dam (DNA adenine methyltransferase) plays a role in regulating gene expression in many bacteria. Each time the bacteria reproduce, Dam modifies the A (adenine) nucleotide in the DNA sequence GATC through a chemical reaction known as methylation. Methylation is a biological process used to tag a variety of molecules, including DNA, and is important in cellular processes such as regulating gene expression, DNA replication and repair. In humans DNA methylation occurs on the C (cytosine) rather than the A (adenine) nucleotide.

Recently scientists have discovered a new role for Dam methylation. Dam also is essential for regulating the expression of genes responsible for bacterial virulence. When the gene responsible for Dam is defective, bacteria lose their disease-causing potency. Using the X-ray diffraction facility at the Argonne National Laboratory in Chicago, Xiaodong Cheng, PhD, professor of biochemistry at Emory University School of Medicine and Georgia Research Alliance Eminent Scholar, and John Horton, PhD, Research Assistant Professor, have now solved the co-crystal structure of the Dam enzyme in complex with DNA, which has allowed them to observe exactly how the enzyme finds its target on bacterial DNA.

The Dam enzyme begins by binding non-specifically to DNA, but once it fastens tightly, it glides smoothly down the entire DNA molecule like fingers sliding down a guitar neck searching for the right chord, examining each base pair as it goes. Each time it finds the sequence GATC it stops and methylates the A nucleotide. Dam must move quickly, because if the bacteria reproduce with the wrong methylation pattern, gene expression will be foiled and they will lose their virulence.

“For the first time, using the 3-D crystal structure, we have been able to see the specific Dam structure in action, including the way it binds to the DNA and moves along the base pairs as it recognizes and methylates the A nucleotides,” says Dr. Cheng. “Using this information we can potentially design a drug to inhibit this particular enzyme’s chemical reaction or its DNA binding process. This kind of rationally designed drug could be an alternative against infections that are resistant to current antibiotics. And because humans don’t have Dam methylation, this kind of drug would not interfere with important biological processes in humans.”

Other coauthors include Dr. Stanley Hattman, professor of biology from University of Rochester, who cloned and sequenced the Dam gene and has been studying the biochemical mechanism of the enzyme and Dr. Albert Jeltsch and his student Kirsten Liebert from International University Bremen in Germany. Dr. Cheng and his colleagues plan to continue their research using structure-based virtual screening techniques and high throughput equipment to screen for potential inhibitor compounds against the Dam enzyme.